Index (MzJava 1.1.1-SNAPSHOT API)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
A

AAMassCalculator - Class in org.expasy.mzjava.proteomics.mol
absolute - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraResult.Intensity
AbsoluteTolerance - Class in org.expasy.mzjava.core.ms: Implementation of Tolerance where the + and - is an absolute value Scaling to get around issues with representing some numbers as doubles.
AbsoluteTolerance(double) - Constructor for class org.expasy.mzjava.core.ms.AbsoluteTolerance
AbstractAminoAcidSequenceReader<O extends AminoAcidSequence> - Class in org.expasy.mzjava.proteomics.avro.io
AbstractAminoAcidSequenceReader() - Constructor for class org.expasy.mzjava.proteomics.avro.io.AbstractAminoAcidSequenceReader
AbstractAminoAcidSequenceWriter<O extends AminoAcidSequence> - Class in org.expasy.mzjava.proteomics.avro.io
AbstractAminoAcidSequenceWriter() - Constructor for class org.expasy.mzjava.proteomics.avro.io.AbstractAminoAcidSequenceWriter
AbstractAvroReader<O> - Class in org.expasy.mzjava.avro.io: Base class for reading objects using the Avro Decoder
AbstractAvroReader() - Constructor for class org.expasy.mzjava.avro.io.AbstractAvroReader
AbstractAvroWritable<T> - Class in org.expasy.mzjava.hadoop.io: Serves as an adapter between Avro and Hadoop serialization.
AbstractAvroWritable(AvroWriter<T>, AvroReader<T>) - Constructor for class org.expasy.mzjava.hadoop.io.AbstractAvroWritable
AbstractAvroWritable(T, AvroWriter<T>, AvroReader<T>) - Constructor for class org.expasy.mzjava.hadoop.io.AbstractAvroWritable
AbstractAvroWriter<O> - Class in org.expasy.mzjava.avro.io: Base class for writing objects using Avro Encoder
AbstractAvroWriter() - Constructor for class org.expasy.mzjava.avro.io.AbstractAvroWriter
AbstractConsensusSpectrumBuilder<A extends LibPeakAnnotation,B extends AbstractConsensusSpectrumBuilder<A,B,C>,C extends ConsensusSpectrum<A>> - Class in org.expasy.mzjava.core.ms.consensus
AbstractConsensusSpectrumBuilder() - Constructor for class org.expasy.mzjava.core.ms.consensus.AbstractConsensusSpectrumBuilder
AbstractContactType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110: A contact is either a person or an organization.
AbstractContactType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AbstractContactType
AbstractIntervalSpectrumLibrary<S extends PeakList> - Class in org.expasy.mzjava.core.ms.library
AbstractIntervalSpectrumLibrary(Collection<S>) - Constructor for class org.expasy.mzjava.core.ms.library.AbstractIntervalSpectrumLibrary
AbstractLibPeakAnnotationWriter<A extends LibPeakAnnotation> - Class in org.expasy.mzjava.avro.io
AbstractLibPeakAnnotationWriter() - Constructor for class org.expasy.mzjava.avro.io.AbstractLibPeakAnnotationWriter
AbstractMapSpectrumLibrary<S extends PeakList> - Class in org.expasy.mzjava.core.ms.library
AbstractMapSpectrumLibrary(Collection<S>) - Constructor for class org.expasy.mzjava.core.ms.library.AbstractMapSpectrumLibrary
AbstractMergePeakFilter<IN extends PeakAnnotation,OUT extends LibPeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist.peakfilter: Class to merge peaks that are close together.
AbstractMergePeakFilter(double, double, AbstractMergePeakFilter.IntensityMode, int) - Constructor for class org.expasy.mzjava.core.ms.peaklist.peakfilter.AbstractMergePeakFilter: Constructor
AbstractMergePeakFilter.IntensityMode - Enum in org.expasy.mzjava.core.ms.peaklist.peakfilter
AbstractMgfReader<A extends PeakAnnotation,S extends Spectrum<A>> - Class in org.expasy.mzjava.core.io.ms.spectrum: To extend how the TITLE line is handled add more TitleParser instances using addTitleParser
AbstractMgfReader(Reader, URI, PeakList.Precision, PeakProcessorChain<A>) - Constructor for class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfReader
AbstractMgfWriter<A extends PeakAnnotation,M,P extends AbstractMgfWriter.Parameters> - Class in org.expasy.mzjava.core.io.ms.spectrum: Abstract implementation of an MGF writer.
AbstractMgfWriter(Writer, P) - Constructor for class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfWriter
AbstractMgfWriter.Parameters - Interface in org.expasy.mzjava.core.io.ms.spectrum
AbstractMsReader<A extends PeakAnnotation,S extends Spectrum<A>> - Class in org.expasy.mzjava.core.io.ms.spectrum
AbstractMsReader(Reader, URI, PeakList.Precision, PeakProcessorChain<A>) - Constructor for class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader
AbstractMsReader.ParseContext - Class in org.expasy.mzjava.core.io.ms.spectrum
AbstractMsReader.ParseContext(URI) - Constructor for class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader.ParseContext
AbstractMsReader.ParseContext(Reader, URI) - Constructor for class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader.ParseContext
AbstractParamType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110: Abstract entity allowing either cvParam or userParam to be referenced in other schemas.
AbstractParamType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AbstractParamType
AbstractPeakList<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist
AbstractPeakList() - Constructor for class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
AbstractPeakList(AbstractPeakList<A>) - Constructor for class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
AbstractPeakList.AbstractMergePeakSink<A extends PeakAnnotation,L extends AbstractPeakList<A>> - Class in org.expasy.mzjava.core.ms.peaklist
AbstractPeakList.AbstractMergePeakSink(L) - Constructor for class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList.AbstractMergePeakSink
AbstractPeakListReader<A extends PeakAnnotation,PL extends PeakList<A>> - Class in org.expasy.mzjava.avro.io
AbstractPeakListReader(AbstractAvroReader<? extends A>[], Optional<PeakList.Precision>, List<PeakProcessor<A, A>>) - Constructor for class org.expasy.mzjava.avro.io.AbstractPeakListReader
AbstractPeakListValue<PL extends PeakList> - Class in org.expasy.mzjava.hadoop.io
AbstractPeakListValue(AbstractPeakListWriter<PL>, AbstractAvroReader<PL>) - Constructor for class org.expasy.mzjava.hadoop.io.AbstractPeakListValue
AbstractPeakListWriter<PL extends PeakList> - Class in org.expasy.mzjava.avro.io
AbstractPeakListWriter(Optional<PeakList.Precision>, AbstractAvroWriter<? extends PeakAnnotation>...) - Constructor for class org.expasy.mzjava.avro.io.AbstractPeakListWriter
AbstractPeakPairProcessor<X extends PeakAnnotation,Y extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor: Peak pair processor that takes care of the sink
AbstractPeakPairProcessor() - Constructor for class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.AbstractPeakPairProcessor
AbstractPeakProcessor<IN extends PeakAnnotation,OUT extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist: Implementation of PeakProcessor that takes care of the reference to the next element in the peak processor chain
AbstractPeakProcessor() - Constructor for class org.expasy.mzjava.core.ms.peaklist.AbstractPeakProcessor
AbstractPsmCsvReader - Class in org.expasy.mzjava.proteomics.io.ms.ident: Abstract implementation of PsmReader with a default parse template method.
AbstractPsmCsvReader() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.AbstractPsmCsvReader
AbstractSimFunc<X extends PeakAnnotation,Y extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.spectrasim: Abstract similarity function.
AbstractSimFunc(Tolerance) - Constructor for class org.expasy.mzjava.core.ms.spectrasim.AbstractSimFunc: Creates a AbstractSimFunc that uses a DefaultPeakListAligner and clear processor chain.
AbstractSimFunc(PeakListAligner<X, Y>, PeakPairProcessor<X, Y>...) - Constructor for class org.expasy.mzjava.core.ms.spectrasim.AbstractSimFunc: Creates a AbstractSimFunc that uses the supplied PeakListAligner and PeakPairProcessor chain.
AbstractSptxtWriter - Class in org.expasy.mzjava.proteomics.io.ms.spectrum
AbstractSptxtWriter(Writer, PeakList.Precision) - Constructor for class org.expasy.mzjava.proteomics.io.ms.spectrum.AbstractSptxtWriter
accept(Monosaccharide, Monosaccharide, GlycosidicLinkage) - Method in interface org.expasy.mzjava.glycomics.mol.LinkageAcceptor
accept(Class<?>) - Method in class org.expasy.mzjava.hadoop.io.MzJavaSerialization
AcceptAllDigestionController - Class in org.expasy.mzjava.proteomics.mol.digest: DigestionController that accepts all peptides and does not interrupt the digestion.
AcceptAllDigestionController() - Constructor for class org.expasy.mzjava.proteomics.mol.digest.AcceptAllDigestionController
acceptUnsortedSpectra - Variable in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader
acceptUnsortedSpectra() - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader
acceptUnsortedSpectra() - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.MspReader.Builder
acceptUnsortedSpectra() - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.SptxtReader.Builder
accession - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.CVParamType
accession - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DBSequenceType
activationMethod - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
ActivationMethodType - Enum in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117: Java class for activationMethodType.
activityDate - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProtocolApplicationType
add(AtomicSymbol) - Method in class org.expasy.mzjava.core.mol.Composition.Builder: Add an atom for the specified AtomicSymbol
add(AtomicSymbol, int) - Method in class org.expasy.mzjava.core.mol.Composition.Builder: Add count atoms for the specified AtomicSymbol
add(Atom, int) - Method in class org.expasy.mzjava.core.mol.Composition.Builder: Add the atom count times.
add(V) - Method in class org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph.AbstractBuilder
add(V, V, double) - Method in class org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph.AbstractBuilder
add(SimEdge<V>) - Method in class org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph.AbstractBuilder
add(V) - Method in interface org.expasy.mzjava.core.ms.cluster.SimilarityGraphBuilder: Add the vertex to the graph
add(V, V, double) - Method in interface org.expasy.mzjava.core.ms.cluster.SimilarityGraphBuilder: Create and add an edge from vertex1 to vertex2 with similarity equal to score to the graph.
add(SimEdge<V>) - Method in interface org.expasy.mzjava.core.ms.cluster.SimilarityGraphBuilder: Add the simEdge to the graph.
add(V) - Method in class org.expasy.mzjava.core.ms.cluster.SparseSimilarityGraph.Builder
add(V, V, double) - Method in class org.expasy.mzjava.core.ms.cluster.SparseSimilarityGraph.Builder
add(SimEdge<V>) - Method in class org.expasy.mzjava.core.ms.cluster.SparseSimilarityGraph.Builder
add(double, double) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
add(double, double, A) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
add(double, double, Collection<? extends A>) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
add(double) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList: Add a mz to this peak list.
add(double) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList: Add a mz to this peak list.
add(double, double, List<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.TopNList: Add a new peak
add(double, double) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList: Add a mz, intensity pair to the peak list
add(double, double, A) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList: Add a mz, intensity pair and associateed annotations to the peak list
add(double, double, Collection<? extends A>) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList: Add a mz, intensity pair and associated annotations to the peak list
add(PeakProcessor<A, A>) - Method in class org.expasy.mzjava.core.ms.peaklist.PeakProcessorChain
add(A) - Method in class org.expasy.mzjava.core.ms.spectrum.AnnotatedPeak: Add annotation to this AnnotatedPeak
add(double, TimeUnit) - Method in class org.expasy.mzjava.core.ms.spectrum.RetentionTimeList
add(double, double, TimeUnit) - Method in class org.expasy.mzjava.core.ms.spectrum.RetentionTimeList
add(int, int) - Method in class org.expasy.mzjava.core.ms.spectrum.ScanNumberList: Add a ScanNumberInterval that starts at minScanNumber and ends at maxScanNumber to this ScanNumberList
add(int) - Method in class org.expasy.mzjava.core.ms.spectrum.ScanNumberList: Add a ScanNumberDiscrete to this ScanNumberList
add(double, double) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
add(double, double, A) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
add(double, double, Collection<? extends A>) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
add(E) - Method in class org.expasy.mzjava.glycomics.mol.NodeSet
add(Monosaccharide, Monosaccharide, GlycosidicLinkage) - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph.AbstractBuilder: Add a Monosaccharide to the Glycan.
add(Monosaccharide, Substituent, Monosaccharide, GlycosidicLinkage, SubstituentLinkage) - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph.AbstractBuilder: Add monosaccharide and substituent to the Glycan being built.
add(Monosaccharide, List<Monosaccharide>, GlycosidicLinkage) - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph.AbstractBuilder: Adda hyper edge from the list of parents to the monosaccharide.
add(Substituent, Monosaccharide, SubstituentLinkage) - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph.AbstractBuilder: Adda substituent to parent
add(Substituent, List<Monosaccharide>, SubstituentLinkage) - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph.AbstractBuilder: Add a hyper edge from parents to substituent.
add(Monosaccharide, List<Monosaccharide>, GlycosidicLinkage) - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph
add(Monosaccharide, Monosaccharide, GlycosidicLinkage) - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph
add(Substituent, List<Monosaccharide>, SubstituentLinkage) - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph
add(Substituent, Monosaccharide, SubstituentLinkage) - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph
add(MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.ModificationMap
add(MsnSpectrum, List<PeptideMatch>) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriter: Collect the list of peptide identifications for the given spectrum
add(MsnSpectrum, PeptideMatch...) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriter: Collect the list of peptide identifications for the given spectrum
add(AminoAcid) - Method in class org.expasy.mzjava.proteomics.mol.PeptideBuilder: Add an amino acid
add(double) - Method in class org.expasy.mzjava.stats.FrequencyTable: Add a value to this table
add(double, Classification) - Method in class org.expasy.mzjava.stats.ROCTable
add(double, double) - Method in class org.expasy.mzjava.stats.ScatterPlotTable
add(double, Classification) - Method in class org.expasy.mzjava.stats.SimROCTable
addAll(Composition) - Method in class org.expasy.mzjava.core.mol.Composition.Builder: Add all of the atoms in composition to this
addAll(FrequencyTable) - Method in class org.expasy.mzjava.stats.FrequencyTable
addAnnotation(int, A) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
addAnnotation(int, A) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList: Add an annotation to the peak at index
addAnnotation(int, A) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
addAnnotations(int, Collection<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
addAnnotations(int, Collection<A>) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList: Set the annotations for the peak at index
addAnnotations(int, Collection<A>) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
addBins(double[]) - Method in class org.expasy.mzjava.stats.HistogramImpl: Add
addC13(int) - Method in class org.expasy.mzjava.glycomics.ms.spectrum.GlycanFragAnnotation.FragBuilder: Add count C13 isotopes
addC13(int) - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation.Builder: Add count C13 isotopes
addCleavedEdge(SEdge) - Method in class org.expasy.mzjava.glycomics.mol.CutDescriptor: Add a cleaved edge to the CutDescriptor.
addCleavedEdge(Monosaccharide, SEdge, IonType) - Method in class org.expasy.mzjava.glycomics.mol.GlycanFragment.Builder: Add a cleaved edge to the fragment.
addCleavedEdges(Set<SEdge>) - Method in class org.expasy.mzjava.glycomics.mol.CutDescriptor: Add a set of cleaved edge to the CutDescriptor.
addCleavedMonosaccharide(Monosaccharide, CutIndexes) - Method in class org.expasy.mzjava.glycomics.mol.CutDescriptor: Add a cleaved monosaccharide edge to the CutDescriptor.
addCleavedMonosaccharide(Monosaccharide, Monosaccharide, GlycosidicLinkage, CutIndexes, IonType) - Method in class org.expasy.mzjava.glycomics.mol.GlycanFragment.Builder: Add a Monosaccharide to the Glycan.
addCleavedMonosaccharide(Monosaccharide, Substituent, Monosaccharide, GlycosidicLinkage, SubstituentLinkage, CutIndexes, IonType) - Method in class org.expasy.mzjava.glycomics.mol.GlycanFragment.Builder: Add cleavedMonosaccharide and substituent to the Glycan being built.
addCleavedMonosaccharide(Monosaccharide, List<Monosaccharide>, GlycosidicLinkage, CutIndexes, IonType) - Method in class org.expasy.mzjava.glycomics.mol.GlycanFragment.Builder: Add an hyper edge from the list of parents to the cleavedMonosaccharide.
addCleavedMonosaccharides(Set<CleavedMonosaccharide>) - Method in class org.expasy.mzjava.glycomics.mol.CutDescriptor: Add a collection of cleaved monosaccharides edge to the CutDescriptor.
addConsistencyChecks(Set<MzxmlReader.ConsistencyCheck>) - Method in class org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader
addData(double, double, Predicate<Double>) - Method in interface org.expasy.mzjava.stats.Histogram: Add the data into this histogram if the given predicate is true
addData(double, double) - Method in interface org.expasy.mzjava.stats.Histogram: Add value contributing with weight
addData(double) - Method in interface org.expasy.mzjava.stats.Histogram: Add one occurrence of value
addData(double[]) - Method in interface org.expasy.mzjava.stats.Histogram: Add one occurrence of each value
addData(double[], double[]) - Method in interface org.expasy.mzjava.stats.Histogram
addData(double) - Method in class org.expasy.mzjava.stats.HistogramImpl
addData(double, double) - Method in class org.expasy.mzjava.stats.HistogramImpl
addData(double[]) - Method in class org.expasy.mzjava.stats.HistogramImpl
addData(double[], double[]) - Method in class org.expasy.mzjava.stats.HistogramImpl
addData(double, double, Predicate<Double>) - Method in class org.expasy.mzjava.stats.HistogramImpl
addDataAtBin(double, int) - Method in interface org.expasy.mzjava.stats.Histogram: Add data at given bin
addDataAtBin(double, int) - Method in class org.expasy.mzjava.stats.HistogramImpl
addEdge(SimEdge<V>, Pair<? extends V>, EdgeType) - Method in class org.expasy.mzjava.core.ms.cluster.JungSimGraphWrapper
addFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.MsnSpectrumMetaDataReader
addFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.MsnSpectrumMetaDataWriter
addFixedMod(AminoAcid, Modification) - Method in class org.expasy.mzjava.proteomics.mol.digest.ProteinDigester.Builder
AddFlankingPeaksTransformer<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist.peaktransformer: Add flanking peaks to all peaks with an intensity higher than a threshold to a binned spectrum.
AddFlankingPeaksTransformer(double, double) - Constructor for class org.expasy.mzjava.core.ms.peaklist.peaktransformer.AddFlankingPeaksTransformer
addH2(int) - Method in class org.expasy.mzjava.glycomics.ms.spectrum.GlycanFragAnnotation.FragBuilder: Add count H2 isotpes
addH2(int) - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation.Builder: Add count H2 isotpes
addHeaderParser(FastaHeaderParser) - Method in class org.expasy.mzjava.proteomics.io.mol.FastaProteinReader: Add a header parser
addIntensity(double, int) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList.AbstractMergePeakSink
addInterval(double, double) - Method in class org.expasy.mzjava.utils.IntervalList: Add new interval to list.
addIsotope(AtomicSymbol, int) - Method in class org.expasy.mzjava.core.mol.Composition.Builder: Add an atom for the specified symbol and isotope
addIsotope(AtomicSymbol, int, int) - Method in class org.expasy.mzjava.core.mol.Composition.Builder: Add an atom count times for the specified symbol and isotope
addIsotope(Atom) - Method in class org.expasy.mzjava.glycomics.ms.spectrum.GlycanFragAnnotation.FragBuilder: Add the isotope
addIsotope(Atom) - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation.Builder: Add the isotope
addIsotopeComposition(Composition) - Method in class org.expasy.mzjava.glycomics.ms.spectrum.GlycanFragAnnotation.FragBuilder: Add all the atoms from isotopeComposition
addIsotopeComposition(Composition) - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation.Builder: Add all the atoms from isotopeComposition
additionalSearchParams - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType
addMemberIds(Collection<UUID>) - Method in class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum
addMod(int, String) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.LibrarySpectrumBuilder
addMod(ModAttachment, String) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.LibrarySpectrumBuilder
addModification(ModAttachment, Modification) - Method in class org.expasy.mzjava.proteomics.mol.PeptideBuilder: Add a the modification to either end of the the peptide.
addModification(int, Modification) - Method in class org.expasy.mzjava.proteomics.mol.PeptideBuilder: Add a the modification to the side chain of residue at index
addModificationMatch(int, ModificationMatch) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch: Add a the modificationMatch to the side chain of residue at index
addModificationMatch(int, double) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch: Convenience method for adding a ModificationMatch.
addModificationMatch(int, Modification) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch: Convenience method for adding a ModificationMatch.
addModificationMatch(ModAttachment, ModificationMatch) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch: Add a the modificationMatch to either end of the this peptide match.
addModificationMatch(ModAttachment, double) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch: Convenience method for adding a ModificationMatch.
addModificationMatch(ModAttachment, Modification) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch: Convenience method for adding a ModificationMatch.
addModificationToAll(Modification, AminoAcid) - Method in class org.expasy.mzjava.proteomics.mol.PeptideBuilder: Add the modification to all amino acids that are equal to aminoAcid
addModificationToAll(Collection<Modification>, AminoAcid) - Method in class org.expasy.mzjava.proteomics.mol.PeptideBuilder: Add all of the Modification's in modifications to all amino acids that are equal to aminoAcid
addModifs(PeptideMatch, double) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader.PeptideInfoParser
addPeak(double, double, String) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.LibrarySpectrumBuilder
addPeaks(PeakList<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
addPeaks(PeakList<T>, Function<List<T>, List<A>>) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
addPeaks(PeakList<A>) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList: Add peaks and annotations in peakList to this peak list.
addPeaks(PeakList<T>, Function<List<T>, List<A>>) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList: Add peaks (mz, intensity pairs) and optional annotations in peakList to this peak list
addPeaks(PeakList<A>) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
addPeaks(PeakList<T>, Function<List<T>, List<A>>) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
addPeaksNoAnnotations(PeakList<T>) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
addPeaksNoAnnotations(PeakList<T>) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList: Add peaks (without annotations) in peakList to this peak list.
addPeaksNoAnnotations(PeakList<T>) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
addPeaksToSpectrum(S, double[], double[], int) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader: Potentially non-order add peaks to spectrum.
addPeakToSpectrum(Spectrum<A>, double, double, AbstractMsReader.ParseContext) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader: Potentially non-order add peak to spectrum.
addPotentialModification(Modification) - Method in class org.expasy.mzjava.proteomics.ms.ident.ModificationMatch: Add a modification to the list of potential modifications
addProteinAccessionNumber(String) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.LibrarySpectrumBuilder
addProteinAccessionNumbers(String...) - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum: Add a protein accession number to the accession number list of this LibrarySpectrum
addProteinAccessionNumbers(Collection<String>) - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum: Add all the accession numbers from accessionNumbers to the accession number list of this LibrarySpectrum
addProteinAccessionNumbers(String...) - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PeptideSpectrum
addProteinAccessionNumbers(Collection<String>) - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PeptideSpectrum
addProteinId(String) - Method in class org.expasy.mzjava.proteomics.ms.dbsearch.Digest: Add a proteinId.
addProteinMatch(PeptideProteinMatch) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch: Add a protein match to this PeptideMatch
addProteinMatches(Collection<PeptideProteinMatch>) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch: Add all the accessions in proteinAC to this PeptideMatch
addRetentionTime(RetentionTime) - Method in class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum: Add the retentionTime to this MsnSpectrum's retention time list
addRetentionTime(double, TimeUnit) - Method in class org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
addRetentionTime(RetentionTime) - Method in class org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
addRetentionTime(RetentionTimeList) - Method in class org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
addRetentionTimes(RetentionTimeList) - Method in class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum: Add all retention times from the retentionTimes to this MsnSpectrum's retention times.
addScanNumber(ScanNumber) - Method in class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum: Add scanNumber to this MsnSpectrum
addScanNumber(int) - Method in class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum: Add scanNumber to this MsnSpectrum
addScanNumber(SpectrumIdentifier, int, int) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader
addScanNumber(ScanNumber) - Method in class org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
addScanNumber(int) - Method in class org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
addScanNumber(ScanNumberList) - Method in class org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
addScanNumbers(Collection<? extends ScanNumber>) - Method in class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum: Add a all scan numbers from scanNumbers to this MsnSpectrum
addScanNumbers(ScanNumberList) - Method in class org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
addScore(String, double) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch: Add the score to the score map
addSequenceFields(List<Schema.Field>) - Method in class org.expasy.mzjava.proteomics.avro.io.AbstractAminoAcidSequenceReader
addSequenceFields(List<Schema.Field>) - Method in class org.expasy.mzjava.proteomics.avro.io.AbstractAminoAcidSequenceWriter
addSorted(double[], double[]) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
addSorted(double[], double[], int) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
addSorted(double[], double[]) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList: Add the pairs of mz and intensities to this peak list.
addSorted(double[], double[], int) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList: Add the pairs of mz and intensities to this peak list.
addSorted(double[], double[]) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
addSorted(double[], double[], int) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
addTarget(Set<AminoAcid>, Modification) - Method in class org.expasy.mzjava.proteomics.mol.ModifiedPeptideFactory.Builder
addTarget(Set<AminoAcid>, ModAttachment, Modification) - Method in class org.expasy.mzjava.proteomics.mol.ModifiedPeptideFactory.Builder
addTarget(ModAttachment, Modification) - Method in class org.expasy.mzjava.proteomics.mol.ModifiedPeptideFactory.Builder
addTitleParser(TitleParser) - Method in class org.expasy.mzjava.core.io.ms.spectrum.MgfReader
addToArray(double, double, int) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList.AbstractMergePeakSink
addVertex(V) - Method in class org.expasy.mzjava.core.ms.cluster.JungSimGraphWrapper
adjustMass(Double, AminoAcid) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader
adjustMass(Double, ModAttachment) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader
affectedChannel - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.IsotopicContributions.ContributingChannel
affiliation - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PersonType
AffiliationType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110: Java class for AffiliationType complex type.
AffiliationType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AffiliationType
AffineTransformer<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist.peaktransformer: Performs affine transformation (slope*Intensity+offset) on peak intensities.
AffineTransformer(double, double) - Constructor for class org.expasy.mzjava.core.ms.peaklist.peaktransformer.AffineTransformer: Make an instance of affine transformer (slope*Intensity+offset) on peak intensities.
align(PeakList<X>, PeakList<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.DefaultPeakListAligner
align(PeakList<X>, PeakList<Y>) - Method in interface org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.PeakListAligner: Align peakListX with peakListY.
all - Static variable in enum org.expasy.mzjava.proteomics.mol.modification.ModAttachment
AllCrossRingCutType - Class in org.expasy.mzjava.glycomics.mol
AllCrossRingCutType() - Constructor for class org.expasy.mzjava.glycomics.mol.AllCrossRingCutType
allNttProb - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.PeptideprophetResult
alternativeProtein - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
altName - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT
ambiguousResidue - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MassTableType
AmbiguousResidueType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110: Ambiguous residues e.g.
AmbiguousResidueType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AmbiguousResidueType
aminoacid - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
AminoAcid - Enum in org.expasy.mzjava.proteomics.mol: Enum that represents the 21 Proteinogenic amino acids and 3 B, Z and X to represent amino acids for which there is ambiguity.
aminoacidModification - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
AminoacidModificationHashable - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml
AminoacidModificationHashable(MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification) - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.AminoacidModificationHashable
AminoAcidSequence - Class in org.expasy.mzjava.proteomics.mol: Abstract amino acid sequence base class.
AminoAcidSequence(AminoAcid, AminoAcid...) - Constructor for class org.expasy.mzjava.proteomics.mol.AminoAcidSequence: Construct an AminoAcidSequence by copying the residues
AminoAcidSequence(AminoAcid[]) - Constructor for class org.expasy.mzjava.proteomics.mol.AminoAcidSequence: Constructs an AminoAcidSequence by copying the residues.
AminoAcidSequence(AminoAcidSequence, int, int) - Constructor for class org.expasy.mzjava.proteomics.mol.AminoAcidSequence: Constructor that copies the residues and modifications from src.
AminoAcidSequence(AminoAcidSequence, Set<AminoAcid>, AminoAcid) - Constructor for class org.expasy.mzjava.proteomics.mol.AminoAcidSequence: Constructor that copies the source AminoAcidSequence and replaces any amino acids in oldAAs with newAA.
AminoAcidSequence(List<AminoAcid>, Multimap<Integer, Modification>, Multimap<ModAttachment, Modification>) - Constructor for class org.expasy.mzjava.proteomics.mol.AminoAcidSequence: Constructs an AminoAcidSequence from the list of residues with the modifications contained in side chain and term mod map.
analysis - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.AnalysisSummary
analysis - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp
analysis - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult
analysis - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.PeptideprophetResult
analysisCollection - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType
AnalysisCollectionType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110: The analyses performed to get the results, which map the input and output data sets.
AnalysisCollectionType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisCollectionType
analysisData - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DataCollectionType
AnalysisDataType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110: Data sets generated by the analyses, including peptide and protein lists.
AnalysisDataType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisDataType
analysisParams - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionProtocolType
analysisProtocolCollection - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType
AnalysisProtocolCollectionType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110: The collection of protocols which include the parameters and settings of the performed analyses.
AnalysisProtocolCollectionType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisProtocolCollectionType
analysisResult - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
analysisSampleCollection - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType
AnalysisSampleCollectionType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110: The samples analysed can optionally be recorded using CV terms for descriptions.
AnalysisSampleCollectionType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisSampleCollectionType
analysisSoftware - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisSoftwareListType
analysisSoftwareList - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType
AnalysisSoftwareListType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110: The software packages used to perform the analyses.
AnalysisSoftwareListType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisSoftwareListType
analysisSoftwareRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionProtocolType
analysisSoftwareRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProviderType
analysisSoftwareRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType
AnalysisSoftwareType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110: The software used for performing the analyses.
AnalysisSoftwareType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisSoftwareType
analysisSummary - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis
analysisTimestamp - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary
AnalystTitleParser - Class in org.expasy.mzjava.core.io.ms.spectrum.mgf: Parser for the title in mgf files exported by the Analyst software
AnalystTitleParser() - Constructor for class org.expasy.mzjava.core.io.ms.spectrum.mgf.AnalystTitleParser
annotate(S, Peptide) - Method in class org.expasy.mzjava.proteomics.ms.fragment.PeptideFragmentAnnotator: Annotate peaklist from peptide at precursor charge
annotate(S, Peptide, int) - Method in class org.expasy.mzjava.proteomics.ms.fragment.PeptideFragmentAnnotator: Annotate peaklist from peptide at specific charge
annotate(S, Peptide, int, int...) - Method in class org.expasy.mzjava.proteomics.ms.fragment.PeptideFragmentAnnotator: Annotate peaklist from peptide at specific charge
AnnotatedPeak<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.spectrum: A peak that has a list of peak annotations.
AnnotatedPeak() - Constructor for class org.expasy.mzjava.core.ms.spectrum.AnnotatedPeak: Default constructor.
AnnotatedPeak(double, double, int, A...) - Constructor for class org.expasy.mzjava.core.ms.spectrum.AnnotatedPeak: Constructs a AnnotatedPeak.
AnnotatedPeak(AnnotatedPeak<A>) - Constructor for class org.expasy.mzjava.core.ms.spectrum.AnnotatedPeak: Copy constructor.
annotationMap - Variable in class org.expasy.mzjava.core.ms.peaklist.ArrayCursor
AnnotationResolver - Interface in org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt
Anomericity - Enum in org.expasy.mzjava.glycomics.mol
any - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.AnalysisSummary
any - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp
any - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult
appendSequence(String) - Method in class org.expasy.mzjava.proteomics.mol.Protein.Builder
apply(PeakProcessor<A, A>) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
apply(PeakList<A>, PeakList<A>, PeakProcessor<A, A>) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
apply(PeakProcessorChain<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
apply(PeakList<A>, PeakList<A>, PeakProcessorChain<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
apply(PeakProcessor<A, A>) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList: Apply the peakProcessor to the peaks in this PeakList
apply(PeakProcessorChain<A>) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList: Apply the peakProcessorChain to the peaks in this PeakList
apply(UnivariateStatistic, double[]) - Method in class org.expasy.mzjava.core.ms.spectrasim.PearsonsSimFunc
apply(PeakProcessor<A, A>) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
apply(PeakProcessorChain<A>) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
apply(PeptideFragment) - Method in class org.expasy.mzjava.proteomics.ms.fragment.PeptideNeutralLossPeakGenerator.ModifiedAaPresencePredicate
apply(V) - Method in interface org.expasy.mzjava.utils.function.DoubleFunction
approved - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT
ArcsinhTransformer<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist.peaktransformer: Following Huber et al.
ArcsinhTransformer(double, double, double) - Constructor for class org.expasy.mzjava.core.ms.peaklist.peaktransformer.ArcsinhTransformer: Constructor
area - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak
area - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak
areaError - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak
areaError - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak
areaFlag - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioPeptideData
areaFlag - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioSummary
arg(int, String) - Method in class org.expasy.mzjava.utils.URIBuilder
array - Variable in class org.expasy.mzjava.utils.ArrayIndexComparator
ArrayCursor<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist: A cursor for traversing an mz and intensity array
ArrayCursor(double[], double[], int) - Constructor for class org.expasy.mzjava.core.ms.peaklist.ArrayCursor
ArrayCursor(double[], double[], Map<Integer, List<A>>, int) - Constructor for class org.expasy.mzjava.core.ms.peaklist.ArrayCursor
ArrayDigestDB - Class in org.expasy.mzjava.proteomics.ms.dbsearch: A peptide digest db that stores peptide digests in ram and is backed by an array.
ArrayDigestDB(IterativeReader<Protein>, ProteinDigester, DigestDB.AmbiguousAminoAcidAction) - Constructor for class org.expasy.mzjava.proteomics.ms.dbsearch.ArrayDigestDB: Construct a new ArrayDigestDB.
ArrayDigestDB.Builder - Class in org.expasy.mzjava.proteomics.ms.dbsearch: Builder
ArrayDigestDB.Builder(IterativeReader<Protein>, Protease, int) - Constructor for class org.expasy.mzjava.proteomics.ms.dbsearch.ArrayDigestDB.Builder: Create a bulder that build a ArrayDigestDB that digests proteins from the reader using the protease with missedCleavages missed cleavages.
arrayEquals(double[], double[], int) - Static method in class org.expasy.mzjava.utils.PrimitiveArrayUtils: Array equals that takes into account the size
arrayEquals(float[], float[], int) - Static method in class org.expasy.mzjava.utils.PrimitiveArrayUtils: Array equals that takes into account the size
arrayHashCode(double[], int) - Static method in class org.expasy.mzjava.utils.PrimitiveArrayUtils: Array hash code that takes into account the peak list size
arrayHashCode(float[], int) - Static method in class org.expasy.mzjava.utils.PrimitiveArrayUtils: Array hash code that takes into account the peak list size
ArrayIndexComparator<T extends Number> - Class in org.expasy.mzjava.utils: Abstract class that compare indices of array of Number.
ArrayIndexComparator(T...) - Constructor for class org.expasy.mzjava.utils.ArrayIndexComparator
ArrayIndexSorter - Class in org.expasy.mzjava.utils: This class sort indices of an array object given an index comparator.
ArrayIndexSorter() - Constructor for class org.expasy.mzjava.utils.ArrayIndexSorter
AsapratioContribution - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117: Java class for anonymous complex type.
AsapratioContribution() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioContribution
asapratioContribution - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioPeptideData
asapratioLcHeavypeak - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioContribution
AsapratioLcHeavypeak - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117: Java class for anonymous complex type.
AsapratioLcHeavypeak() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak
asapratioLcLightpeak - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioContribution
AsapratioLcLightpeak - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117: Java class for anonymous complex type.
AsapratioLcLightpeak() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak
AsapratioPeptideData - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117: Java class for anonymous complex type.
AsapratioPeptideData() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioPeptideData
asapratioPeptideData - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioResult
AsapratioResult - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117: Java class for anonymous complex type.
AsapratioResult() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioResult
AsapratioSummary - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117: Java class for anonymous complex type.
AsapratioSummary() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioSummary
AsapratioTimestamp - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117: Java class for anonymous complex type.
AsapratioTimestamp() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioTimestamp
assertConsistent(double, double, float) - Method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.MzmlSpectrumCheck
assumedCharge - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
Atom - Class in org.expasy.mzjava.core.mol
atomCounterMap - Variable in class org.expasy.mzjava.core.mol.Composition
AtomicCompositionParser - Class in org.expasy.mzjava.core.mol: Parsing atomic composition.
AtomicSymbol - Enum in org.expasy.mzjava.core.mol
auditCollection - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType
AuditCollectionType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110: The complete set of Contacts (people and organisations) for this file.
AuditCollectionType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AuditCollectionType
author - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioSummary
author - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioSummary
authors - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType
avgeMass - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.CompositionT
avgMassDelta - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ModificationType
avgMassDelta - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SubstitutionModificationType
AvroExternalizable - Interface in org.expasy.mzjava.avro.io: Base interface for classes that serialize and de-serialize using the MzJava Avro classes.
AvroIO<U extends AvroExternalizable> - Class in org.expasy.mzjava.avro.io: Base class for MzJava Hadoop Avro IO.
AvroIO() - Constructor for class org.expasy.mzjava.avro.io.AvroIO
avroRead(Decoder) - Method in class org.expasy.mzjava.hadoop.io.AbstractAvroWritable
avroRead(Decoder) - Method in class org.expasy.mzjava.hadoop.io.AbstractPeakListValue
avroRead(Decoder) - Method in class org.expasy.mzjava.hadoop.io.AvroWritable
AvroReader<O> - Interface in org.expasy.mzjava.avro.io
AvroWritable - Class in org.expasy.mzjava.hadoop.io
AvroWritable() - Constructor for class org.expasy.mzjava.hadoop.io.AvroWritable
avroWrite(Encoder) - Method in class org.expasy.mzjava.hadoop.io.AbstractAvroWritable
avroWrite(Encoder) - Method in class org.expasy.mzjava.hadoop.io.AbstractPeakListValue
avroWrite(Encoder) - Method in class org.expasy.mzjava.hadoop.io.AvroWritable
AvroWriter<O> - Interface in org.expasy.mzjava.avro.io




B

BackbonePeakGenerator - Class in org.expasy.mzjava.proteomics.ms.fragment
 
BackbonePeakGenerator(Set<IonType>, double) - Constructor for class org.expasy.mzjava.proteomics.ms.fragment.BackbonePeakGenerator
 
background - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak
 
background - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak
 
baseName - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary
 
baseName - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
 
begin(PeakList<X>, PeakList<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.AbstractSimFunc
 
begin(PeakList<X>, PeakList<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.DelayedPeakPairProcessor
 
begin(PeakList<X>, PeakList<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.filter.ThresholdPeakPairFilter
 
begin(PeakList<X>, PeakList<Y>) - Method in interface org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.PeakPairSink

Called before a new PeakList pair is processed

begin(PeakList<X>, PeakList<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.PeakCountEqualizer
 
begin(PeakList<X>, PeakList<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.PeakPairIntensityLog10Transformer
 
begin(PeakList<X>, PeakList<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.PeakPairIntensityLogETransformer
 
begin(PeakList<X>, PeakList<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.PeakPairIntensitySqrtTransformer
 
begin(PeakList<X>, PeakList<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.PeakPairIonCurrentNormalizer
 
begin(PeakList<X>, PeakList<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.TopPeakPairTransformer
 
bibliographicReference - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType
 
BibliographicReferenceType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

Represents bibliographic references.

BibliographicReferenceType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType
 
binary - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
 
BinnedSpectrumFilter<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist.peakfilter

Class to bin a spectrum.

BinnedSpectrumFilter(double, double, double, BinnedSpectrumFilter.IntensityMode) - Constructor for class org.expasy.mzjava.core.ms.peaklist.peakfilter.BinnedSpectrumFilter

Constructor class for binned spectrum.

BinnedSpectrumFilter.IntensityMode - Enum in org.expasy.mzjava.core.ms.peaklist.peakfilter
 
BinomialUtils - Class in org.expasy.mzjava.stats
 
BioJavaFastaProteinReader - Class in org.expasy.mzjava.core.mol.polymer.prot

A Protein reader based on biojava3 FastaReader object.

BioJavaFastaProteinReader(File) - Constructor for class org.expasy.mzjava.core.mol.polymer.prot.BioJavaFastaProteinReader
 
BioJavaFastaProteinReader(InputStream) - Constructor for class org.expasy.mzjava.core.mol.polymer.prot.BioJavaFastaProteinReader
 
breaks - Variable in class org.expasy.mzjava.stats.HistogramImpl
 
build() - Method in class org.expasy.mzjava.core.mol.Composition.Builder

Build the composition

build() - Method in class org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph.AbstractBuilder
 
build(List<S>, SimFunc<A, A>, Tolerance, double) - Static method in class org.expasy.mzjava.core.ms.cluster.PeakListSimGraphFactory

Build a new DenseSimilarityGraph

build(List<S>, SimilarityGraphBuilder<S, G>, SimFunc<A, A>, Tolerance, double) - Static method in class org.expasy.mzjava.core.ms.cluster.PeakListSimGraphFactory

Build a new SimilarityGraph

build() - Method in interface org.expasy.mzjava.core.ms.cluster.SimilarityGraphBuilder
 
build() - Method in class org.expasy.mzjava.core.ms.cluster.SparseSimilarityGraph.Builder
 
build() - Method in class org.expasy.mzjava.core.ms.consensus.AbstractConsensusSpectrumBuilder
 
build() - Method in class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum.Builder
 
build() - Method in class org.expasy.mzjava.glycomics.mol.Glycan.Builder

Build the Glycan.

build() - Method in class org.expasy.mzjava.glycomics.mol.GlycanFragment.Builder

Build the Glycosidic Fragments Fragment.

build() - Method in class org.expasy.mzjava.glycomics.ms.spectrum.GlycanFragAnnotation.FragBuilder

Build the CrossRingFragAnnotation annotation.

build() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder.Builder

Build a PepXmlWriter

build() - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.MspReader.Builder
 
build(PeakList.Precision, ModificationResolver, AnnotationResolver, boolean) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.LibrarySpectrumBuilder
 
build() - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.SptxtReader.Builder
 
build() - Method in class org.expasy.mzjava.proteomics.mol.digest.ProteinDigester.Builder
 
build() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodMod.Builder

Build the UnimodMod.

build() - Method in class org.expasy.mzjava.proteomics.mol.ModifiedPeptideFactory.Builder
 
build() - Method in class org.expasy.mzjava.proteomics.mol.PeptideBuilder

Build a Peptide

build() - Method in class org.expasy.mzjava.proteomics.mol.Protein.Builder
 
build() - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.BuilderOld
 
build() - Method in class org.expasy.mzjava.proteomics.ms.dbsearch.ArrayDigestDB.Builder

Build the ArrayDigestDB

build() - Method in interface org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumDB.EndDSL

Build the PeptideSpectrumDB

build() - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation.Builder

Build the PepFragAnnotation annotation.

build() - Method in class org.expasy.mzjava.spark.Cached
 
build() - Method in class org.expasy.mzjava.spark.CachedAbsoluteTolerance
 
build() - Method in class org.expasy.mzjava.spark.CachedPpmTolerance
 
build() - Method in class org.expasy.mzjava.utils.URIBuilder
 
buildConsensus(int, Peptide, Collection<S>, Set<String>, RetentionTimeList) - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.Builder
 
buildConsensus(int, Peptide, Collection<S>, Set<String>) - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.Builder
 
builder() - Static method in class org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph
 
builder(int) - Static method in class org.expasy.mzjava.core.ms.cluster.SparseSimilarityGraph
 
builder() - Static method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum
 
builder(PeakList.Precision, URI) - Static method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum
 
buildFragment(FragmentType) - Method in class org.expasy.mzjava.proteomics.mol.PeptideBuilder

Build a PeptideFragment

buildSate - Variable in class org.expasy.mzjava.glycomics.mol.SaccharideGraph.AbstractBuilder
 
buildSpectrumQuerySpectrumAttribute(MsnSpectrum) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriter

Format MsnSpectrum id for element spectrum attribute of spectrum_query element.

BytesUtils - Class in org.expasy.mzjava.core.io.ms.spectrum
 




C

C - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
C13 - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
C13_MASS - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
C_MASS - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
Ca - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
Ca_MASS - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
cache - Variable in class org.expasy.mzjava.proteomics.ms.dbsearch.SoftRefPepSpectrumCache
 
Cached<T> - Class in org.expasy.mzjava.spark
 
Cached() - Constructor for class org.expasy.mzjava.spark.Cached
 
CachedAbsoluteTolerance - Class in org.expasy.mzjava.spark
 
CachedAbsoluteTolerance(double) - Constructor for class org.expasy.mzjava.spark.CachedAbsoluteTolerance
 
CachedPpmTolerance - Class in org.expasy.mzjava.spark
 
CachedPpmTolerance(double) - Constructor for class org.expasy.mzjava.spark.CachedPpmTolerance
 
cachePeptideSpectrumWith(PeptideSpectrumCache) - Method in interface org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumDB.FragmentDSL
 
calcCentroidMz(TDoubleArrayList, TDoubleArrayList, CentroidFilter.PeakIntensityInfo) - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.CentroidFilter

Given the index-bounds of a centroid, the centroid mass and intensity is calculated.

calcFMeasure(Collection<Set<E>>, Collection<Set<E>>) - Static method in class org.expasy.mzjava.core.ms.cluster.FMeasure
 
calcIsotopeDelta(Composition) - Static method in class org.expasy.mzjava.core.mol.MassCalculator
 
calcLength(double[], int) - Static method in class org.expasy.mzjava.core.ms.peaklist.PeakListUtils
 
calcLength(float[], int) - Static method in class org.expasy.mzjava.core.ms.peaklist.PeakListUtils
 
calcMzSamplingDist(TDoubleArrayList) - Static method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.CentroidFilter
 
calcNeutralPepMass - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
calcPI - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
calcR(TDoubleList, TDoubleList) - Static method in class org.expasy.mzjava.stats.PearsonsCorrelationCoeff
 
calcR(double[], double[]) - Static method in class org.expasy.mzjava.stats.PearsonsCorrelationCoeff
 
calcR(TDoubleArrayList, TDoubleArrayList, TDoubleArrayList) - Static method in class org.expasy.mzjava.stats.WeightedPearsonsCorrelationCoeff
 
calcSimilarity(PeakList<X>, PeakList<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.DpSimFunc
 
calcSimilarity(PeakList<X>, PeakList<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.McNdpSimFunc
 
calcSimilarity(PeakList<X>, PeakList<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.NdpSimFunc
 
calcSimilarity(PeakList<X>, PeakList<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.PearsonsSimFunc
 
calcSimilarity(PeakList<X>, PeakList<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.PspcSimFunc
 
calcSimilarity(PeakList<X>, PeakList<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.SharedPeakSimFunc
 
calcSimilarity(PeakList<X>, PeakList<Y>) - Method in interface org.expasy.mzjava.core.ms.spectrasim.SimFunc

Calculate the similarity score of the two vectors.

calcSimilarity(PeakList<X>, PeakList<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.WeightedPearsonsSimFunc
 
calcTheoreticalMz() - Method in class org.expasy.mzjava.glycomics.ms.spectrum.GlycanFragAnnotation

Returns the theoretical m/z for this annotation.

calcTotalMembers(Collection<? extends Set>) - Static method in class org.expasy.mzjava.core.ms.cluster.FMeasure
 
calculateAverageMass(Atom) - Static method in class org.expasy.mzjava.core.mol.MassCalculator

Calculates average mass of Atom

calculateAverageMass(Composition) - Static method in class org.expasy.mzjava.core.mol.MassCalculator

Calculates the sum of the average mass of each Atom in this
 Composition.

calculatedMassToCharge - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType
 
calculatedPI - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType
 
calculateFDR() - Method in class org.expasy.mzjava.stats.statscores.FirstRankScoreStatistics
 
calculateFDR() - Method in class org.expasy.mzjava.stats.statscores.FitDecoyScoreStatistics
 
calculateFDR() - Method in class org.expasy.mzjava.stats.statscores.ScoreStatistics
 
calculateMass() - Method in class org.expasy.mzjava.glycomics.mol.Glycan

Return the molecular mass of this glycan.

calculateMass(IonType) - Method in class org.expasy.mzjava.proteomics.mol.PeptideFragment

Calculate the mass of this PeptideFragment given the ionType

calculateMolecularMass() - Method in class org.expasy.mzjava.glycomics.mol.GlycanFragment

Return the mass of the this fragment.

calculateMonomerMassDefect() - Method in class org.expasy.mzjava.proteomics.mol.AminoAcidSequence
 
calculateMonomerMassSum() - Method in class org.expasy.mzjava.proteomics.mol.AminoAcidSequence

Sums the mass of all the monomers

calculateMz(double, int, IonType) - Method in class org.expasy.mzjava.core.mol.MassCalculator

Calculate the m/z for the given neutral molecular weight.

calculateMz(double, int, FragmentType) - Method in class org.expasy.mzjava.glycomics.mol.DefaultGlycanMassCalculator

Return the value of the mass over charge.

calculateMz(int) - Method in class org.expasy.mzjava.glycomics.mol.Glycan

Return the mass/charge of this glycan.

calculateMz(double, int, FragmentType) - Method in interface org.expasy.mzjava.glycomics.mol.GlycanMassCalculator

Return the value of the mass over charge.

calculateMz(double, int, IonType) - Method in class org.expasy.mzjava.proteomics.mol.AAMassCalculator
 
calculateMz(int) - Method in class org.expasy.mzjava.proteomics.mol.Peptide

Calculate the m/z of this peptide at the given charge

calculateMz(IonType, int) - Method in class org.expasy.mzjava.proteomics.mol.PeptideFragment

Calculate the m/z of this PeptideFragment given the charge and
 ionType

calculateNeutralMolecularMass(double, int) - Method in class org.expasy.mzjava.core.mol.MassCalculator

Calculate the neutral molecular weight given a m/z, charge and mass of the charge carrying particle.

calculateNeutralMolecularMass(Peak) - Method in class org.expasy.mzjava.core.mol.MassCalculator
 
calculateNeutralMolecularMass(double, int) - Method in class org.expasy.mzjava.proteomics.mol.AAMassCalculator

Calculate the neutral molecular weight given a m/z, charge and mass of the charge carrying particle.

calculateNeutralMolecularMass(Peak) - Method in class org.expasy.mzjava.proteomics.mol.AAMassCalculator
 
calculatePrecursor(ConsensusSpectrum<? extends LibPeakAnnotation>) - Method in class org.expasy.mzjava.core.ms.consensus.AbstractConsensusSpectrumBuilder
 
calculatePrecursor(ConsensusSpectrum<? extends LibPeakAnnotation>) - Method in class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum.Builder
 
calculatePrecursor(ConsensusSpectrum<? extends LibPeakAnnotation>) - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.BuilderOld
 
calculateQValue() - Method in class org.expasy.mzjava.stats.statscores.ScoreStatistics
 
calculateTotalSaccharideMass() - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph

Returns the total mass of the Saccharide Graph.

calcVectorLength() - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList
 
calcVectorLength() - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleFloatPeakList
 
calcVectorLength() - Method in class org.expasy.mzjava.core.ms.peaklist.DoublePeakList
 
calcVectorLength() - Method in class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList
 
calcVectorLength() - Method in class org.expasy.mzjava.core.ms.peaklist.FloatPeakList
 
calcVectorLength() - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Calculates the vector length of this peak list

calcVectorLength() - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
canFragmentCrossRing(Monosaccharide) - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph

Return a boolean value that show if the glycan is fragmentable.

canPeek(int) - Method in class org.expasy.mzjava.core.ms.peaklist.ArrayCursor
 
canPeek(int) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakCursor

Returns true if there are n more peaks in the peak list

CentroidFilter<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist.peakfilter

Class to select all peaks that are local maxima and replace their
 mass/intensity values by the centroid values calculated within a
 neighborhood.

CentroidFilter(double, CentroidFilter.IntensityMode) - Constructor for class org.expasy.mzjava.core.ms.peaklist.peakfilter.CentroidFilter
 
CentroidFilter.IntensityMode - Enum in org.expasy.mzjava.core.ms.peaklist.peakfilter
 
CentroidFilter.PeakIntensityInfo - Class in org.expasy.mzjava.core.ms.peaklist.peakfilter
 
CentroidFilter.PeakIntensityInfo() - Constructor for class org.expasy.mzjava.core.ms.peaklist.peakfilter.CentroidFilter.PeakIntensityInfo
 
centroidingPreference - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary
 
channel - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraResult.Intensity
 
channel - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.FragmentMasses
 
channel - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.IsotopicContributions.ContributingChannel.AffectedChannel
 
channel - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.IsotopicContributions.ContributingChannel
 
channelCode - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary
 
charge(int) - Method in class org.expasy.mzjava.core.mol.Composition.Builder

Set the charge.

charge - Variable in class org.expasy.mzjava.core.mol.Composition
 
charge - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.IonTypeType
 
charge - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioContribution
 
ChargeMzSplitter<V> - Class in org.expasy.mzjava.utils.function

Base class for splitter that splits on charge and m/z

ChargeMzSplitter(Tolerance) - Constructor for class org.expasy.mzjava.utils.function.ChargeMzSplitter
 
chargeState - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType
 
check(double, double) - Method in class org.expasy.mzjava.core.ms.AbsoluteTolerance
 
check(double, double) - Method in class org.expasy.mzjava.core.ms.PpmTolerance
 
check(double, double) - Method in class org.expasy.mzjava.core.ms.Tolerance
 
check(double, double, int) - Method in class org.expasy.mzjava.core.ms.Tolerance
 
checkConsistencies(MsnSpectrum, Spectrum) - Method in class org.expasy.mzjava.external.io.ms.spectrum.ConsistencyChecker

Check strict and tolerant consistencies on spectrum

checkConsistencies(S, Spectrum) - Method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.EbiMzmlReader
 
checkConsistency(MsnSpectrum, Spectrum, float) - Method in interface org.expasy.mzjava.external.io.ms.spectrum.ConsistencyCheck

Check consistency

checkConsistency(MsnSpectrum, Spectrum, float) - Method in enum org.expasy.mzjava.external.io.ms.spectrum.mzml.MzmlConsistencyCheck
 
checkConsistency(MsnSpectrum, Spectrum, float) - Method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.MzmlSpectrumCheck
 
checkIsBuilding() - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph.AbstractBuilder
 
checkLinkedCarbon(CutIndexes, CutDirection, int) - Method in class org.expasy.mzjava.glycomics.mol.Monosaccharide

Check if a carbon of the ring is in the fragment specified by the cutIndexes and the cutDirection.

checkMonosaccharidesPresence(List<Monosaccharide>) - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph.AbstractBuilder

Check for the presence of all cleaved monosaccharides inside the graph.

cidIndex - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioPeptideData
 
classification - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.SpecificityT
 
Classification - Enum in org.expasy.mzjava.stats
 
Classifier<E> - Interface in org.expasy.mzjava.stats
 
classify(E, E) - Method in interface org.expasy.mzjava.stats.Classifier
 
clear() - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList

Clears the peak list, the size is set to 0 and the backing arrays are set to an clear array

clear() - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.TopNList

Remove all peaks

clear() - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Clears the peak list, the size is set to 0 and objects used to store peaks are unreferenced to allow
 garbage collection

clear() - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
clear() - Method in class org.expasy.mzjava.glycomics.mol.NodeSet
 
clear() - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.LibrarySpectrumBuilder
 
clear() - Method in class org.expasy.mzjava.proteomics.mol.PeptideBuilder

Reset this builder

clear() - Method in interface org.expasy.mzjava.stats.Histogram

Empty data

clear() - Method in class org.expasy.mzjava.stats.HistogramImpl
 
clear() - Method in class org.expasy.mzjava.utils.MixedRadixNtupleGenerator.NtupleContainer
 
clearAnnotations() - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
 
clearAnnotations() - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Remove all annotations from this PeakList

clearAnnotations() - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
clearAnnotationsAt(int) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
 
clearAnnotationsAt(int) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Remove all annotations for the peak at index

clearAnnotationsAt(int) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
clearOverrides() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodModificationResolver
 
clearProteinAccessionNumber() - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum

Clear the accession number list //review should this class be mutable?

clearTranslations() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodModificationResolver
 
CleavageSiteFinder - Interface in org.expasy.mzjava.proteomics.mol.digest
 
CleavageSiteFinderImpl - Class in org.expasy.mzjava.proteomics.mol.digest

The default implementation of CleavageSiteFinder

CleavageSiteFinderImpl(CleavageSiteMatcher) - Constructor for class org.expasy.mzjava.proteomics.mol.digest.CleavageSiteFinderImpl
 
cleavageSiteIteration(ProteinDigester.CleavageSiteIteration) - Method in class org.expasy.mzjava.proteomics.mol.digest.ProteinDigester.Builder
 
CleavageSiteMatcher - Class in org.expasy.mzjava.proteomics.mol.digest

This matcher is used to find the sites of cleavage in an amino-acid sequence.

CleavageSiteMatcher(String) - Constructor for class org.expasy.mzjava.proteomics.mol.digest.CleavageSiteMatcher

Pattern has a special format:
 
 Pn ...

CleavageSiteMatcher(String, Optional<Modification>, Optional<Modification>) - Constructor for class org.expasy.mzjava.proteomics.mol.digest.CleavageSiteMatcher
 
CleavageSiteParseException - Exception in org.expasy.mzjava.proteomics.mol.digest
 
CleavageSiteParseException(String) - Constructor for exception org.expasy.mzjava.proteomics.mol.digest.CleavageSiteParseException
 
CleavageSiteParseException(String, int) - Constructor for exception org.expasy.mzjava.proteomics.mol.digest.CleavageSiteParseException
 
CleavageSiteVisitor - Interface in org.expasy.mzjava.proteomics.mol.digest
 
CleavedMonosaccharide - Class in org.expasy.mzjava.glycomics.mol
 
CleavedMonosaccharide(Monosaccharide, CutIndexes) - Constructor for class org.expasy.mzjava.glycomics.mol.CleavedMonosaccharide
 
close() - Method in class org.expasy.mzjava.app.io.MonitoredIterativeReader
 
close() - Method in class org.expasy.mzjava.core.io.ConcatIterativeReader
 
close() - Method in interface org.expasy.mzjava.core.io.IterativeReader

Closes the reader and releases any system resources associated with
 it.

close() - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfWriter
 
close() - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader
 
close() - Method in class org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader
 
close() - Method in class org.expasy.mzjava.core.mol.polymer.prot.BioJavaFastaProteinReader
 
close() - Method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.EbiMzmlReader
 
close() - Method in class org.expasy.mzjava.glycomics.io.ms.gwp.GWPWriter
 
close() - Method in class org.expasy.mzjava.hadoop.io.HadoopSpectraReader
 
close() - Method in class org.expasy.mzjava.hadoop.io.HadoopSpectraWriter
 
close() - Method in class org.expasy.mzjava.proteomics.io.mol.FastaProteinReader
 
close() - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.AbstractSptxtWriter
 
cluster(SimilarityGraph<V>) - Method in interface org.expasy.mzjava.core.ms.cluster.ClusterBuilder

Cluster the vertices given a SimilarityGraph

cluster(SimilarityGraph<V>, Collection<Set<V>>) - Method in interface org.expasy.mzjava.core.ms.cluster.ClusterBuilder

Cluster the vertices in graph using the startingClusters as a starting point.

cluster(SimilarityGraph<V>) - Method in class org.expasy.mzjava.core.ms.cluster.CompoundClusterBuilder
 
cluster(SimilarityGraph<V>, Collection<Set<V>>) - Method in class org.expasy.mzjava.core.ms.cluster.CompoundClusterBuilder
 
cluster(SimilarityGraph<V>) - Method in class org.expasy.mzjava.core.ms.cluster.GlobalThresholdClusterBuilder
 
cluster(SimilarityGraph<V>, Collection<Set<V>>) - Method in class org.expasy.mzjava.core.ms.cluster.GlobalThresholdClusterBuilder
 
cluster(SimilarityGraph<V>) - Method in class org.expasy.mzjava.core.ms.cluster.KMeansPlusPlusClusterBuilder
 
cluster(SimilarityGraph<V>, Collection<Set<V>>) - Method in class org.expasy.mzjava.core.ms.cluster.KMeansPlusPlusClusterBuilder
 
cluster(SimilarityGraph<V>) - Method in class org.expasy.mzjava.core.ms.cluster.MSTClusterBuilder
 
cluster(SimilarityGraph<V>, Collection<Set<V>>) - Method in class org.expasy.mzjava.core.ms.cluster.MSTClusterBuilder
 
ClusterBuilder<V> - Interface in org.expasy.mzjava.core.ms.cluster

Interface for any object that can cluster the vertexes of a SimilarityGraph

code - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AmbiguousResidueType
 
code - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ResidueType
 
collisionEnergy - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
 
compact() - Method in class org.expasy.mzjava.proteomics.ms.dbsearch.Digest

Free up any resources that are no longer needed.

compare(PeakList, PeakList) - Method in class org.expasy.mzjava.core.ms.peaklist.PeakListComparator
 
compare(RetentionTime, RetentionTime) - Method in class org.expasy.mzjava.core.ms.spectrum.RetentionTimeComparator
 
compare(Monosaccharide, GlycosidicLinkage, Monosaccharide, GlycosidicLinkage) - Method in interface org.expasy.mzjava.glycomics.mol.TraversalComparator

Compares two children of a node in a SaccharideGraph for order.

compare(SpectrumKey, SpectrumKey) - Method in class org.expasy.mzjava.hadoop.io.DefaultSpectrumKeyRawComparator
 
compare(byte[], int, int, byte[], int, int) - Method in class org.expasy.mzjava.hadoop.io.DefaultSpectrumKeyRawComparator
 
compare(PeptideMatch, PeptideMatch) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatchComparator
 
compare(Integer, Integer) - Method in class org.expasy.mzjava.utils.ArrayIndexComparator
 
compareTo(Atom) - Method in class org.expasy.mzjava.core.mol.Atom
 
compareTo(Peak) - Method in class org.expasy.mzjava.core.ms.peaklist.Peak
 
compareTo(SNode) - Method in class org.expasy.mzjava.glycomics.mol.SNode
 
compareTo(SpectrumKey) - Method in class org.expasy.mzjava.hadoop.io.SpectrumKey
 
compareTo(PeptideMatch) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch
 
compensationVoltage - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
 
CompositeModResolver - Class in org.expasy.mzjava.proteomics.mol.modification
 
CompositeModResolver(ModificationResolver, ModificationResolver...) - Constructor for class org.expasy.mzjava.proteomics.mol.modification.CompositeModResolver
 
Composition - Class in org.expasy.mzjava.core.mol

A collection of atoms and charge

Composition(TObjectIntMap<Atom>, int) - Constructor for class org.expasy.mzjava.core.mol.Composition

Construct a new composition that contains the charge and the atoms in the atomCounterMap.

Composition(String, TObjectIntMap<Atom>, int) - Constructor for class org.expasy.mzjava.core.mol.Composition
 
Composition(Composition...) - Constructor for class org.expasy.mzjava.core.mol.Composition

Constructs a composition that is the sum of the compositions

composition - Variable in class org.expasy.mzjava.glycomics.mol.GlycanNode
 
composition - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.CompositionT
 
Composition.Builder - Class in org.expasy.mzjava.core.mol

Class to build a Composition

Composition.Builder() - Constructor for class org.expasy.mzjava.core.mol.Composition.Builder

Construct a new Builder

Composition.Builder(AtomicSymbol) - Constructor for class org.expasy.mzjava.core.mol.Composition.Builder

Construct a new Builder and add the atom

Composition.Builder(AtomicSymbol, int) - Constructor for class org.expasy.mzjava.core.mol.Composition.Builder

Construct a new Builder and add the atom count times

CompositionReader - Class in org.expasy.mzjava.avro.io
 
CompositionReader() - Constructor for class org.expasy.mzjava.avro.io.CompositionReader
 
CompositionT - Class in org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb

Java class for composition_t complex type.

CompositionT() - Constructor for class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.CompositionT
 
CompositionWriter - Class in org.expasy.mzjava.avro.io
 
CompositionWriter() - Constructor for class org.expasy.mzjava.avro.io.CompositionWriter
 
CompoundClusterBuilder<V> - Class in org.expasy.mzjava.core.ms.cluster

Cluster builder that uses the output of builder1 as the starting clusters of builder2.

CompoundClusterBuilder(ClusterBuilder<V>, ClusterBuilder<V>) - Constructor for class org.expasy.mzjava.core.ms.cluster.CompoundClusterBuilder

Construct a new CompoundClusterBuilder

compress(byte[]) - Static method in class org.expasy.mzjava.core.io.ms.spectrum.BytesUtils
 
ConcatIterativeReader<T> - Class in org.expasy.mzjava.core.io

Combines multiple IterativeReaders into a single IterativeReader.

ConcatIterativeReader(IterativeReader<T>...) - Constructor for class org.expasy.mzjava.core.io.ConcatIterativeReader

Create an IterativeReader that iterates over the readers in readers

ConcatIterativeReader(Collection<IterativeReader<T>>) - Constructor for class org.expasy.mzjava.core.io.ConcatIterativeReader

Create an IterativeReader that iterates over the readers in inputs

confidenceInterval(int, double) - Static method in class org.expasy.mzjava.stats.PoissonUtils

Calculates a confidence interval for a poisson distribution.

confidenceInterval95(int, int) - Static method in class org.expasy.mzjava.stats.BinomialUtils

Calculates the 95% confidence interval for the ratio of the two menas.

confidenceInterval95(int) - Static method in class org.expasy.mzjava.stats.PoissonUtils

See http://www.math.mcmaster.ca/peter/s743/poissonalpha.html.

ConsensusPeakSink<A extends LibPeakAnnotation> - Class in org.expasy.mzjava.core.ms.consensus

Peak filter that retains peaks that have a mergedPeakCount that is >= absoluteMinPeakCount && >= peakFraction*consensusSize.

ConsensusPeakSink(ConsensusSpectrum<A>, double, int) - Constructor for class org.expasy.mzjava.core.ms.consensus.ConsensusPeakSink
 
ConsensusSpectrum<A extends LibPeakAnnotation> - Class in org.expasy.mzjava.core.ms.consensus
 
ConsensusSpectrum(int, PeakList.Precision, Set<UUID>) - Constructor for class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum
 
ConsensusSpectrum(ConsensusSpectrum<A>, PeakProcessor<A, A>) - Constructor for class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum
 
ConsensusSpectrum(ConsensusSpectrum<A>, PeakProcessorChain<A>) - Constructor for class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum
 
ConsensusSpectrum.Builder - Class in org.expasy.mzjava.core.ms.consensus
 
ConsensusSpectrum.Builder() - Constructor for class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum.Builder
 
ConsistencyCheck - Interface in org.expasy.mzjava.external.io.ms.spectrum

A consistency check interface

ConsistencyChecker<C extends ConsistencyCheck> - Class in org.expasy.mzjava.external.io.ms.spectrum

ConsistencyChecker checks for consistencies on MsnSpectrum.

ConsistencyChecker(Set<C>) - Constructor for class org.expasy.mzjava.external.io.ms.spectrum.ConsistencyChecker

Create an instance of ConsistencyChecker composed of a given strict consistencies

ConsistencyCheckException - Exception in org.expasy.mzjava.external.io.ms.spectrum
 
ConsistencyCheckException(String, String, String) - Constructor for exception org.expasy.mzjava.external.io.ms.spectrum.ConsistencyCheckException
 
ConsistencyCheckHandler<C extends ConsistencyCheck> - Interface in org.expasy.mzjava.external.io.ms.spectrum

Class implementing this interface are able to control the ConsistencyCheck behavior

consistencyChecks(MsnSpectrum) - Method in class org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader

Check for all spectrum consistencies

ConsoleProgressBar - Class in org.expasy.mzjava.app.pb

A simple terminal progress bar.

ConsoleProgressBar(ConsoleProgressBar.View) - Constructor for class org.expasy.mzjava.app.pb.ConsoleProgressBar
 
ConsoleProgressBar.View - Class in org.expasy.mzjava.app.pb
 
ConsoleProgressBar.View() - Constructor for class org.expasy.mzjava.app.pb.ConsoleProgressBar.View
 
CONSTANT_RESOLVER - Static variable in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader
 
contactRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ContactRoleType
 
contactRole - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisSoftwareType
 
contactRole - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProviderType
 
contactRole - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SampleType
 
ContactRoleType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

The role that a Contact plays in an organization or with respect to the associating class.

ContactRoleType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ContactRoleType
 
contains(V) - Method in class org.expasy.mzjava.core.ms.cluster.SimEdge
 
contains(RetentionTime) - Method in interface org.expasy.mzjava.core.ms.spectrum.RetentionTime
 
contains(RetentionTime) - Method in class org.expasy.mzjava.core.ms.spectrum.RetentionTimeDiscrete
 
contains(RetentionTime) - Method in class org.expasy.mzjava.core.ms.spectrum.RetentionTimeInterval
 
contains(Object) - Method in class org.expasy.mzjava.core.ms.spectrum.RetentionTimeList
 
contains(ScanNumber) - Method in interface org.expasy.mzjava.core.ms.spectrum.ScanNumber

Return true if this scan number contains the scanNumber, false otherwise

contains(ScanNumber) - Method in class org.expasy.mzjava.core.ms.spectrum.ScanNumberDiscrete
 
contains(ScanNumber) - Method in class org.expasy.mzjava.core.ms.spectrum.ScanNumberInterval
 
contains(Object) - Method in class org.expasy.mzjava.core.ms.spectrum.ScanNumberList
 
contains(Monosaccharide) - Method in class org.expasy.mzjava.glycomics.mol.CutDescriptor

Check if the CutDescriptor contains the specified monosaccharide.

contains(SEdge) - Method in class org.expasy.mzjava.glycomics.mol.CutDescriptor

Check if the CutDescriptor contains the specified edge.

contains(Object) - Method in class org.expasy.mzjava.glycomics.mol.NodeSet
 
contains(double) - Method in class org.expasy.mzjava.utils.IntervalList

Checks whether value is included in any of the intervals

containsAll(Collection<?>) - Method in class org.expasy.mzjava.glycomics.mol.NodeSet
 
containsEdge(SimEdge<V>) - Method in class org.expasy.mzjava.core.ms.cluster.JungSimGraphWrapper
 
containsNode(GlycanNode) - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph

This method check if a glycan contains a specific node.

containsOnlyProteinMatch(String) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Returns true if this PeptideMatch contains only ProteinMatch's that have an accession
 in which the regex pattern can be found.

containsOnlyProteinMatch(Pattern) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Returns true if this PeptideMatch contains only ProteinMatch's that have an accession
 in which the regex pattern can be found.

containsProtein(String) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Returns true if this PeptideMatch contains the proteinAcs protein accession, false otherwise.

containsProteinMatch(String) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Returns true if this PeptideMatch contains a ProteinMatch that has an accession
 in which the regex pattern can be found.

containsProteinMatch(Pattern) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Returns true if this PeptideMatch contains a ProteinMatch that has an accession
 in which the regex pattern can be found.

containsUnknownAA(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader
 
containsVertex(V) - Method in class org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph
 
containsVertex(V) - Method in class org.expasy.mzjava.core.ms.cluster.JungSimGraphWrapper
 
containsVertex(V) - Method in interface org.expasy.mzjava.core.ms.cluster.SimilarityGraph

Returns true if this graph contains vertex, false otherwise.

containsVertex(V) - Method in class org.expasy.mzjava.core.ms.cluster.SparseSimilarityGraph
 
ContrastEnhancingTransformer<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist.peaktransformer

As described in Eng et al., Journal Proteome Research, 2008, this transformation subtracts the average intensity
 within a window of width 2*mvAvgWindow from every peak intensity.

ContrastEnhancingTransformer(double) - Constructor for class org.expasy.mzjava.core.ms.peaklist.peaktransformer.ContrastEnhancingTransformer
 
contributingChannel - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.IsotopicContributions
 
controller(DigestionController) - Method in class org.expasy.mzjava.proteomics.mol.digest.ProteinDigester.Builder
 
convert(double, TimeUnit) - Method in enum org.expasy.mzjava.core.ms.spectrum.TimeUnit
 
convert64bitsAndPopulate(byte[], double[], double[], int) - Static method in class org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader
 
copy(PeakProcessor<A, A>) - Method in class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum
 
copy(PeakProcessorChain<A>) - Method in class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum
 
copy(PeakProcessor<A, A>) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList
 
copy(PeakProcessorChain<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList
 
copy(PeakProcessor<A, A>) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleFloatPeakList
 
copy(PeakProcessorChain<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleFloatPeakList
 
copy(PeakProcessor<A, A>) - Method in class org.expasy.mzjava.core.ms.peaklist.DoublePeakList
 
copy(PeakProcessorChain<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.DoublePeakList
 
copy(PeakProcessor<A, A>) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList
 
copy(PeakProcessorChain<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList
 
copy(PeakProcessor<A, A>) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatPeakList
 
copy(PeakProcessorChain<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatPeakList
 
copy() - Method in class org.expasy.mzjava.core.ms.peaklist.Peak
 
copy(PeakProcessor<A, A>) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Return PeakList copy processed with PeakProcessor

copy(PeakProcessorChain<A>) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Return PeakList copy processed with PeakProcessorChain

copy() - Method in class org.expasy.mzjava.core.ms.spectrum.AnnotatedPeak
 
copy() - Method in class org.expasy.mzjava.core.ms.spectrum.LibPeakAnnotation
 
copy(PeakProcessor<PeakAnnotation, PeakAnnotation>) - Method in class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum
 
copy(PeakProcessorChain<PeakAnnotation>) - Method in class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum
 
copy(PeakProcessor<PeakAnnotation, PeakAnnotation>, Function<Double, Double>) - Method in class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum
 
copy(PeakProcessorChain<PeakAnnotation>, Function<Double, Double>) - Method in class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum
 
copy(Function<Double, Double>) - Method in class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum
 
copy() - Method in interface org.expasy.mzjava.core.ms.spectrum.RetentionTime
 
copy() - Method in class org.expasy.mzjava.core.ms.spectrum.RetentionTimeDiscrete
 
copy() - Method in class org.expasy.mzjava.core.ms.spectrum.RetentionTimeInterval
 
copy() - Method in class org.expasy.mzjava.core.ms.spectrum.RetentionTimeList
 
copy() - Method in class org.expasy.mzjava.core.ms.spectrum.ScanNumberList
 
copy() - Method in class org.expasy.mzjava.glycomics.ms.spectrum.GlycanFragAnnotation
 
copy(PeakProcessor<GlycanFragAnnotation, GlycanFragAnnotation>) - Method in class org.expasy.mzjava.glycomics.ms.spectrum.GlycanSpectrum
 
copy(PeakProcessorChain<GlycanFragAnnotation>) - Method in class org.expasy.mzjava.glycomics.ms.spectrum.GlycanSpectrum
 
copy(PeakProcessor<PepLibPeakAnnotation, PepLibPeakAnnotation>) - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum
 
copy(PeakProcessorChain<PepLibPeakAnnotation>) - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum
 
copy() - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation
 
copy() - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PepLibPeakAnnotation
 
copy(PeakProcessor<PepFragAnnotation, PepFragAnnotation>) - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PeptideSpectrum
 
copy(PeakProcessorChain<PepFragAnnotation>) - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PeptideSpectrum
 
copy() - Method in class org.expasy.mzjava.stats.HistogramImpl
 
copy() - Method in interface org.expasy.mzjava.utils.Copyable

Creates and returns a copy of this object.

Copyable<T> - Interface in org.expasy.mzjava.utils
 
copyArray(double[], int, double[], int, int) - Static method in class org.expasy.mzjava.utils.PrimitiveArrayUtils

Wraps System.arrayCopy and creates a new array if required

copyArray(float[], int, double[], int, int) - Static method in class org.expasy.mzjava.utils.PrimitiveArrayUtils

Copies an array from the specified source array, beginning at the
 specified position, to the specified position of the destination array.

copyEdgeList() - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph

Returns a new list of all the edges.

copyModInfo(PeptideMatch, MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader
 
correction - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.IsotopicContributions.ContributingChannel.AffectedChannel
 
CorruptedPSMFileException - Exception in org.expasy.mzjava.proteomics.io.ms.ident
 
CorruptedPSMFileException(String) - Constructor for exception org.expasy.mzjava.proteomics.io.ms.ident.CorruptedPSMFileException
 
cosim(TDoubleList, TDoubleList) - Static method in class org.expasy.mzjava.stats.NormalizedDotProduct
 
cosim(double[], double[]) - Static method in class org.expasy.mzjava.stats.NormalizedDotProduct
 
countAminoAcidsIn(Set<AminoAcid>) - Method in class org.expasy.mzjava.proteomics.mol.AminoAcidSequence

Counts sums the number of times each of the amino acid in aminoAcidSet is contained in this Peptide.

countCleavageSites(SymbolSequence<AminoAcid>) - Method in interface org.expasy.mzjava.proteomics.mol.digest.CleavageSiteFinder

Get the number of potential cleavage sites

countCleavageSites(SymbolSequence<AminoAcid>) - Method in class org.expasy.mzjava.proteomics.mol.digest.CleavageSiteFinderImpl
 
countCleavageSites(SymbolSequence<AminoAcid>) - Method in enum org.expasy.mzjava.proteomics.mol.digest.Protease
 
countCleavageSites(SymbolSequence<AminoAcid>) - Method in class org.expasy.mzjava.proteomics.mol.digest.ProteinDigester
 
Counter - Class in org.expasy.mzjava.utils

Counter is a simple counter and a better alternative than Integer as a new instance is created each time you want to set the value.

Counter() - Constructor for class org.expasy.mzjava.utils.Counter
 
Counter(int) - Constructor for class org.expasy.mzjava.utils.Counter
 
countNtuples(int[]) - Static method in class org.expasy.mzjava.utils.MixedRadixNtupleGenerator

Compute the number of n-tuples given the radices.

create(EngineType, String) - Static method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder

Main entry point to build PepXmlWriter

create(EngineType, Comparator<PeptideMatch>) - Static method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder

Main entry point to build PepXmlWriter

createAffiliationType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of AffiliationType

createAmbiguousResidueType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of AmbiguousResidueType

createAnalysisCollectionType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of AnalysisCollectionType

createAnalysisDataType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of AnalysisDataType

createAnalysisProtocolCollectionType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of AnalysisProtocolCollectionType

createAnalysisSampleCollectionType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of AnalysisSampleCollectionType

createAnalysisSoftwareListType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of AnalysisSoftwareListType

createAnalysisSoftwareType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of AnalysisSoftwareType

createAsapratioContribution() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of AsapratioContribution

createAsapratioLcHeavypeak() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of AsapratioLcHeavypeak

createAsapratioLcLightpeak() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of AsapratioLcLightpeak

createAsapratioPeptideData() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of AsapratioPeptideData

createAsapratioResult() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of AsapratioResult

createAsapratioSummary() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of AsapratioSummary

createAsapratioTimestamp() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of AsapratioTimestamp

createAuditCollectionType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of AuditCollectionType

createBibliographicReferenceType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of BibliographicReferenceType

createCompositionT() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ObjectFactory

Create an instance of CompositionT

createContactRoleType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of ContactRoleType

createCVListType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of CVListType

createCVParamType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of CVParamType

createCvType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of CvType

createDatabaseFiltersType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of DatabaseFiltersType

createDatabaseRefreshTimestamp() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of DatabaseRefreshTimestamp

createDatabaseTranslationType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of DatabaseTranslationType

createDataCollectionType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of DataCollectionType

createDBSequenceType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of DBSequenceType

createElemRefT() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ObjectFactory

Create an instance of ElemRefT

createEnumSchema(Class<? extends Enum>, Enum...) - Method in class org.expasy.mzjava.avro.io.AvroIO
 
createEnzyme(String) - Static method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder

Static factory method that create a SampleEnzyme builder

createEnzymesType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of EnzymesType

createEnzymeType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of EnzymeType

createExternalDataType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of ExternalDataType

createFileFormatType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of FileFormatType

createFilterType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of FilterType

createFragment(int, int, FragmentType) - Method in class org.expasy.mzjava.proteomics.mol.Peptide

Returns a new peptide fragment that is a subsequence of this peptide.

createFragment(IonType, int) - Method in class org.expasy.mzjava.proteomics.mol.Peptide

Create PeptideFragment that is sub sequence for the give ion type and residue number

 Given peptide CERVILAS createFragment(y, 1) will return S, createFragment(b, 1) will return C
 createFragment(b, 3) will return CER.

createFragmentArrayType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of FragmentArrayType

createFragmentationTableType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of FragmentationTableType

createFragmentationType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of FragmentationType

createIndexArray() - Method in class org.expasy.mzjava.utils.ArrayIndexComparator
 
createInputSpectraType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of InputSpectraType

createInputSpectrumIdentificationsType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of InputSpectrumIdentificationsType

createInputsType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of InputsType

createInteractSummary() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of InteractSummary

createInteractSummaryInputfile() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of InteractSummary.Inputfile

createIonTypeType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of IonTypeType

createLibraResult() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of LibraResult

createLibraResultIntensity() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of LibraResult.Intensity

createLibraSummary() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of LibraSummary

createLibraSummaryFragmentMasses() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of LibraSummary.FragmentMasses

createLibraSummaryIsotopicContributions() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of LibraSummary.IsotopicContributions

createLibraSummaryIsotopicContributionsContributingChannel() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of LibraSummary.IsotopicContributions.ContributingChannel

createLibraSummaryIsotopicContributionsContributingChannelAffectedChannel() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of LibraSummary.IsotopicContributions.ContributingChannel.AffectedChannel

createMassTableType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of MassTableType

createMeasureType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of MeasureType

createModificationParamsType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of ModificationParamsType

createModificationsT() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ObjectFactory

Create an instance of ModificationsT

createModificationType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of ModificationType

createModT() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ObjectFactory

Create an instance of ModT

createMsmsPipelineAnalysis() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of MsmsPipelineAnalysis

createMsmsPipelineAnalysisAnalysisSummary() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of MsmsPipelineAnalysis.AnalysisSummary

createMsmsPipelineAnalysisDatasetDerivation() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of MsmsPipelineAnalysis.DatasetDerivation

createMsmsPipelineAnalysisDatasetDerivationDataFilter() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of MsmsPipelineAnalysis.DatasetDerivation.DataFilter

createMsmsPipelineAnalysisMsmsRunSummary() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of MsmsPipelineAnalysis.MsmsRunSummary

createMsmsPipelineAnalysisMsmsRunSummaryAnalysisTimestamp() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp

createMsmsPipelineAnalysisMsmsRunSummarySampleEnzyme() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme

createMsmsPipelineAnalysisMsmsRunSummarySampleEnzymeSpecificity() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity

createMsmsPipelineAnalysisMsmsRunSummarySearchSummary() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary

createMsmsPipelineAnalysisMsmsRunSummarySearchSummaryAminoacidModification() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification

createMsmsPipelineAnalysisMsmsRunSummarySearchSummaryEnzymaticSearchConstraint() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint

createMsmsPipelineAnalysisMsmsRunSummarySearchSummarySearchDatabase() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase

createMsmsPipelineAnalysisMsmsRunSummarySearchSummarySequenceSearchConstraint() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SequenceSearchConstraint

createMsmsPipelineAnalysisMsmsRunSummarySearchSummaryTerminalModification() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification

createMsmsPipelineAnalysisMsmsRunSummarySpectrumQuery() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery

createMsmsPipelineAnalysisMsmsRunSummarySpectrumQuerySearchResult() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult

createMsmsPipelineAnalysisMsmsRunSummarySpectrumQuerySearchResultSearchHit() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

createMsmsPipelineAnalysisMsmsRunSummarySpectrumQuerySearchResultSearchHitAlternativeProtein() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein

createMsmsPipelineAnalysisMsmsRunSummarySpectrumQuerySearchResultSearchHitAnalysisResult() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult

createMsmsPipelineAnalysisMsmsRunSummarySpectrumQuerySearchResultSearchHitModificationInfo() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo

createMsmsPipelineAnalysisMsmsRunSummarySpectrumQuerySearchResultSearchHitModificationInfoModAminoacidMass() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo.ModAminoacidMass

createMzIdentML(MzIdentMLType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of JAXBElement<MzIdentMLType>}

createMzIdentMLType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of MzIdentMLType

createNameValueType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of NameValueType

createNeutralLossT() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ObjectFactory

Create an instance of NeutralLossT

createOrganizationType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of OrganizationType

createParamListType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of ParamListType

createParamType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of ParamType

createParentOrganizationType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of ParentOrganizationType

createPeakAnnotation(int, double, double) - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.AbstractMergePeakFilter
 
createPeakAnnotation(int, double, double) - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.LibraryMergePeakFilter
 
createPepNeutralLossT() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ObjectFactory

Create an instance of PepNeutralLossT

createPeptideEvidenceRefType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of PeptideEvidenceRefType

createPeptideEvidenceType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of PeptideEvidenceType

createPeptideHypothesisType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of PeptideHypothesisType

createPeptideprophetResult() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of PeptideprophetResult

createPeptideprophetResultSearchScoreSummary() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of PeptideprophetResult.SearchScoreSummary

createPeptideprophetSummary(Object) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of JAXBElement<Object>}

createPeptideType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of PeptideType

createPersonType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of PersonType

createProteinAmbiguityGroupType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of ProteinAmbiguityGroupType

createProteinDetectionHypothesisType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of ProteinDetectionHypothesisType

createProteinDetectionListType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of ProteinDetectionListType

createProteinDetectionProtocolType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of ProteinDetectionProtocolType

createProteinDetectionType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of ProteinDetectionType

createProviderType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of ProviderType

createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.AbstractLibPeakAnnotationWriter
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.AbstractPeakListReader
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.AbstractPeakListWriter
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.AvroIO

Create a list containing the Schema.Fields for the fields that this class writes

createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.CompositionReader
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.CompositionWriter
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.LibPeakAnnotationReader
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.MsnSpectrumReader
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.MsnSpectrumWriter
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.NumericMassReader
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.NumericMassWriter
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.PeakListReader
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.PeakListWriter
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.PeakReader
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.PeakWriter
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.RetentionTimeDiscreteReader
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.RetentionTimeDiscreteWriter
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.RetentionTimeIntervalReader
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.RetentionTimeIntervalWriter
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.RetentionTimeListReader
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.RetentionTimeListWriter
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.ScanNumberDiscreteReader
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.ScanNumberDiscreteWriter
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.ScanNumberIntervalReader
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.ScanNumberIntervalWriter
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.ScanNumberListReader
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.ScanNumberListWriter
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.UUIDReader
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.avro.io.UUIDWriter
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.proteomics.avro.io.ModificationReader
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.proteomics.avro.io.ModificationWriter
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.proteomics.avro.io.PepFragAnnotationReader
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.proteomics.avro.io.PepFragAnnotationWriter
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.proteomics.avro.io.PepLibPeakAnnotationReader
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.proteomics.avro.io.PepLibPeakAnnotationWriter
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.proteomics.avro.io.PeptideConsensusSpectrumReader
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.proteomics.avro.io.PeptideConsensusSpectrumWriter
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.proteomics.avro.io.PeptideFragmentReader
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.proteomics.avro.io.PeptideFragmentWriter
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.proteomics.avro.io.PeptideReader
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.proteomics.avro.io.PeptideSpectrumReader
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.proteomics.avro.io.PeptideSpectrumWriter
 
createRecordFields(List<Schema.Field>) - Method in class org.expasy.mzjava.proteomics.avro.io.PeptideWriter
 
createResidueType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of ResidueType

createRoleType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of RoleType

createSampleType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of SampleType

createSchema() - Method in interface org.expasy.mzjava.avro.io.AvroExternalizable
 
createSchema() - Method in class org.expasy.mzjava.avro.io.AvroIO

Creates a schema for this reader or writer

createSchema() - Method in class org.expasy.mzjava.avro.io.RetentionTimeListReader
 
createSchema() - Method in class org.expasy.mzjava.avro.io.RetentionTimeListWriter
 
createSchema() - Method in class org.expasy.mzjava.avro.io.ScanNumberListReader
 
createSchema() - Method in class org.expasy.mzjava.avro.io.ScanNumberListWriter
 
createSchemaField(String, Schema) - Method in class org.expasy.mzjava.avro.io.AvroIO

Utility method for creating a Field

createSearchDatabaseRefType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of SearchDatabaseRefType

createSearchDatabaseType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of SearchDatabaseType

createSearchModificationType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of SearchModificationType

createSequenceCollectionType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of SequenceCollectionType

createSourceFileType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of SourceFileType

createSpecificityRulesType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of SpecificityRulesType

createSpecificityT() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ObjectFactory

Create an instance of SpecificityT

createSpectraDataType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of SpectraDataType

createSpectrumIdentificationItemRefType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of SpectrumIdentificationItemRefType

createSpectrumIdentificationItemType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of SpectrumIdentificationItemType

createSpectrumIdentificationListType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of SpectrumIdentificationListType

createSpectrumIdentificationProtocolType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of SpectrumIdentificationProtocolType

createSpectrumIdentificationResultType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of SpectrumIdentificationResultType

createSpectrumIdentificationType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of SpectrumIdentificationType

createSpectrumIDFormatType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of SpectrumIDFormatType

createSubSampleType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of SubSampleType

createSubstitutionModificationType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of SubstitutionModificationType

createToleranceType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of ToleranceType

createTranslationTableType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of TranslationTableType

createTrypsin() - Static method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder

Static factory method that create the default SampleEnzyme

createUnimod(UnimodT) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ObjectFactory

Create an instance of JAXBElement<UnimodT>}

createUnimodT() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ObjectFactory

Create an instance of UnimodT

createUnionSchema(Class) - Method in class org.expasy.mzjava.avro.io.AvroIO

Utility method for creating a schema for the union for the recordSuperclass for unions that were registered with
 registerUnion

createUnionSchema(Class, AvroExternalizable...) - Method in class org.expasy.mzjava.avro.io.AvroIO

Utility method for creating a schema for the union for the recordSuperclass for unions that were registered with
 registerUnion

createUserParamType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create an instance of UserParamType

createVarModPeptides(Peptide) - Method in class org.expasy.mzjava.proteomics.mol.ModifiedPeptideFactory
 
createXpressratioResult() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of XpressratioResult

createXpressratioSummary() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of XpressratioSummary

createXpressratioTimestamp() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create an instance of XpressratioTimestamp

createXrefT() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ObjectFactory

Create an instance of XrefT

creationDate - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType
 
CrossRingCutType - Interface in org.expasy.mzjava.glycomics.mol

The CrossRingCutType interface allows you to get specific Crossring cleavage sites.

cTermGain - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymeType
 
cTermSet - Static variable in enum org.expasy.mzjava.proteomics.mol.modification.ModAttachment
 
Cu - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
Cu_MASS - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
cumulFrequencies - Variable in class org.expasy.mzjava.stats.HistogramImpl
 
currAnnotations() - Method in class org.expasy.mzjava.core.ms.peaklist.ArrayCursor
 
currAnnotations() - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakCursor

Returns the annotations of the peak that this cursor is currently pointing at

currAnnotations() - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.TopNList

Return the current annotation

currIntensity() - Method in class org.expasy.mzjava.core.ms.peaklist.ArrayCursor
 
currIntensity() - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakCursor

Returns the intensity of the peak that this cursor is currently pointing at

currIntensity() - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.TopNList

Return the intensity of the current peak

currMz() - Method in class org.expasy.mzjava.core.ms.peaklist.ArrayCursor
 
currMz() - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakCursor

Returns the m/z of the peak that this cursor is currently pointing at

currMz() - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.TopNList

Return the m/z of the current peak

cursor() - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
 
cursor() - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Returns a cursor over the peaks in this peak list in proper sequence.

cursor() - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
cursorIndex - Variable in class org.expasy.mzjava.core.ms.peaklist.ArrayCursor
 
customizations - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisSoftwareType
 
cut - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity
 
CutDescriptor - Class in org.expasy.mzjava.glycomics.mol
 
CutDescriptor() - Constructor for class org.expasy.mzjava.glycomics.mol.CutDescriptor
 
CutDescriptor(Set<CleavedMonosaccharide>, Set<SEdge>) - Constructor for class org.expasy.mzjava.glycomics.mol.CutDescriptor
 
CutDescriptorGenerator - Class in org.expasy.mzjava.glycomics.mol
 
CutDescriptorGenerator() - Constructor for class org.expasy.mzjava.glycomics.mol.CutDescriptorGenerator
 
CutDirection - Enum in org.expasy.mzjava.glycomics.mol

Because the CutIndexes have the first index always lower than the second, the cutDirection will select the part
 between the two indexes if it is CLOCK_WISE otherwise it will select the other part of the whole.

CutIndexes - Class in org.expasy.mzjava.glycomics.mol

This class contains the two carbons where the carbon ring is cut.

CutIndexes(int, int) - Constructor for class org.expasy.mzjava.glycomics.mol.CutIndexes
 
cv - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.CVListType
 
cvList - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType
 
CVListType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

The list of controlled vocabularies used in the file.

CVListType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.CVListType
 
cvParam - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FileFormatType
 
cvParam - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.IonTypeType
 
cvParam - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MeasureType
 
cvParam - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ModificationType
 
cvParam - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ParamType
 
cvParam - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.RoleType
 
cvParam - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchDatabaseType
 
cvParam - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchModificationType
 
cvParam - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpecificityRulesType
 
cvParam - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIDFormatType
 
cvParam - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ToleranceType
 
cvParam - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.TranslationTableType
 
CVParamHelper - Class in org.expasy.mzjava.external.io.ms.spectrum.mzml

A bunch of static utility methods for CVParam

CVParamType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

A single entry from an ontology or a controlled
 vocabulary.

CVParamType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.CVParamType
 
cvRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.CVParamType
 
CvType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

A source controlled vocabulary from which cvParams will be obtained.

CvType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.CvType
 




D

database - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.DatabaseRefreshTimestamp
 
databaseFilters - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType
 
DatabaseFiltersType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

The specification of filters applied to the database searched.

DatabaseFiltersType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DatabaseFiltersType
 
databaseName - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchDatabaseType
 
databaseName - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
 
DatabaseRefreshTimestamp - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

DatabaseRefreshTimestamp() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.DatabaseRefreshTimestamp
 
databaseReleaseDate - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
 
databaseReleaseIdentifier - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
 
databaseTranslation - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType
 
DatabaseTranslationType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

A specification of how a nucleic acid sequence database was translated for searching.

DatabaseTranslationType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DatabaseTranslationType
 
dataCollection - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType
 
DataCollectionType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

The collection of input and output data sets of the analyses.

DataCollectionType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DataCollectionType
 
dataFilter - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.DatasetDerivation
 
datasetDerivation - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis
 
date - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis
 
dateTimeModified - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT
 
dateTimePosted - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT
 
DbSearchPaperExample - Class in org.expasy.mzjava.proteomics.cookbook
 
DbSearchPaperExample() - Constructor for class org.expasy.mzjava.proteomics.cookbook.DbSearchPaperExample
 
dbSequence - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SequenceCollectionType
 
dbSequenceRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType
 
dbSequenceRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionHypothesisType
 
DBSequenceType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

A database sequence from the specified SearchDatabase (nucleic acid or amino acid).

DBSequenceType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DBSequenceType
 
decimalRatio - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult
 
decoyScores - Variable in class org.expasy.mzjava.stats.statscores.ScoreStatistics
 
decrement() - Method in class org.expasy.mzjava.utils.Counter

Decrement counter by 1.

decrement(int) - Method in class org.expasy.mzjava.utils.Counter

Decrement counter by dec.

DefaultGlycanMassCalculator - Class in org.expasy.mzjava.glycomics.mol
 
DefaultGlycanMassCalculator() - Constructor for class org.expasy.mzjava.glycomics.mol.DefaultGlycanMassCalculator
 
DefaultGlycoCtResolver - Class in org.expasy.mzjava.glycomics.io.mol.glycoct
 
DefaultGlycoCtResolver() - Constructor for class org.expasy.mzjava.glycomics.io.mol.glycoct.DefaultGlycoCtResolver
 
DefaultMonosaccharideLookup - Class in org.expasy.mzjava.glycomics.mol
 
DefaultMonosaccharideLookup() - Constructor for class org.expasy.mzjava.glycomics.mol.DefaultMonosaccharideLookup
 
DefaultPeakListAligner<X extends PeakAnnotation,Y extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor

Aligns two peak lists.

DefaultPeakListAligner(Tolerance) - Constructor for class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.DefaultPeakListAligner
 
DefaultPeakListAligner(Tolerance, PeakPairSink<X, Y>) - Constructor for class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.DefaultPeakListAligner
 
DefaultPeakListAligner.OverlapListener - Interface in org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor
 
DefaultSpectrumKeyRawComparator - Class in org.expasy.mzjava.hadoop.io
 
DefaultSpectrumKeyRawComparator() - Constructor for class org.expasy.mzjava.hadoop.io.DefaultSpectrumKeyRawComparator
 
DefaultSpectrumLibrary<S extends PeakList> - Class in org.expasy.mzjava.core.ms.library
 
DefaultSpectrumLibrary(Tolerance, Collection<S>) - Constructor for class org.expasy.mzjava.core.ms.library.DefaultSpectrumLibrary
 
DefaultSubstituentLookup - Class in org.expasy.mzjava.glycomics.mol
 
DefaultSubstituentLookup() - Constructor for class org.expasy.mzjava.glycomics.mol.DefaultSubstituentLookup
 
degree(V) - Method in class org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph
 
degree(V) - Method in interface org.expasy.mzjava.core.ms.cluster.SimilarityGraph

Return the number of edges incident to vertex.

degree(V) - Method in class org.expasy.mzjava.core.ms.cluster.SparseSimilarityGraph
 
DelayedPeakPairProcessor<X extends PeakAnnotation,Y extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor

A peak pair processor that caches all the peaks that are pushed to it by the processPeakPair method.

DelayedPeakPairProcessor() - Constructor for class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.DelayedPeakPairProcessor
 
DelayedPeakProcessor<IN extends PeakAnnotation,OUT extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist

A peak processor that caches all the peaks that are pushed to it by the processPeak method.

DelayedPeakProcessor() - Constructor for class org.expasy.mzjava.core.ms.peaklist.DelayedPeakProcessor
 
DelegatingRegexTitleParser - Class in org.expasy.mzjava.core.io.ms.spectrum.mgf

A title parser that delegates

DelegatingRegexTitleParser() - Constructor for class org.expasy.mzjava.core.io.ms.spectrum.mgf.DelegatingRegexTitleParser
 
deletePath(String) - Static method in class org.expasy.mzjava.utils.PathUtils
 
delta - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT
 
DenseSimilarityGraph<V> - Class in org.expasy.mzjava.core.ms.cluster

A similarity graph that is backed by a matrix

DenseSimilarityGraph(TObjectIntMap<V>, SimEdge<V>[][], int) - Constructor for class org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph
 
DenseSimilarityGraph.AbstractBuilder<V,G extends SimilarityGraph<V>> - Class in org.expasy.mzjava.core.ms.cluster
 
DenseSimilarityGraph.AbstractBuilder(boolean) - Constructor for class org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph.AbstractBuilder
 
DenseSimilarityGraph.Builder<V> - Class in org.expasy.mzjava.core.ms.cluster
 
DenseSimilarityGraph.Builder() - Constructor for class org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph.Builder
 
DenseSimilarityGraph.Builder(boolean) - Constructor for class org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph.Builder
 
description - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.DatasetDerivation.DataFilter
 
description - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme
 
description - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
 
description - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
 
digest(Protein) - Method in class org.expasy.mzjava.proteomics.mol.digest.ProteinDigester

Digest protein

digest(Protein, Collection<Peptide>) - Method in class org.expasy.mzjava.proteomics.mol.digest.ProteinDigester

Digest protein given a container for digests

Digest - Class in org.expasy.mzjava.proteomics.ms.dbsearch

A wrapper for Peptide that has a set to hold the ids of the proteins that
 the peptide belongs to.

DigestDB - Interface in org.expasy.mzjava.proteomics.ms.dbsearch

A database that stores digested peptides

DigestDB.AmbiguousAminoAcidAction - Enum in org.expasy.mzjava.proteomics.ms.dbsearch

The action to take if a peptide that have amino acids that are ambiguous (Z, B etc) are returned by the digester

DigestionController - Interface in org.expasy.mzjava.proteomics.mol.digest

This interface delegates to callbacks to control the digestion handled by ProteinDigester.

digestWith(Protease) - Method in interface org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumDB.DigestDSL

Set the Protease that is used to digest the proteins.

directory - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.InteractSummary
 
discardAmbiguous - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader
 
DiscreteSpectrumLibrary<S extends PeakList> - Class in org.expasy.mzjava.core.ms.library
 
DiscreteSpectrumLibrary(double[], Tolerance, Collection<S>) - Constructor for class org.expasy.mzjava.core.ms.library.DiscreteSpectrumLibrary
 
doAppend(double, double) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList

Append the peak to the end of the peak list

doAppend(double, double) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList

Add a mz to this peak list.

doAppend(double, double) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleFloatPeakList

Add a mz, intensity pair to the peak list

doAppend(double, double) - Method in class org.expasy.mzjava.core.ms.peaklist.DoublePeakList

Add a mz, intensity pair to the peak list

doAppend(double, double) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList

Add a mz to this peak list.

doAppend(double, double) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatPeakList

Add a mz, intensity pair to the peak list

doBFS(LinkageAcceptor, Deque<Monosaccharide>, Comparator<GlycosidicEdge>) - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph
 
doBuild(TObjectIntMap<V>, int, SimEdge<V>[][]) - Method in class org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph.AbstractBuilder
 
doBuild(TObjectIntMap<V>, int, SimEdge<V>[][]) - Method in class org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph.Builder
 
doDFS(LinkageAcceptor, Deque<Monosaccharide>, Comparator<GlycosidicEdge>) - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph
 
doi - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType
 
doInsert(double, double) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList

Insert the peak so that the m/z are still sorted

doInsert(double, double) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList
 
doInsert(double, double) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleFloatPeakList
 
doInsert(double, double) - Method in class org.expasy.mzjava.core.ms.peaklist.DoublePeakList
 
doInsert(double, double) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList
 
doInsert(double, double) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatPeakList
 
doPut(SpectrumIdentifier, PeptideMatch) - Method in class org.expasy.mzjava.proteomics.ms.ident.ScanNumberIndexSearchResultMap
 
doPut(SpectrumIdentifier, PeptideMatch) - Method in class org.expasy.mzjava.proteomics.ms.ident.ScanNumberSearchResultMap
 
doPut(SpectrumIdentifier, PeptideMatch) - Method in class org.expasy.mzjava.proteomics.ms.ident.SearchResultMap
 
doPut(SpectrumIdentifier, PeptideMatch) - Method in class org.expasy.mzjava.proteomics.ms.ident.TitleSearchResultMap
 
DOUBLE_PRECISION - Static variable in class org.expasy.mzjava.utils.NumberFormatFactory
 
DoubleConstantPeakList<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist

PeakList that stores the m/z values as doubles and the intensities as a constant double value

DoubleConstantPeakList(double) - Constructor for class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList

Create an clear peak list

DoubleConstantPeakList(double, int) - Constructor for class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList

Create a peak list that has a capacity set to initialCapacity

DoubleConstantPeakList(DoubleConstantPeakList<A>, PeakProcessor<A, A>) - Constructor for class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList
 
DoubleConstantPeakList(DoubleConstantPeakList<A>, PeakProcessorChain<A>) - Constructor for class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList
 
DoubleFloatPeakList<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist

PeakList that stores the m/z values as doubles and the intensities as floats

DoubleFloatPeakList() - Constructor for class org.expasy.mzjava.core.ms.peaklist.DoubleFloatPeakList

Create an clear peak list

DoubleFloatPeakList(int) - Constructor for class org.expasy.mzjava.core.ms.peaklist.DoubleFloatPeakList

Create a peak list that has a capacity set to initialCapacity

DoubleFloatPeakList(DoubleFloatPeakList<A>, PeakProcessor<A, A>) - Constructor for class org.expasy.mzjava.core.ms.peaklist.DoubleFloatPeakList
 
DoubleFloatPeakList(DoubleFloatPeakList<A>, PeakProcessorChain<A>) - Constructor for class org.expasy.mzjava.core.ms.peaklist.DoubleFloatPeakList
 
DoubleFunction<V> - Interface in org.expasy.mzjava.utils.function
 
DoublePeakList<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist

PeakList that stores the m/z and intensity values as doubles

DoublePeakList() - Constructor for class org.expasy.mzjava.core.ms.peaklist.DoublePeakList

Create an clear peak list

DoublePeakList(int) - Constructor for class org.expasy.mzjava.core.ms.peaklist.DoublePeakList

Create a peak list that has a capacity set to initialCapacity

DoublePeakList(DoublePeakList<A>, PeakProcessor<A, A>) - Constructor for class org.expasy.mzjava.core.ms.peaklist.DoublePeakList
 
DoublePeakList(DoublePeakList<A>, PeakProcessorChain<A>) - Constructor for class org.expasy.mzjava.core.ms.peaklist.DoublePeakList
 
doublesToOctets(double[]) - Static method in class org.expasy.mzjava.core.io.ms.spectrum.BytesUtils
 
doubleToOctet(double) - Static method in class org.expasy.mzjava.core.io.ms.spectrum.BytesUtils

Convert one double into eight bytes

DpSimFunc<X extends PeakAnnotation,Y extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.spectrasim

Calculates the similarity between two PeakLists using the dot product (dp).

DpSimFunc(int, Tolerance) - Constructor for class org.expasy.mzjava.core.ms.spectrasim.DpSimFunc

Construct a NdpSimFunc that uses the default peak list aligner.

DpSimFunc(int, PeakListAligner<X, Y>, PeakPairProcessor<X, Y>...) - Constructor for class org.expasy.mzjava.core.ms.spectrasim.DpSimFunc

Construct a NdpSimFunc that uses the supplied PeakListAligner and PeakPairProcessor chain to process
 and align the peak lists.

DtaReader - Class in org.expasy.mzjava.proteomics.io.ms.spectrum

A simple DTA reader.

DtaReader(File, PeakList.Precision) - Constructor for class org.expasy.mzjava.proteomics.io.ms.spectrum.DtaReader
 
DtaReader(Reader, PeakList.Precision) - Constructor for class org.expasy.mzjava.proteomics.io.ms.spectrum.DtaReader
 
DtaReader(Reader, URI, PeakList.Precision) - Constructor for class org.expasy.mzjava.proteomics.io.ms.spectrum.DtaReader
 
DtaReader(Reader, URI, PeakList.Precision, PeakProcessorChain<PeakAnnotation>) - Constructor for class org.expasy.mzjava.proteomics.io.ms.spectrum.DtaReader
 




E

EbiMzmlReader<S extends MsnSpectrum> - Class in org.expasy.mzjava.external.io.ms.spectrum.mzml

EbiMzmlReader is a wrapper over jmzml reader provided by EBI (https://code.google.com/p/jmzml/)
 that fully support mzML 1.1.0 specifications (http://www.psidev.info/mzml_1_0_0%20).

EbiMzmlReader(MzMLUnmarshaller, PeakList.Precision) - Constructor for class org.expasy.mzjava.external.io.ms.spectrum.mzml.EbiMzmlReader
 
EbiMzmlReader(MzMLUnmarshaller, PeakList.Precision, PeakProcessorChain<PeakAnnotation>) - Constructor for class org.expasy.mzjava.external.io.ms.spectrum.mzml.EbiMzmlReader
 
edgeCount() - Method in class org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph.AbstractBuilder
 
edgeCount() - Method in interface org.expasy.mzjava.core.ms.cluster.SimilarityGraphBuilder

Return the number of edges currently in the graph

edgeCount() - Method in class org.expasy.mzjava.core.ms.cluster.SparseSimilarityGraph.Builder
 
edges - Variable in class org.expasy.mzjava.glycomics.mol.SaccharideGraph
 
editor - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType
 
ELECTRON_MASS - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
element - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.CompositionT
 
ElemRefT - Class in org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb

Java class for elem_ref_t complex type.

ElemRefT() - Constructor for class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ElemRefT
 
elution - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioSummary
 
empty() - Static method in class org.expasy.mzjava.core.io.IterativeReaders
 
EMPTY_COMPOSITION - Static variable in class org.expasy.mzjava.glycomics.ms.spectrum.GlycanFragAnnotation
 
EMPTY_COMPOSITION - Static variable in class org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation
 
EMPTY_MOD_LIST - Static variable in class org.expasy.mzjava.proteomics.mol.modification.ModificationLists
 
EMPTY_READER - Static variable in interface org.expasy.mzjava.core.io.IterativeReader

The empty IterativeReader.

end() - Method in class org.expasy.mzjava.core.ms.consensus.ConsensusPeakSink
 
end() - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList.AbstractMergePeakSink
 
end() - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakProcessor
 
end() - Method in class org.expasy.mzjava.core.ms.peaklist.DelayedPeakProcessor
 
end() - Method in class org.expasy.mzjava.core.ms.peaklist.PeakCollectorSink
 
end() - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.NPeaksFilter
 
end() - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.NPeaksPerBinFilter
 
end() - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakSink

Called after a PeakList is processed

end() - Method in class org.expasy.mzjava.core.ms.spectrasim.AbstractSimFunc
 
end() - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.DelayedPeakPairProcessor
 
end() - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.filter.ThresholdPeakPairFilter
 
end() - Method in interface org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.PeakPairSink

Called when all the peak pairs in the PeakList pair have been processed

end() - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.PeakCountEqualizer
 
end() - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.PeakPairIntensityLog10Transformer
 
end() - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.PeakPairIntensityLogETransformer
 
end() - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.PeakPairIntensitySqrtTransformer
 
end() - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.PeakPairIonCurrentNormalizer
 
end - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType
 
end() - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusPeakSink
 
endElement(String, String, String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.NamespaceFilterXMLReader
 
endEnzyme() - Method in interface org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder.EnzymeEnd
 
endEnzyme() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder.SampleEnzymeBuilder
 
endEnzyme() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder.SpecificityBuilder
 
endScan - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
 
EngineType - Enum in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for engineType.

ensureCapacity(int) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList

Increases the capacity of this DoublePeakList instance, if
 necessary, to ensure that it can hold at least the number of peaks
 specified by the minimum capacity argument.

ensureCapacity(int) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleFloatPeakList

Increases the capacity of this DoublePeakList instance, if
 necessary, to ensure that it can hold at least the number of peaks
 specified by the minimum capacity argument.

ensureCapacity(int) - Method in class org.expasy.mzjava.core.ms.peaklist.DoublePeakList

Increases the capacity of this DoublePeakList instance, if
 necessary, to ensure that it can hold at least the number of peaks
 specified by the minimum capacity argument.

ensureCapacity(int) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList

Increases the capacity of this DoublePeakList instance, if
 necessary, to ensure that it can hold at least the number of peaks
 specified by the minimum capacity argument.

ensureCapacity(int) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatPeakList

Increases the capacity of this DoublePeakList instance, if
 necessary, to ensure that it can hold at least the number of peaks
 specified by the minimum capacity argument.

ensureCapacity(int) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Increases the capacity of this DoublePeakList instance, if
 necessary, to ensure that it can hold at least the number of peaks
 specified by the minimum capacity argument.

ensureCapacity(int) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
ensureCapacity(int) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.LibrarySpectrumBuilder
 
enzymaticSearchConstraint - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
 
enzymaticSearchConstraint(int, int) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder.Builder

Set the enzymatic_search_constraint child element of search_summary

enzyme - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymesType
 
enzyme - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint
 
enzyme(MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder.Builder

Set the sample_enzyme element of msms_run_summary (else enzyme by default)

enzymeName - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymeType
 
enzymes - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType
 
EnzymesType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

The list of enzymes used in experiment

EnzymesType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymesType
 
EnzymeType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

The details of an individual cleavage enzyme should be provided by giving a regular expression or a CV term if a "standard" enzyme cleavage has been performed.

EnzymeType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymeType
 
equals(Object) - Method in class org.expasy.mzjava.core.mol.Atom
 
equals(Object) - Method in class org.expasy.mzjava.core.mol.Composition
 
equals(Object) - Method in class org.expasy.mzjava.core.mol.NumericMass
 
equals(Object) - Method in class org.expasy.mzjava.core.ms.cluster.SimEdge
 
equals(Object) - Method in class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum
 
equals(Object) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
 
equals(Object) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList
 
equals(Object) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleFloatPeakList
 
equals(Object) - Method in class org.expasy.mzjava.core.ms.peaklist.DoublePeakList
 
equals(Object) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList
 
equals(Object) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatPeakList
 
equals(Object) - Method in class org.expasy.mzjava.core.ms.peaklist.Peak
 
equals(Object) - Method in class org.expasy.mzjava.core.ms.spectrum.AnnotatedPeak
 
equals(Object) - Method in class org.expasy.mzjava.core.ms.spectrum.LibPeakAnnotation
 
equals(Object) - Method in class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum
 
equals(Object) - Method in class org.expasy.mzjava.core.ms.spectrum.RetentionTimeDiscrete
 
equals(Object) - Method in class org.expasy.mzjava.core.ms.spectrum.RetentionTimeInterval
 
equals(Object) - Method in class org.expasy.mzjava.core.ms.spectrum.ScanNumberDiscrete
 
equals(Object) - Method in class org.expasy.mzjava.core.ms.spectrum.ScanNumberInterval
 
equals(Object) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
equals(Object) - Method in class org.expasy.mzjava.glycomics.mol.CleavedMonosaccharide
 
equals(Object) - Method in class org.expasy.mzjava.glycomics.mol.CutDescriptor
 
equals(Object) - Method in class org.expasy.mzjava.glycomics.mol.CutIndexes
 
equals(Object) - Method in class org.expasy.mzjava.glycomics.mol.Glycan
 
equals(Object) - Method in class org.expasy.mzjava.glycomics.mol.GlycanFragment
 
equals(Object) - Method in class org.expasy.mzjava.glycomics.mol.GlycosidicLinkage
 
equals(Object) - Method in class org.expasy.mzjava.glycomics.mol.Monosaccharide
 
equals(Object) - Method in class org.expasy.mzjava.glycomics.mol.NodeSet
 
equals(Object) - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph
 
equals(Object) - Method in class org.expasy.mzjava.glycomics.mol.SEdge
 
equals(Object) - Method in class org.expasy.mzjava.glycomics.mol.SNode
 
equals(Object) - Method in class org.expasy.mzjava.glycomics.mol.Substituent
 
equals(Object) - Method in class org.expasy.mzjava.glycomics.mol.SubstituentLinkage
 
equals(Object) - Method in class org.expasy.mzjava.glycomics.ms.spectrum.GlycanFragAnnotation
 
equals(Object) - Method in class org.expasy.mzjava.glycomics.ms.spectrum.GlycanSpectrum
 
equals(Object) - Method in class org.expasy.mzjava.hadoop.io.AbstractPeakListValue
 
equals(Object) - Method in class org.expasy.mzjava.hadoop.io.SpectrumKey
 
equals(Object) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.AminoacidModificationHashable
 
equals(Object) - Method in class org.expasy.mzjava.proteomics.mol.AminoAcidSequence
 
equals(Object) - Method in class org.expasy.mzjava.proteomics.mol.modification.Modification
 
equals(Object) - Method in class org.expasy.mzjava.proteomics.mol.modification.NeutralLoss
 
equals(Object) - Method in class org.expasy.mzjava.proteomics.mol.PeptideFragment
 
equals(Object) - Method in class org.expasy.mzjava.proteomics.mol.Protein
 
equals(Object) - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum
 
equals(Object) - Method in class org.expasy.mzjava.proteomics.ms.dbsearch.Digest
 
equals(Object) - Method in class org.expasy.mzjava.proteomics.ms.ident.ModificationMatch
 
equals(Object) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch
 
equals(Object) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideProteinMatch
 
equals(Object) - Method in class org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
 
equals(Object) - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation
 
equals(Object) - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PepLibPeakAnnotation
 
equals(Object) - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PeptideSpectrum
 
equals(Object) - Method in class org.expasy.mzjava.stats.Histogram.Normalization
 
equals(Object) - Method in class org.expasy.mzjava.stats.HistogramImpl
 
equals(Object) - Method in class org.expasy.mzjava.utils.Counter
 
error - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioContribution
 
error - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioResult
 
evaluate(Collection<S>) - Method in class org.expasy.mzjava.core.ms.cluster.SpectrumClusterEvaluator
 
exclude - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FilterType
 
excludeProteinPattern - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader
 
exCodeName - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT
 
execute(LPL) - Method in class org.expasy.mzjava.core.ms.library.SimFuncProcedure
 
execute(T) - Method in interface org.expasy.mzjava.utils.function.Procedure

Executes this procedure.

experimentalMassToCharge - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType
 
ExternalDataType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

Data external to the XML instance document.

ExternalDataType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ExternalDataType
 
externalFormatDocumentation - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ExternalDataType
 
extractCharge(V) - Method in class org.expasy.mzjava.utils.function.ChargeMzSplitter
 
extractCharge(PeakList) - Method in class org.expasy.mzjava.utils.function.PrecursorSplitter
 
extractChargeList(PeakList, M) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfWriter
 
extractChargeList(PeakList, MsnSpectrum) - Method in class org.expasy.mzjava.core.io.ms.spectrum.MgfWriter
 
extractMz(V) - Method in class org.expasy.mzjava.utils.function.ChargeMzSplitter
 
extractMz(PeakList) - Method in class org.expasy.mzjava.utils.function.PrecursorSplitter
 
extractRetentionTime(M) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfWriter
 
extractRetentionTime(MsnSpectrum) - Method in class org.expasy.mzjava.core.io.ms.spectrum.MgfWriter
 
extractScanNumbers(M) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfWriter
 
extractScanNumbers(MsnSpectrum) - Method in class org.expasy.mzjava.core.io.ms.spectrum.MgfWriter
 
extractTitle(M) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfWriter
 
extractTitle(MsnSpectrum) - Method in class org.expasy.mzjava.core.io.ms.spectrum.MgfWriter
 




F

falseNegatives - Variable in class org.expasy.mzjava.stats.ROCTable
 
falsePositives - Variable in class org.expasy.mzjava.stats.ROCTable
 
FastaHeaderParser - Interface in org.expasy.mzjava.proteomics.io.mol.fasta

This interface has to be implemented by parsers that can extract information from
 the Fasta header line.

FastaProteinReader - Class in org.expasy.mzjava.proteomics.io.mol

A reader for FASTA formatted files.

FastaProteinReader(Reader) - Constructor for class org.expasy.mzjava.proteomics.io.mol.FastaProteinReader

Construct a FastaReader that reads from a Reader

FastaProteinReader(File) - Constructor for class org.expasy.mzjava.proteomics.io.mol.FastaProteinReader

Constructs a FastaReader that reads from a file.

fdrValues - Variable in class org.expasy.mzjava.stats.statscores.ScoreStatistics
 
Fe - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
Fe_MASS - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
fidelity - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme
 
fileFormat - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ExternalDataType
 
FileFormatType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

The format of the ExternalData file, for example "tiff" for image files.

FileFormatType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FileFormatType
 
filename - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.InteractSummary
 
filter - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DatabaseFiltersType
 
FilterType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

Filters applied to the search database.

FilterType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FilterType
 
filterType - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FilterType
 
find(SymbolSequence<AminoAcid>, TIntList) - Method in interface org.expasy.mzjava.proteomics.mol.digest.CleavageSiteFinder

Find potential cleavage sites over the given amino-acid sequence

find(SymbolSequence<AminoAcid>, TIntList) - Method in class org.expasy.mzjava.proteomics.mol.digest.CleavageSiteFinderImpl
 
find(SymbolSequence<AminoAcid>, Optional<CleavageSiteVisitor>) - Method in class org.expasy.mzjava.proteomics.mol.digest.CleavageSiteFinderImpl

Find potential cleavage sites over the given amino-acid sequence

find(SymbolSequence<AminoAcid>, TIntList) - Method in enum org.expasy.mzjava.proteomics.mol.digest.Protease
 
findEdge(V, V) - Method in class org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph
 
findEdge(V, V) - Method in class org.expasy.mzjava.core.ms.cluster.JungSimGraphWrapper
 
findEdge(V, V) - Method in interface org.expasy.mzjava.core.ms.cluster.SimilarityGraph

Find the edge between vertex1 and vertex2.

findEdge(V, V) - Method in class org.expasy.mzjava.core.ms.cluster.SparseSimilarityGraph
 
findLinkages(Map<Integer, String>, int) - Method in class org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCTReader
 
FirstMzCheck - Class in org.expasy.mzjava.external.io.ms.spectrum.mzml
 
FirstMzCheck() - Constructor for class org.expasy.mzjava.external.io.ms.spectrum.mzml.FirstMzCheck
 
firstName - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PersonType
 
FirstRankScoreStatistics - Class in org.expasy.mzjava.stats.statscores

This class calculates FDRs and qValues for searches where each spectrum matches only one - either target or
 decoy - entry.

FirstRankScoreStatistics(float[], float[]) - Constructor for class org.expasy.mzjava.stats.statscores.FirstRankScoreStatistics
 
FirstRankScoreStatistics(float[], float[], ScoreStatistics.SortAction) - Constructor for class org.expasy.mzjava.stats.statscores.FirstRankScoreStatistics
 
FirstRankScoreStatistics(double[], double[]) - Constructor for class org.expasy.mzjava.stats.statscores.FirstRankScoreStatistics
 
FirstRankScoreStatistics(double[], double[], ScoreStatistics.SortAction) - Constructor for class org.expasy.mzjava.stats.statscores.FirstRankScoreStatistics
 
FirstRankScoreStatistics(TFloatList, TFloatList) - Constructor for class org.expasy.mzjava.stats.statscores.FirstRankScoreStatistics
 
FirstRankScoreStatistics(TFloatList, TFloatList, ScoreStatistics.SortAction) - Constructor for class org.expasy.mzjava.stats.statscores.FirstRankScoreStatistics
 
FirstRankScoreStatistics(TDoubleList, TDoubleList) - Constructor for class org.expasy.mzjava.stats.statscores.FirstRankScoreStatistics
 
FirstRankScoreStatistics(TDoubleList, TDoubleList, ScoreStatistics.SortAction) - Constructor for class org.expasy.mzjava.stats.statscores.FirstRankScoreStatistics
 
FitDecoyScoreStatistics - Class in org.expasy.mzjava.stats.statscores

This method is appropriate if for separate decoy and target searches and if more than one hit
 is considered.

FitDecoyScoreStatistics(float[], float[]) - Constructor for class org.expasy.mzjava.stats.statscores.FitDecoyScoreStatistics
 
FitDecoyScoreStatistics(float[], float[], ScoreStatistics.SortAction) - Constructor for class org.expasy.mzjava.stats.statscores.FitDecoyScoreStatistics
 
FitDecoyScoreStatistics(double[], double[]) - Constructor for class org.expasy.mzjava.stats.statscores.FitDecoyScoreStatistics
 
FitDecoyScoreStatistics(double[], double[], ScoreStatistics.SortAction) - Constructor for class org.expasy.mzjava.stats.statscores.FitDecoyScoreStatistics
 
FitDecoyScoreStatistics(TFloatList, TFloatList) - Constructor for class org.expasy.mzjava.stats.statscores.FitDecoyScoreStatistics
 
FitDecoyScoreStatistics(TFloatList, TFloatList, ScoreStatistics.SortAction) - Constructor for class org.expasy.mzjava.stats.statscores.FitDecoyScoreStatistics
 
FitDecoyScoreStatistics(TDoubleList, TDoubleList) - Constructor for class org.expasy.mzjava.stats.statscores.FitDecoyScoreStatistics
 
FitDecoyScoreStatistics(TDoubleList, TDoubleList, ScoreStatistics.SortAction) - Constructor for class org.expasy.mzjava.stats.statscores.FitDecoyScoreStatistics
 
fixedMod - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchModificationType
 
fixedModResidues - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader
 
flag - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.NeutralLossT
 
FLOAT_PRECISION - Static variable in class org.expasy.mzjava.utils.NumberFormatFactory
 
FloatConstantPeakList<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist

PeakList that stores the m/z values as floats and the intensities as a constant double value

FloatConstantPeakList(double) - Constructor for class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList

Create an clear peak list

FloatConstantPeakList(double, int) - Constructor for class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList

Create a peak list that has a capacity set to initialCapacity

FloatConstantPeakList(FloatConstantPeakList<A>) - Constructor for class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList
 
FloatConstantPeakList(FloatConstantPeakList<A>, PeakProcessor<A, A>) - Constructor for class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList
 
FloatConstantPeakList(FloatConstantPeakList<A>, PeakProcessorChain<A>) - Constructor for class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList
 
FloatConstantPeakList(float[], double) - Constructor for class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList
 
FloatPeakList<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist

PeakList that stores the m/z and intensity values as floats

FloatPeakList() - Constructor for class org.expasy.mzjava.core.ms.peaklist.FloatPeakList

Create an clear peak list

FloatPeakList(int) - Constructor for class org.expasy.mzjava.core.ms.peaklist.FloatPeakList

Create a peak list that has a capacity set to initialCapacity

FloatPeakList(FloatPeakList<A>, PeakProcessor<A, A>) - Constructor for class org.expasy.mzjava.core.ms.peaklist.FloatPeakList
 
FloatPeakList(FloatPeakList<A>, PeakProcessorChain<A>) - Constructor for class org.expasy.mzjava.core.ms.peaklist.FloatPeakList
 
floatsToQuads(float[]) - Static method in class org.expasy.mzjava.core.io.ms.spectrum.BytesUtils
 
floatToQuad(float) - Static method in class org.expasy.mzjava.core.io.ms.spectrum.BytesUtils

Convert one float into four bytes

FMeasure - Class in org.expasy.mzjava.core.ms.cluster
 
forEach(Peak, Procedure<S>) - Method in class org.expasy.mzjava.core.ms.library.AbstractIntervalSpectrumLibrary
 
forEach(Peak, Procedure<S>) - Method in class org.expasy.mzjava.core.ms.library.DiscreteSpectrumLibrary
 
forEach(Peak, Procedure<S>) - Method in interface org.expasy.mzjava.core.ms.library.SpectrumLibrary
 
forEachEdge(Procedure<SimEdge<V>>) - Method in class org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph
 
forEachEdge(V, Procedure<SimEdge<V>>) - Method in class org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph
 
forEachEdge(Procedure<SimEdge<V>>) - Method in interface org.expasy.mzjava.core.ms.cluster.SimilarityGraph

Applies the procedure to each edge in this graph

forEachEdge(V, Procedure<SimEdge<V>>) - Method in interface org.expasy.mzjava.core.ms.cluster.SimilarityGraph

Applies the procedure to each edge that is connected to vertex

forEachEdge(Procedure<SimEdge<V>>) - Method in class org.expasy.mzjava.core.ms.cluster.SparseSimilarityGraph
 
forEachEdge(V, Procedure<SimEdge<V>>) - Method in class org.expasy.mzjava.core.ms.cluster.SparseSimilarityGraph
 
forEachLinkage(SaccharideGraph.Traversal, LinkageAcceptor) - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph

Traverses the saccharide graph starting at the root.

forEachLinkage(SaccharideGraph.Traversal, TraversalComparator, LinkageAcceptor) - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph

Traverses the saccharide graph starting at the root.

forEachNeighbour(V, Procedure<V>) - Method in class org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph
 
forEachNeighbour(V, Procedure<V>) - Method in interface org.expasy.mzjava.core.ms.cluster.SimilarityGraph

Applies the procedure to each vertex that is a neighbour of vertex

forEachNeighbour(V, Procedure<V>) - Method in class org.expasy.mzjava.core.ms.cluster.SparseSimilarityGraph
 
forEachVertex(Procedure<V>) - Method in class org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph
 
forEachVertex(Procedure<V>) - Method in interface org.expasy.mzjava.core.ms.cluster.SimilarityGraph

Applies the procedure to each vertex in this graph

forEachVertex(Procedure<V>) - Method in class org.expasy.mzjava.core.ms.cluster.SparseSimilarityGraph
 
formatAnnotations(int, PeakList<? extends PeakAnnotation>) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.AbstractSptxtWriter
 
formatAnnotations(int, PeakList<? extends PeakAnnotation>) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.SptxtWriter
 
formatIntensity(double) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.AbstractSptxtWriter
 
formatMz(double) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.AbstractSptxtWriter
 
fragMassType(MassType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder.Builder

Set the fragment_mass_type attribute of element search_summary

fragment(Glycan, int) - Method in class org.expasy.mzjava.glycomics.ms.fragment.GlycanFragmenter

Generate a GlycanSpectrum from the fragment in input.

fragment(Glycan, int, CrossRingCutType) - Method in class org.expasy.mzjava.glycomics.ms.fragment.GlycanFragmenter

Generate a GlycanSpectrum from the fragment in input.

fragment(Glycan, int, int[], CrossRingCutType) - Method in class org.expasy.mzjava.glycomics.ms.fragment.GlycanFragmenter

Generate a GlycanSpectrum from the fragment in input.

fragment(Glycan, int, List<GlycanFragment>, int[]) - Method in class org.expasy.mzjava.glycomics.ms.fragment.GlycanFragmenter

Generate a GlycanSpectrum from the fragment in input.

fragment(Peptide, int) - Method in class org.expasy.mzjava.proteomics.ms.fragment.PeptideFragmentAnnotator
 
fragment(Peptide, int, int...) - Method in class org.expasy.mzjava.proteomics.ms.fragment.PeptideFragmentAnnotator
 
fragment(Peptide, int) - Method in class org.expasy.mzjava.proteomics.ms.fragment.PeptideFragmenter
 
fragment(Peptide, int, int[]) - Method in class org.expasy.mzjava.proteomics.ms.fragment.PeptideFragmenter
 
fragment(Peptide, int, List<PeptideFragment>, int[]) - Method in class org.expasy.mzjava.proteomics.ms.fragment.PeptideFragmenter
 
FragmentAnnotationFilter<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist.peakfilter

Retain annotated peaks which the given predicate is true.

FragmentAnnotationFilter(Predicate<A>) - Constructor for class org.expasy.mzjava.core.ms.peaklist.peakfilter.FragmentAnnotationFilter
 
fragmentArray - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.IonTypeType
 
FragmentArrayType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

An array of values for a given type of measure and for a particular ion type, in parallel to the index of ions identified.

FragmentArrayType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FragmentArrayType
 
fragmentation - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType
 
fragmentationTable - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationListType
 
FragmentationTableType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

Contains the types of measures that will be reported in generic arrays for each SpectrumIdentificationItem e.g.

FragmentationTableType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FragmentationTableType
 
FragmentationType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

The product ions identified in this result.

FragmentationType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FragmentationType
 
fragmenter - Variable in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.Builder
 
fragmenter(PeptideFragmenter) - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.BuilderOld
 
fragmentMasses - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary
 
fragmentMassType - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
 
fragmentTolerance - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType
 
fragmentTolerance - Variable in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.Builder
 
FragmentType - Enum in org.expasy.mzjava.core.ms.spectrum

An enum to represent the types of fragments

fragMzTolerance - Variable in class org.expasy.mzjava.core.ms.consensus.AbstractConsensusSpectrumBuilder
 
fragMzTolerance(double) - Method in class org.expasy.mzjava.core.ms.consensus.AbstractConsensusSpectrumBuilder
 
frame - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType
 
frames - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DatabaseTranslationType
 
FrequencyTable - Class in org.expasy.mzjava.stats

A table to hold the frequency distribution of values from one variable.

FrequencyTable(double) - Constructor for class org.expasy.mzjava.stats.FrequencyTable

Construct a new FrequencyTable that has intervals that have a width of binSize

FrequencyTable(double, String) - Constructor for class org.expasy.mzjava.stats.FrequencyTable

Construct a new FrequencyTable that has intervals that have a width of binSize

fromCollection(Collection<T>) - Static method in class org.expasy.mzjava.core.io.IterativeReaders
 
fromIterator(Iterator<T>) - Static method in class org.expasy.mzjava.core.io.IterativeReaders
 
fromValue(String) - Static method in enum org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ActivationMethodType
 
fromValue(String) - Static method in enum org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.EngineType
 
fromValue(String) - Static method in enum org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MassType
 
fromValue(String) - Static method in enum org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ModelDisType
 
fromValue(String) - Static method in enum org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.PositionT
 
fullName - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.CvType
 
fullName - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT
 




G

generate(int, int) - Method in class org.expasy.mzjava.utils.MixedRadixNtupleGenerator

This algorithm generate all n-tuples with the same radix at
 any positions.

generate(int[]) - Method in class org.expasy.mzjava.utils.MixedRadixNtupleGenerator

This algorithm generates all n-tuples with different radices
 and give them to the Handler

 [from knuth the AOCP, section 7.1.1 : Algorithm M]


generateCutDescriptor(Glycan, int, int) - Method in class org.expasy.mzjava.glycomics.mol.CutDescriptorGenerator
 
generateCutDescriptor(Glycan, int, int, CrossRingCutType) - Method in class org.expasy.mzjava.glycomics.mol.CutDescriptorGenerator
 
generateForward(Peptide, List<PeptideFragment>) - Method in class org.expasy.mzjava.proteomics.ms.fragment.PeptideFragmenter
 
generateImmonium(Peptide, List<PeptideFragment>) - Method in class org.expasy.mzjava.proteomics.ms.fragment.PeptideFragmenter
 
generatePeaks(Glycan, GlycanFragment, int[], List<AnnotatedPeak<GlycanFragAnnotation>>) - Method in class org.expasy.mzjava.glycomics.ms.fragment.GlycanFragmentPeakGenerator

Generate peaks that are observed for the fragment at the supplied charge states.

generatePeaks(Glycan, GlycanFragment, int[], List<AnnotatedPeak<GlycanFragAnnotation>>) - Method in interface org.expasy.mzjava.glycomics.ms.fragment.GlycanPeakGenerator

Generate peaks that are observed for the fragment at the supplied charge states.

generatePeaks(Peptide, PeptideFragment, int[], List<AnnotatedPeak<PepFragAnnotation>>) - Method in class org.expasy.mzjava.proteomics.ms.fragment.BackbonePeakGenerator
 
generatePeaks(Peptide, PeptideFragment, int[], List<AnnotatedPeak<PepFragAnnotation>>) - Method in class org.expasy.mzjava.proteomics.ms.fragment.PeptideNeutralLossPeakGenerator
 
generatePeaks(Peptide, PeptideFragment, int[], List<AnnotatedPeak<A>>) - Method in interface org.expasy.mzjava.proteomics.ms.fragment.PeptidePeakGenerator

Generate peaks that are observed for the fragment at the supplied charge states.

generateReverse(Peptide, List<PeptideFragment>) - Method in class org.expasy.mzjava.proteomics.ms.fragment.PeptideFragmenter
 
generateSequestCidSpectra(PeakList.Precision) - Method in interface org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumDB.FragmentDSL

Creates a new PeptideFragmenter that generates theoretical spectra like SEQUEST does.

generateSpectra(PeakList.Precision, IonType, IonType...) - Method in interface org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumDB.FragmentDSL

Set the precision of the spectra and ion types that are generated when a theoretical spectrum is created.

generateSpectraWith(PeptideFragmenter) - Method in interface org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumDB.FragmentDSL

Set the PeptideFragmenter that is used to generate the theoretical spectra.

generateSpectraWithIons(IonType, IonType...) - Method in interface org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumDB.FragmentDSL

Creates a new PeptideFragmenter that generates theoretical spectra using the provided ions.

generationNo - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.DatasetDerivation
 
get(Monosaccharide) - Method in class org.expasy.mzjava.glycomics.mol.AllCrossRingCutType

Return an array of all possible Crossiring cleavage indexes for the specific input.

get(Monosaccharide) - Method in interface org.expasy.mzjava.glycomics.mol.CrossRingCutType

Return an array of Crossring indexes.

get() - Method in class org.expasy.mzjava.glycomics.mol.SNode
 
get() - Method in class org.expasy.mzjava.hadoop.io.AbstractAvroWritable
 
get() - Method in class org.expasy.mzjava.hadoop.io.AbstractPeakListValue

Returns the read peak list

get(int) - Method in interface org.expasy.mzjava.proteomics.mol.modification.ModificationList
 
get(Peptide, int) - Method in interface org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumCache
 
get(Peptide, int) - Method in class org.expasy.mzjava.proteomics.ms.dbsearch.SoftRefPepSpectrumCache
 
get() - Method in class org.expasy.mzjava.spark.Cached
 
getAbsolute() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraResult.Intensity

Gets the value of the absolute property.

getAbsoluteBinFreq(int) - Method in interface org.expasy.mzjava.stats.Histogram

Get the absolute frequency at given bin

getAbsoluteBinFreq(int) - Method in class org.expasy.mzjava.stats.HistogramImpl
 
getAbsoluteBinFreqs(double[]) - Method in interface org.expasy.mzjava.stats.Histogram
 
getAbsoluteBinFreqs(double[]) - Method in class org.expasy.mzjava.stats.HistogramImpl
 
getAbundance() - Method in class org.expasy.mzjava.core.mol.Atom
 
getAccession() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.CVParamType

Gets the value of the accession property.

getAccession() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DBSequenceType

Gets the value of the accession property.

getAccession() - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideProteinMatch

Returns the protein accession number

getAccessionId() - Method in class org.expasy.mzjava.proteomics.mol.Protein.Builder
 
getAccessionId() - Method in class org.expasy.mzjava.proteomics.mol.Protein
 
getAccessionNumbers(ResultSet) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.AbstractPsmCsvReader

Extract accession numbers

getAccessionNumbers(ResultSet) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.MaxQuantPsmReader
 
getAccessionNumbers(ResultSet) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.ProteinPilotPsmReader
 
getActivationMethod() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery

Gets the value of the activationMethod property.

getActivityDate() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProtocolApplicationType

Gets the value of the activityDate property.

getAdditionalSearchParams() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType

Gets the value of the additionalSearchParams property.

getAffectedChannel() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.IsotopicContributions.ContributingChannel

Gets the value of the affectedChannel property.

getAffiliation() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PersonType

Gets the value of the affiliation property.

getAllInternalTypeCleavage(Monosaccharide) - Method in class org.expasy.mzjava.glycomics.mol.DefaultGlycanMassCalculator

Return all possible type of internal cleavage for the monosaccharide of interest
 Before call this method be sure that the molecularMass it is correct.

getAllInternalTypeCleavage(Monosaccharide) - Method in interface org.expasy.mzjava.glycomics.mol.GlycanMassCalculator

Return all possible type of internal cleavage for the monosaccharide of interest
 Before call this method be sure that the molecularMass it is correct.

getAllNttProb() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.PeptideprophetResult

Gets the value of the allNttProb property.

getAlternativeProtein() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Gets the value of the alternativeProtein property.

getAltName() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT

Gets the value of the altName property.

getAmbiguousAminoAcids() - Method in class org.expasy.mzjava.proteomics.mol.AminoAcidSequence

Returns a set containing all the amino acids that are ambiguous.

getAmbiguousResidue() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MassTableType

Gets the value of the ambiguousResidue property.

getAminoacid() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification

Gets the value of the aminoacid property.

getAminoacidModification() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary

Gets the value of the aminoacidModification property.

getAminoacidModificationMap() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.ModificationMap
 
getAminoacidModificationSet(AminoAcid) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.ModificationMap
 
getAnalysis() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.AnalysisSummary

Gets the value of the analysis property.

getAnalysis() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp

Gets the value of the analysis property.

getAnalysis() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult

Gets the value of the analysis property.

getAnalysis() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.PeptideprophetResult

Gets the value of the analysis property.

getAnalysisCollection() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType

Gets the value of the analysisCollection property.

getAnalysisData() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DataCollectionType

Gets the value of the analysisData property.

getAnalysisParams() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionProtocolType

Gets the value of the analysisParams property.

getAnalysisProtocolCollection() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType

Gets the value of the analysisProtocolCollection property.

getAnalysisResult() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Gets the value of the analysisResult property.

getAnalysisSampleCollection() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType

Gets the value of the analysisSampleCollection property.

getAnalysisSoftware() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisSoftwareListType

Gets the value of the analysisSoftware property.

getAnalysisSoftwareList() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType

Gets the value of the analysisSoftwareList property.

getAnalysisSoftwareRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionProtocolType

Gets the value of the analysisSoftwareRef property.

getAnalysisSoftwareRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProviderType

Gets the value of the analysisSoftwareRef property.

getAnalysisSoftwareRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType

Gets the value of the analysisSoftwareRef property.

getAnalysisSummary() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis

Gets the value of the analysisSummary property.

getAnalysisTimestamp() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary

Gets the value of the analysisTimestamp property.

getAnnotation(int) - Method in class org.expasy.mzjava.core.ms.spectrum.AnnotatedPeak

Returns the annotation at the specified position in this peak.

getAnnotationCount() - Method in class org.expasy.mzjava.core.ms.spectrum.AnnotatedPeak

Returns the number of annotations in this peak.

getAnnotationIndexes() - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
 
getAnnotationIndexes() - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Returns an array containing the sorted indexes of the peaks that are annotated.

getAnnotationIndexes() - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
getAnnotations(int) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
 
getAnnotations(int) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Returns an unmodifiable list containing the annotations for the peak at index

getAnnotations(int, TIntObjectHashMap<List<T>>) - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.DelayedPeakPairProcessor

Returns the cached annotations for the peak at index for the given annotationMap

getAnnotations() - Method in class org.expasy.mzjava.core.ms.spectrum.AnnotatedPeak

Returns an unmodifiable list containing this peaks annotations

getAnnotations(int) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
getAnomericCarbon(String) - Method in class org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCTReader
 
getAnomericCarbon() - Method in class org.expasy.mzjava.glycomics.mol.GlycosidicLinkage
 
getAnomericComposition() - Method in class org.expasy.mzjava.glycomics.mol.GlycosidicLinkage
 
getAnomericCompsition(String) - Method in class org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCTReader
 
getAnomericity(String) - Method in class org.expasy.mzjava.glycomics.io.mol.glycoct.DefaultGlycoCtResolver

Returns the appropriate Anomericity instance for the given glycoct code.

getAnomericity(String) - Method in interface org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCtResolver
 
getAnomericity() - Method in class org.expasy.mzjava.glycomics.mol.GlycosidicLinkage
 
getAnomericResidueId(String) - Method in class org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCTReader
 
getAny() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.AnalysisSummary

Gets the value of the any property.

getAny() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp

Gets the value of the any property.

getAny() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult

Gets the value of the any property.

getArea() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak

Gets the value of the area property.

getArea() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak

Gets the value of the area property.

getAreaError() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak

Gets the value of the areaError property.

getAreaError() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak

Gets the value of the areaError property.

getAreaFlag() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioPeptideData

Gets the value of the areaFlag property.

getAreaFlag() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioSummary

Gets the value of the areaFlag property.

getAsapratioContribution() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioPeptideData

Gets the value of the asapratioContribution property.

getAsapratioLcHeavypeak() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioContribution

Gets the value of the asapratioLcHeavypeak property.

getAsapratioLcLightpeak() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioContribution

Gets the value of the asapratioLcLightpeak property.

getAsapratioPeptideData() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioResult

Gets the value of the asapratioPeptideData property.

getAssumedCharge() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery

Gets the value of the assumedCharge property.

getAssumedCharge() - Method in class org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
 
getAtom(AtomicSymbol, int) - Method in class org.expasy.mzjava.core.mol.PeriodicTable

Return the atom for the atomicSymbol with the number of neutrons given by massNumber

getAtom(AtomicSymbol) - Method in class org.expasy.mzjava.core.mol.PeriodicTable

Return the default isotope for the atomicSymbol

getAtom(String) - Method in class org.expasy.mzjava.core.mol.PeriodicTable

Parse the symbol and return the corresponding Atom.

getAtoms() - Method in class org.expasy.mzjava.core.mol.Composition

Returns a set containing  all the Atoms in this composition.

getAtoms(AtomicSymbol) - Method in class org.expasy.mzjava.core.mol.PeriodicTable

Return all the atoms for the given symbol sorted by mass
 
 For example AtomicSymbol.C will return {C12, C13, C14}

getAuditCollection() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType

Gets the value of the auditCollection property.

getAuthor() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioSummary

Gets the value of the author property.

getAuthor() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioSummary

Gets the value of the author property.

getAuthors() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType

Gets the value of the authors property.

getAvgeMass() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.CompositionT

Gets the value of the avgeMass property.

getAvgMassDelta() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ModificationType

Gets the value of the avgMassDelta property.

getAvgMassDelta() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SubstitutionModificationType

Gets the value of the avgMassDelta property.

getBackground() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak

Gets the value of the background property.

getBackground() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak

Gets the value of the background property.

getBaseName() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary

Gets the value of the baseName property.

getBaseName() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary

Gets the value of the baseName property.

getBasePeakIntensity() - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
 
getBasePeakIntensity() - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Get the intensity of the most intense peak

getBasePeakIntensity() - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
getBasePeakMz() - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
 
getBasePeakMz() - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Get the m/z of the most intense peak

getBasePeakMz() - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
getBestScore() - Method in class org.expasy.mzjava.core.ms.spectrasim.DpSimFunc
 
getBestScore() - Method in class org.expasy.mzjava.core.ms.spectrasim.McNdpSimFunc
 
getBestScore() - Method in class org.expasy.mzjava.core.ms.spectrasim.NdpSimFunc
 
getBestScore() - Method in class org.expasy.mzjava.core.ms.spectrasim.PearsonsSimFunc
 
getBestScore() - Method in class org.expasy.mzjava.core.ms.spectrasim.PspcSimFunc
 
getBestScore() - Method in class org.expasy.mzjava.core.ms.spectrasim.SharedPeakSimFunc
 
getBestScore() - Method in interface org.expasy.mzjava.core.ms.spectrasim.SimFunc

Return the best score that can be returned by calls to calcSimilarity.

getBestScore() - Method in class org.expasy.mzjava.core.ms.spectrasim.WeightedPearsonsSimFunc
 
getBibliographicReference() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType

Gets the value of the bibliographicReference property.

getBinary() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification

Gets the value of the binary property.

getBinId(double) - Method in class org.expasy.mzjava.stats.FrequencyTable

Return the id of the bin (interval) that the value falls in.

getBinIds() - Method in class org.expasy.mzjava.stats.FrequencyTable

Returns an array that holds the ids of the bins (intervals) that contain values.

getBinIndex(double) - Method in interface org.expasy.mzjava.stats.Histogram

Get the bin index containing the given value (else must return -1)

getBinIndex(double) - Method in class org.expasy.mzjava.stats.HistogramImpl
 
getBinIntensity() - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.BinnedSpectrumFilter
 
getBinSize() - Method in class org.expasy.mzjava.stats.FrequencyTable

Return the bin size.

getBinWidth() - Method in interface org.expasy.mzjava.stats.Histogram

Get the bin width

getBinWidth() - Method in class org.expasy.mzjava.stats.HistogramImpl
 
getBinWidth() - Method in class org.expasy.mzjava.utils.IntervalList
 
getBreaks(double[]) - Method in interface org.expasy.mzjava.stats.Histogram

Get the n+1 cells boundaries

getBreaks(double[]) - Method in class org.expasy.mzjava.stats.HistogramImpl
 
getBuilder() - Static method in class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum.Builder
 
getCalcNeutralPepMass() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Gets the value of the calcNeutralPepMass property.

getCalcPI() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Gets the value of the calcPI property.

getCalculatedMassToCharge() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType

Gets the value of the calculatedMassToCharge property.

getCalculatedPI() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType

Gets the value of the calculatedPI property.

getCandidateCount() - Method in class org.expasy.mzjava.proteomics.ms.ident.ModificationMatch

Returns the number of modification candidates

getCenter(int) - Method in class org.expasy.mzjava.stats.FrequencyTable

Return the center value of the bin at index binId

getCentroidingPreference() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary

Gets the value of the centroidingPreference property.

getCentroidIntensity(CentroidFilter.PeakIntensityInfo) - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.CentroidFilter
 
getChannel() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraResult.Intensity

Gets the value of the channel property.

getChannel() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.FragmentMasses

Gets the value of the channel property.

getChannel() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.IsotopicContributions.ContributingChannel.AffectedChannel

Gets the value of the channel property.

getChannel() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.IsotopicContributions.ContributingChannel

Gets the value of the channel property.

getChannelCode() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary

Gets the value of the channelCode property.

getCharge() - Method in class org.expasy.mzjava.core.mol.Composition

Return the charge for this composition.

getCharge() - Method in class org.expasy.mzjava.core.ms.peaklist.Peak

Return the default chargeList of this peak

getCharge() - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakAnnotation

Return this peaks charge

getCharge() - Method in class org.expasy.mzjava.core.ms.spectrum.LibPeakAnnotation
 
getCharge() - Method in class org.expasy.mzjava.glycomics.ms.spectrum.GlycanFragAnnotation

Return the charge for this annotation.

getCharge() - Method in class org.expasy.mzjava.glycomics.ms.spectrum.GlycanSpectrum

Returns the charge of the peaks in the spectrum.

getCharge() - Method in class org.expasy.mzjava.hadoop.io.SpectrumKey
 
getCharge() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.IonTypeType

Gets the value of the charge property.

getCharge() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioContribution

Gets the value of the charge property.

getCharge() - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation.Builder
 
getCharge() - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation
 
getCharge() - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PepLibPeakAnnotation
 
getCharge() - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PeptideSpectrum
 
getChargeList() - Method in class org.expasy.mzjava.core.ms.peaklist.Peak

Return an array containing this peaks charges.

getChargeState() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType

Gets the value of the chargeState property.

getChecker() - Method in enum org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader.ConsistencyCheck
 
getChild() - Method in class org.expasy.mzjava.glycomics.mol.SEdge
 
getChildren(Monosaccharide) - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph

Returns a the children of parent

getCidIndex() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioPeptideData

Gets the value of the cidIndex property.

getClassification() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.SpecificityT

Gets the value of the classification property.

getCleavageSiteMatcher() - Method in interface org.expasy.mzjava.proteomics.mol.digest.CleavageSiteFinder

Get the cleavage site matcher

getCleavageSiteMatcher() - Method in class org.expasy.mzjava.proteomics.mol.digest.CleavageSiteFinderImpl
 
getCleavageSiteMatcher() - Method in enum org.expasy.mzjava.proteomics.mol.digest.Protease
 
getCleavedEdges() - Method in class org.expasy.mzjava.glycomics.mol.CutDescriptor

Return a set of all the cleaved edges in the CutDescriptor.

getCleavedEdges() - Method in class org.expasy.mzjava.glycomics.mol.GlycanFragment

Return a set of cleaved edge in the fragment

getCleavedMonosaccharides() - Method in class org.expasy.mzjava.glycomics.mol.CutDescriptor

Return a set of all the cleaved monosaccharides in the CutDescriptor with their CutIndex.

getCleavedNodes() - Method in class org.expasy.mzjava.glycomics.mol.CutDescriptor

Return a set of all the cleaved monosaccharides in the CutDescriptor.

getCleavedNodes() - Method in class org.expasy.mzjava.glycomics.mol.GlycanFragment

Return a set of cleaved nodes in the fragment

getClosestIndex(double) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
 
getClosestIndex(double) - Method in class org.expasy.mzjava.core.ms.peaklist.ArrayCursor
 
getClosestIndex(double) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakCursor

Returns the index of the peak which is closest to mz.

getClosestIndex(double) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Returns the index of the peak that is closest to the supplied mz.

getClosestIndex(double) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
getCode() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AmbiguousResidueType

Gets the value of the code property.

getCode() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ResidueType

Gets the value of the code property.

getCollisionEnergy() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery

Gets the value of the collisionEnergy property.

getColumnNumber() - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader.ParseContext
 
getComment() - Method in class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum

Return the comment associated with this MsnSpectrum.

getComment() - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum

Return the comment

getCompensationVoltage() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery

Gets the value of the compensationVoltage property.

getComplement() - Method in enum org.expasy.mzjava.core.ms.spectrum.IonType
 
getComplement() - Method in enum org.expasy.mzjava.glycomics.mol.CutDirection
 
getComposition() - Method in class org.expasy.mzjava.glycomics.mol.GlycanNode

Return the composition of the GlycanNode

getComposition() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.CompositionT

Gets the value of the composition property.

getComposition() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodMod

Returns the Composition associated with this UnimodMod.

getCompositionOfMonomer() - Method in enum org.expasy.mzjava.proteomics.mol.AminoAcid

Returns the composition of this amino acid when it is part of a polymer.

getConfigurationClass() - Method in interface org.expasy.mzjava.script.ScriptConfiguredTool

Returns the interface that the configuration implements

getContactRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ContactRoleType

Gets the value of the contactRef property.

getContactRole() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisSoftwareType

Gets the value of the contactRole property.

getContactRole() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProviderType

Gets the value of the contactRole property.

getContactRole() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SampleType

Gets the value of the contactRole property.

getContext() - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader
 
getContributingChannel() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.IsotopicContributions

Gets the value of the contributingChannel property.

getCorrection() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.IsotopicContributions.ContributingChannel.AffectedChannel

Gets the value of the correction property.

getCount(Atom) - Method in class org.expasy.mzjava.core.mol.Composition

Counts the number of times atom occurs in this Composition

getCount() - Method in class org.expasy.mzjava.utils.Counter
 
getCreationDate() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType

Gets the value of the creationDate property.

getCrossRingLossMass(IonType, int, Monosaccharide, CutIndexes) - Method in class org.expasy.mzjava.glycomics.mol.DefaultGlycanMassCalculator

Return the value of mass that the glycan have lost during the crossring fragmentation depending on the ion type.

getCrossRingLossMass(IonType, int, Monosaccharide, CutIndexes) - Method in interface org.expasy.mzjava.glycomics.mol.GlycanMassCalculator

Return the value of mass that the glycan have lost during the crossring fragmentation depending on the ion type.

getCTermGain() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymeType

Gets the value of the cTermGain property.

getCterminalModification() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.ModificationMap
 
getCtermMod() - Method in class org.expasy.mzjava.proteomics.mol.digest.CleavageSiteMatcher
 
getCumulFreqs() - Method in interface org.expasy.mzjava.stats.Histogram

Get the counts of the cumulative number of observations in all bins

getCumulFreqs(int, int) - Method in interface org.expasy.mzjava.stats.Histogram

Get the counts of the cumulative number of weighed observations in all of the bins in the specifed range

getCumulFreqs() - Method in class org.expasy.mzjava.stats.HistogramImpl
 
getCumulFreqs(int, int) - Method in class org.expasy.mzjava.stats.HistogramImpl
 
getCurrentReader() - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader.ParseContext
 
getCustomizations() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisSoftwareType

Gets the value of the customizations property.

getCut() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity

Gets the value of the cut property.

getCutIndexes() - Method in class org.expasy.mzjava.glycomics.mol.CleavedMonosaccharide
 
getCutIndexesForMonosaccharide(Monosaccharide) - Method in class org.expasy.mzjava.glycomics.mol.CutDescriptor

Return the CutIndex related with the specified monosaccharide.

getCv() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.CVListType

Gets the value of the cv property.

getCvList() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType

Gets the value of the cvList property.

getCvParam() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FileFormatType

Gets the value of the cvParam property.

getCvParam() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.IonTypeType

Gets the value of the cvParam property.

getCvParam() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MeasureType

Gets the value of the cvParam property.

getCvParam() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ModificationType

Gets the value of the cvParam property.

getCvParam() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ParamType

Gets the value of the cvParam property.

getCvParam() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.RoleType

Gets the value of the cvParam property.

getCvParam() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchDatabaseType

Gets the value of the cvParam property.

getCvParam() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchModificationType

Gets the value of the cvParam property.

getCvParam() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpecificityRulesType

Gets the value of the cvParam property.

getCvParam() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIDFormatType

Gets the value of the cvParam property.

getCvParam() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ToleranceType

Gets the value of the cvParam property.

getCvParam() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.TranslationTableType

Gets the value of the cvParam property.

getCVParamDoubleValue(List<CVParam>, String...) - Static method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.CVParamHelper
 
getCvRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.CVParamType

Gets the value of the cvRef property.

getDatabase() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.DatabaseRefreshTimestamp

Gets the value of the database property.

getDatabaseFilters() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType

Gets the value of the databaseFilters property.

getDatabaseIdentifier() - Method in class org.expasy.mzjava.glycomics.mol.Glycan

Return the database identifier associated with this glycan.

getDatabaseName() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchDatabaseType

Gets the value of the databaseName property.

getDatabaseName() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase

Gets the value of the databaseName property.

getDatabaseReleaseDate() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase

Gets the value of the databaseReleaseDate property.

getDatabaseReleaseIdentifier() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase

Gets the value of the databaseReleaseIdentifier property.

getDatabaseTranslation() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType

Gets the value of the databaseTranslation property.

getDataCollection() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType

Gets the value of the dataCollection property.

getDataFilter() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.DatasetDerivation

Gets the value of the dataFilter property.

getDatasetDerivation() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis

Gets the value of the datasetDerivation property.

getDate() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis

Gets the value of the date property.

getDateTimeModified() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT

Gets the value of the dateTimeModified property.

getDateTimePosted() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT

Gets the value of the dateTimePosted property.

getDBSequence() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SequenceCollectionType

Gets the value of the dbSequence property.

getDBSequenceRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType

Gets the value of the dbSequenceRef property.

getDBSequenceRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionHypothesisType

Gets the value of the dbSequenceRef property.

getDecimalRatio() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult

Gets the value of the decimalRatio property.

getDecoyScores() - Method in class org.expasy.mzjava.stats.statscores.ScoreStatistics
 
getDefaultPrecision() - Static method in class org.expasy.mzjava.utils.NumberFormatFactory
 
getDelta() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT

Gets the value of the delta property.

getDeltaComposition(IonType) - Method in class org.expasy.mzjava.proteomics.mol.AAMassCalculator
 
getDeltaMass(IonType) - Method in class org.expasy.mzjava.core.mol.MassCalculator
 
getDeltaMass(IonType) - Method in class org.expasy.mzjava.proteomics.mol.AAMassCalculator
 
getDescription() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.DatasetDerivation.DataFilter

Gets the value of the description property.

getDescription() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme

Gets the value of the description property.

getDescription() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification

Gets the value of the description property.

getDescription() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification

Gets the value of the description property.

getDeserializer(Class<Object>) - Method in class org.expasy.mzjava.hadoop.io.MzJavaSerialization
 
getDest(SimEdge<V>) - Method in class org.expasy.mzjava.core.ms.cluster.JungSimGraphWrapper
 
getDirectory() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.InteractSummary

Gets the value of the directory property.

getDoi() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType

Gets the value of the doi property.

getDotBias() - Method in class org.expasy.mzjava.core.ms.spectrasim.NdpSimFunc

Returns the dot bias for the last calculated ndp

getEdgeCount() - Method in class org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph
 
getEdgeCount() - Method in class org.expasy.mzjava.core.ms.cluster.JungSimGraphWrapper
 
getEdgeCount() - Method in interface org.expasy.mzjava.core.ms.cluster.SimilarityGraph

Returns the number of edges in this graph

getEdgeCount() - Method in class org.expasy.mzjava.core.ms.cluster.SparseSimilarityGraph
 
getEdges() - Method in class org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph
 
getEdges(V) - Method in class org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph
 
getEdges() - Method in class org.expasy.mzjava.core.ms.cluster.JungSimGraphWrapper
 
getEdges() - Method in interface org.expasy.mzjava.core.ms.cluster.SimilarityGraph

Return an Iterable that iterates over the SimEdge's in this graph.

getEdges(V) - Method in interface org.expasy.mzjava.core.ms.cluster.SimilarityGraph

Return an Iterable that iterates over all the edges connected to vertex.

getEdges() - Method in class org.expasy.mzjava.core.ms.cluster.SparseSimilarityGraph
 
getEdges(V) - Method in class org.expasy.mzjava.core.ms.cluster.SparseSimilarityGraph
 
getEditor() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType

Gets the value of the editor property.

getElement() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.CompositionT

Gets the value of the element property.

getElution() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioSummary

Gets the value of the elution property.

getEnd() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType

Gets the value of the end property.

getEnd() - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideProteinMatch

Returns the end position of the peptide within the protein.

getEndComposition() - Method in class org.expasy.mzjava.glycomics.mol.Glycan

Return the composition of the end of the glycan.

getEndComposition() - Method in class org.expasy.mzjava.glycomics.mol.GlycanFragment

Return the composition of the end of the glycan.

getEndpoints(SimEdge<V>) - Method in class org.expasy.mzjava.core.ms.cluster.JungSimGraphWrapper
 
getEndScan() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery

Gets the value of the endScan property.

getEnzymaticSearchConstraint() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary

Gets the value of the enzymaticSearchConstraint property.

getEnzyme() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymesType

Gets the value of the enzyme property.

getEnzyme() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint

Gets the value of the enzyme property.

getEnzymeName() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymeType

Gets the value of the enzymeName property.

getEnzymes() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType

Gets the value of the enzymes property.

getError(double, double) - Method in class org.expasy.mzjava.core.ms.AbsoluteTolerance
 
getError(double, double) - Method in class org.expasy.mzjava.core.ms.PpmTolerance
 
getError(double, double) - Method in class org.expasy.mzjava.core.ms.Tolerance
 
getError() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioContribution

Gets the value of the error property.

getError() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioResult

Gets the value of the error property.

getError(int) - Method in class org.expasy.mzjava.stats.ROCTable
 
getExclude() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FilterType

Gets the value of the exclude property.

getExCodeName() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT

Gets the value of the exCodeName property.

getExpectedScanCount() - Method in class org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader
 
getExpectedValue(Spectrum) - Method in interface org.expasy.mzjava.external.io.ms.spectrum.ConsistencyCheck

Get expected value from a container

getExpectedValue(Spectrum) - Method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.FirstMzCheck
 
getExpectedValue(Spectrum) - Method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.LastMzCheck
 
getExpectedValue(Spectrum) - Method in enum org.expasy.mzjava.external.io.ms.spectrum.mzml.MzmlConsistencyCheck
 
getExpectedValue(Spectrum, String) - Method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.MzmlSpectrumCheck
 
getExpectedValue(Spectrum) - Method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.TicCheck
 
getExperimentalMassToCharge() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType

Gets the value of the experimentalMassToCharge property.

getExtension() - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfReader
 
getExternalFormatDocumentation() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ExternalDataType

Gets the value of the externalFormatDocumentation property.

getFalseNegative(int) - Method in class org.expasy.mzjava.stats.ROCTable
 
getFalsePositive(int) - Method in class org.expasy.mzjava.stats.ROCTable
 
getFalsePositiveRate(int) - Method in class org.expasy.mzjava.stats.ROCTable
 
getFidelity() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme

Gets the value of the fidelity property.

getFile(String) - Static method in class org.expasy.mzjava.utils.PathUtils
 
getFileFormat() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ExternalDataType

Gets the value of the fileFormat property.

getFilename() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.InteractSummary

Gets the value of the filename property.

getFilter() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DatabaseFiltersType

Gets the value of the filter property.

getFilterType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FilterType

Gets the value of the filterType property.

getFirst() - Method in class org.expasy.mzjava.core.ms.spectrum.RetentionTimeList
 
getFirst() - Method in class org.expasy.mzjava.core.ms.spectrum.ScanNumberList

Return the first scan number in this ScanNumberList

getFirstAnnotation(int) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
 
getFirstAnnotation(int) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Return the first annotation in the list of annotations for the peak at index.

getFirstAnnotation(int) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
getFirstCarbonRing() - Method in class org.expasy.mzjava.glycomics.mol.Monosaccharide

Return the number of the first carbon in the ring of the Monosaccharide.

getFirstIndex() - Method in class org.expasy.mzjava.glycomics.mol.CutIndexes

Return the first index of the cleavage

getFirstName() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PersonType

Gets the value of the firstName property.

getFormat() - Method in class org.expasy.mzjava.proteomics.mol.digest.CleavageSiteMatcher
 
getFormula() - Method in class org.expasy.mzjava.core.mol.Composition

Return the formula for this composition.

getFormula() - Method in class org.expasy.mzjava.core.mol.Mass
 
getFormula() - Method in class org.expasy.mzjava.core.mol.NumericMass
 
getFragment(CutDescriptor) - Method in class org.expasy.mzjava.glycomics.mol.Glycan
 
getFragment() - Method in class org.expasy.mzjava.glycomics.ms.spectrum.GlycanFragAnnotation

Return the glycan fragment associated with this annotation

getFragment() - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation

Return the peptide fragment associated with this annotation

getFragmentArray() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.IonTypeType

Gets the value of the fragmentArray property.

getFragmentation() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType

Gets the value of the fragmentation property.

getFragmentationTable() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationListType

Gets the value of the fragmentationTable property.

getFragmentMasses() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary

Gets the value of the fragmentMasses property.

getFragmentMassType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary

Gets the value of the fragmentMassType property.

getFragmentTolerance() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType

Gets the value of the fragmentTolerance property.

getFragmentType() - Method in enum org.expasy.mzjava.core.ms.spectrum.IonType
 
getFragmentType() - Method in class org.expasy.mzjava.glycomics.mol.GlycanFragment

Return the fragment type.

getFragmentType() - Method in class org.expasy.mzjava.proteomics.mol.PeptideFragment

Return the fragmentType

getFragmentTypes() - Method in class org.expasy.mzjava.glycomics.ms.fragment.GlycanFragmentPeakGenerator

Return the set of fragment type used in the peak generator.

getFragmentTypes() - Method in interface org.expasy.mzjava.glycomics.ms.fragment.GlycanPeakGenerator

Return the set of fragment type used in the peak generator.

getFragmentTypes() - Method in class org.expasy.mzjava.proteomics.ms.fragment.BackbonePeakGenerator
 
getFragmentTypes() - Method in class org.expasy.mzjava.proteomics.ms.fragment.PeptideNeutralLossPeakGenerator
 
getFragmentTypes() - Method in interface org.expasy.mzjava.proteomics.ms.fragment.PeptidePeakGenerator
 
getFragMethod() - Method in class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum

Return the fragmentation method

getFrame() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType

Gets the value of the frame property.

getFrames() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DatabaseTranslationType

Gets the value of the frames property.

getFrequency(int) - Method in class org.expasy.mzjava.stats.FrequencyTable

Return the number of values that fall in the bin (interval) for the given binId

getFullName() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.CvType

Gets the value of the fullName property.

getFullName() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT

Gets the value of the fullName property.

getFullName() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodMod

Returns the UniMod full name.

getGenerationNo() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.DatasetDerivation

Gets the value of the generationNo property.

getGlycan() - Method in class org.expasy.mzjava.glycomics.ms.spectrum.GlycanSpectrum

Returns the glycan used for creating the spectrum.

getGlycoctIndex(String) - Method in class org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCTReader
 
getGlycoctResidueAnomer(String) - Method in class org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCTReader
 
getGlycoctResidueType(String) - Method in class org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCTReader
 
getGlycoLinkage(GlycanNode, GlycanNode) - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph

Return the linkage between parentNode and childNode

getGlycosidicDeltaComposition(IonType) - Method in class org.expasy.mzjava.glycomics.mol.DefaultGlycanMassCalculator

Return the value of mass that the glycan have lost during the glycosidic fragmentation depending on the ion type.

getGlycosidicDeltaComposition(IonType) - Method in interface org.expasy.mzjava.glycomics.mol.GlycanMassCalculator

Return the composition that the glycan have lost during the glycosidic fragmentation depending on the ion type.

getGlycosidicDeltaMass(IonType) - Method in class org.expasy.mzjava.glycomics.mol.DefaultGlycanMassCalculator

Return the value of mass that the glycan have lost during the glycosidic fragmentation depending on the ion type.

getGlycosidicDeltaMass(IonType) - Method in interface org.expasy.mzjava.glycomics.mol.GlycanMassCalculator

Return the value of mass that the glycan have lost during the glycosidic fragmentation depending on the ion type.

getGroupOfPoster() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT

Gets the value of the groupOfPoster property.

getHeader() - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader
 
getHeaderData() - Method in class org.expasy.mzjava.core.io.ms.spectrum.MgfParameters
 
getHeavy2LightError() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioResult

Gets the value of the heavy2LightError property.

getHeavy2LightMean() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioResult

Gets the value of the heavy2LightMean property.

getHeavy2LightRatio() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult

Gets the value of the heavy2LightRatio property.

getHeavyArea() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult

Gets the value of the heavyArea property.

getHeavyFirstscan() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult

Gets the value of the heavyFirstscan property.

getHeavyLastscan() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult

Gets the value of the heavyLastscan property.

getHeavyMass() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioPeptideData

Gets the value of the heavyMass property.

getHeavyMass() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult

Gets the value of the heavyMass property.

getHighestIntensity() - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.CentroidFilter.PeakIntensityInfo
 
getHitRank() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Gets the value of the hitRank property.

getHitType() - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideProteinMatch

Returns the HitType.

getId() - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
 
getId() - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList
 
getId() - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
getId(GlycanNode) - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph.AbstractBuilder

Return the id of the node

getId() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.CvType

Gets the value of the id property.

getId() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.IdentifiableType

Gets the value of the id property.

getId() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp

Gets the value of the id property.

getId() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult

Gets the value of the id property.

getIdentifier(PeptideMatch) - Method in class org.expasy.mzjava.proteomics.ms.ident.SearchResultMap
 
getIgnore() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT

Gets the value of the ignore property.

getIncidentEdges(V) - Method in class org.expasy.mzjava.core.ms.cluster.JungSimGraphWrapper
 
getInclude() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FilterType

Gets the value of the include property.

getIndex() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.IonTypeType

Gets the value of the index property.

getIndex() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery

Gets the value of the index property.

getIndex() - Method in class org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
 
getInEdges(V) - Method in class org.expasy.mzjava.core.ms.cluster.JungSimGraphWrapper
 
getInputfile() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.InteractSummary

Gets the value of the inputfile property.

getInputs() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DataCollectionType

Gets the value of the inputs property.

getInputSpectra() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationType

Gets the value of the inputSpectra property.

getInputSpectrumIdentifications() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionType

Gets the value of the inputSpectrumIdentifications property.

getInstance() - Static method in class org.expasy.mzjava.core.mol.AtomicCompositionParser
 
getInstance() - Static method in class org.expasy.mzjava.core.mol.PeriodicTable
 
getInstance() - Static method in class org.expasy.mzjava.proteomics.mol.AAMassCalculator
 
getInstance() - Static method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodManager
 
getInstance() - Static method in class org.expasy.mzjava.utils.NumberFormatFactory
 
getIntensities(double[]) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList

Copies an the intensities from this peak list, beginning at 0,
 to the destination array.

getIntensities(double[], int) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList

Copies an the intensities from this peak list, beginning at 0,
 to the specified position of the destination array.

getIntensities(int, double[], int, int) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList

Copies an the intensities from this peak list, beginning at the specified position,
 to the specified position of the destination array.

getIntensities(double[]) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleFloatPeakList

Copies an the intensities from this peak list, beginning at 0,
 to the destination array.

getIntensities(double[], int) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleFloatPeakList

Copies an the intensities from this peak list, beginning at 0,
 to the specified position of the destination array.

getIntensities(int, double[], int, int) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleFloatPeakList

Copies an the intensities from this peak list, beginning at the specified position,
 to the specified position of the destination array.

getIntensities(double[]) - Method in class org.expasy.mzjava.core.ms.peaklist.DoublePeakList

Copies an the intensities from this peak list, beginning at 0,
 to the destination array.

getIntensities(double[], int) - Method in class org.expasy.mzjava.core.ms.peaklist.DoublePeakList

Copies an the intensities from this peak list, beginning at 0,
 to the specified position of the destination array.

getIntensities(int, double[], int, int) - Method in class org.expasy.mzjava.core.ms.peaklist.DoublePeakList

Copies an the intensities from this peak list, beginning at the specified position,
 to the specified position of the destination array.

getIntensities(double[]) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList

Copies an the intensities from this peak list, beginning at 0,
 to the destination array.

getIntensities(double[], int) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList

Copies an the intensities from this peak list, beginning at 0,
 to the specified position of the destination array.

getIntensities(int, double[], int, int) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList

Copies an the intensities from this peak list, beginning at the specified position,
 to the specified position of the destination array.

getIntensities(double[]) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatPeakList

Copies an the intensities from this peak list, beginning at 0,
 to the destination array.

getIntensities(double[], int) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatPeakList

Copies an the intensities from this peak list, beginning at 0,
 to the specified position of the destination array.

getIntensities(int, double[], int, int) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatPeakList

Copies an the intensities from this peak list, beginning at the specified position,
 to the specified position of the destination array.

getIntensities(double[]) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Copies an the intensities from this peak list, beginning at 0,
 to the destination array.

getIntensities(double[], int) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Copies an the intensities from this peak list, beginning at 0,
 to the specified position of the destination array.

getIntensities(int, double[], int, int) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Copies an the intensities from this peak list, beginning at the specified position,
 to the specified position of the destination array.

getIntensities(double[]) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
getIntensities(double[], int) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
getIntensities(int, double[], int, int) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
getIntensity(int) - Method in class org.expasy.mzjava.core.ms.peaklist.ArrayCursor
 
getIntensity() - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList
 
getIntensity(int) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList

Returns the intensity of the peak at index

getIntensity(int) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleFloatPeakList

Returns the intensity of the peak at index

getIntensity(int) - Method in class org.expasy.mzjava.core.ms.peaklist.DoublePeakList

Returns the intensity of the peak at index

getIntensity() - Method in class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList
 
getIntensity(int) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList

Returns the intensity of the peak at index

getIntensity(int) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatPeakList

Returns the intensity of the peak at index

getIntensity() - Method in class org.expasy.mzjava.core.ms.peaklist.Peak

Return the peak intensity

getIntensity(int) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakCursor

Returns the intensity of the peak at index

getIntensity(int) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Returns the intensity of the peak at index

getIntensity(int) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
getIntensity() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraResult

Gets the value of the intensity property.

getIntensityFormat() - Method in interface org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfWriter.Parameters
 
getIntensityFormat() - Method in class org.expasy.mzjava.core.io.ms.spectrum.MgfParameters
 
getIntensityFormat(PeakList.Precision) - Static method in class org.expasy.mzjava.core.io.ms.spectrum.PeakListPrecisionFormat
 
getIntensityStd() - Method in class org.expasy.mzjava.core.ms.spectrum.LibPeakAnnotation
 
getInterimName() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodMod

Returns the UniMod interim name.

getIonType(SEdge) - Method in class org.expasy.mzjava.glycomics.mol.GlycanFragment
 
getIonType(CleavedMonosaccharide) - Method in class org.expasy.mzjava.glycomics.mol.GlycanFragment
 
getIonType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FragmentationType

Gets the value of the ionType property.

getIonType() - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation

Return the peaks ion type

getIonTypes() - Method in class org.expasy.mzjava.glycomics.mol.GlycanFragment
 
getIsHeavy() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak

Gets the value of the isHeavy property.

getIsHeavy() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak

Gets the value of the isHeavy property.

getIsotopeComposition() - Method in class org.expasy.mzjava.glycomics.ms.spectrum.GlycanFragAnnotation

Return the Composition that contains the isotopes.

getIsotopeComposition() - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation

Return the Composition that contains the isotopes.

getIsotopeCount() - Method in class org.expasy.mzjava.glycomics.ms.spectrum.GlycanFragAnnotation

Return the number of isotopes

getIsotopeCount() - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation

Return the number of isotopes

getIsotopicContributions() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary

Gets the value of the isotopicContributions property.

getIsRejected() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Gets the value of the isRejected property.

getIssue() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType

Gets the value of the issue property.

getLabel() - Method in class org.expasy.mzjava.proteomics.mol.modification.Modification
 
getLabeledResidues() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioSummary

Gets the value of the labeledResidues property.

getLabeledResidues() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioSummary

Gets the value of the labeledResidues property.

getLast() - Method in class org.expasy.mzjava.core.ms.spectrum.RetentionTimeList
 
getLast() - Method in class org.expasy.mzjava.core.ms.spectrum.ScanNumberList

Return the last scan number in this ScanNumberList

getLastCarbonRing() - Method in class org.expasy.mzjava.glycomics.mol.Monosaccharide

Return the number of the last carbon in the ring of the Monosaccharide.

getLastIntensity() - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.TopNList

Returns the intensity of the last peak

getLastName() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PersonType

Gets the value of the lastName property.

getLeftValley() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak

Gets the value of the leftValley property.

getLeftValley() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak

Gets the value of the leftValley property.

getLength() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DBSequenceType

Gets the value of the length property.

getLightArea() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult

Gets the value of the lightArea property.

getLightFirstscan() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult

Gets the value of the lightFirstscan property.

getLightLastscan() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult

Gets the value of the lightLastscan property.

getLightMass() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioPeptideData

Gets the value of the lightMass property.

getLightMass() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult

Gets the value of the lightMass property.

getLineNumber() - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader.ParseContext
 
getLineNumber() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.AbstractPsmCsvReader
 
getLink() - Method in class org.expasy.mzjava.glycomics.mol.SEdge
 
getLinkageComposition(String) - Method in class org.expasy.mzjava.glycomics.io.mol.glycoct.DefaultGlycoCtResolver

Returns the appropriate LinkageComposition instance for the given GlycoCT code.

getLinkageComposition(String) - Method in interface org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCtResolver
 
getLinkedCarbon(String) - Method in class org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCTReader
 
getLinkedCarbon() - Method in class org.expasy.mzjava.glycomics.mol.GlycosidicLinkage
 
getLinkedCarbon() - Method in interface org.expasy.mzjava.glycomics.mol.Linkage

Return the number of the linked carbon.

getLinkedCarbon() - Method in class org.expasy.mzjava.glycomics.mol.SubstituentLinkage
 
getLinkedComposition() - Method in class org.expasy.mzjava.glycomics.mol.GlycosidicLinkage
 
getLinkedComposition() - Method in interface org.expasy.mzjava.glycomics.mol.Linkage

Return the composition of the linkage.

getLinkedComposition() - Method in class org.expasy.mzjava.glycomics.mol.SubstituentLinkage
 
getLinkedCompsition(String) - Method in class org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCTReader
 
getLinkedResidueId(String) - Method in class org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCTReader
 
getLoadFactor() - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList

Returns the current load factor, which is the number of elements that are added to the mz and intensity arrays
 when they are full

getLocal(Configuration) - Static method in class org.expasy.mzjava.hadoop.io.HadoopSpectraReader
 
getLocalPath() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase

Gets the value of the localPath property.

getLocation() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ExternalDataType

Gets the value of the location property.

getLocation() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ModificationType

Gets the value of the location property.

getLocation() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SubstitutionModificationType

Gets the value of the location property.

getLowerBound() - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.AbstractMergePeakFilter

Return the current lower bound peak index

getMajorVersion() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.UnimodT

Gets the value of the majorVersion property.

getMandatoryAttribute(StartElement, String, String...) - Static method in class org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader.XMLEventUtils
 
getMandatoryXMLEvent(Optional<E>, String) - Static method in class org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader.XMLEventUtils
 
getMass() - Method in class org.expasy.mzjava.core.mol.Atom
 
getMass() - Method in class org.expasy.mzjava.core.ms.peaklist.Peak

Returns mass of this peak

getMass() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ResidueType

Gets the value of the mass property.

getMass() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification

Gets the value of the mass property.

getMass() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification

Gets the value of the mass property.

getMass() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo.ModAminoacidMass

Gets the value of the mass property.

getMass() - Method in class org.expasy.mzjava.proteomics.mol.modification.Modification
 
getMassDefect() - Method in class org.expasy.mzjava.core.mol.Composition
 
getMassDefect() - Method in class org.expasy.mzjava.core.mol.Mass

The amount by which the mass of all atomic nuclei in this composition differs
 from the sum of the masses of its constituent protons, neutrons and electrons.

getMassDefect() - Method in class org.expasy.mzjava.core.mol.NumericMass
 
getMassDelta() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchModificationType

Gets the value of the massDelta property.

getMassdiff() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification

Gets the value of the massdiff property.

getMassdiff() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification

Gets the value of the massdiff property.

getMassdiff() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Gets the value of the massdiff property.

getMassdiff() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioSummary

Gets the value of the massdiff property.

getMassDiff() - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Returns the difference between the theoretical and experimental mass.

getMassNumber() - Method in class org.expasy.mzjava.core.mol.Atom
 
getMassOfMonomer() - Method in enum org.expasy.mzjava.proteomics.mol.AminoAcid

Returns the mass of this amino acid when it is part of a polymer.

getMassShift() - Method in class org.expasy.mzjava.proteomics.ms.ident.ModificationMatch

Returns the mass shift

getMassTable() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType

Gets the value of the massTable property.

getMassTableRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType

Gets the value of the massTableRef property.

getMassTol() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult

Gets the value of the massTol property.

getMasstol() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioSummary

Gets the value of the masstol property.

getMassTolerance() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary

Gets the value of the massTolerance property.

getMatch() - Method in exception org.expasy.mzjava.proteomics.ms.ident.UnresolvableModificationMatchException
 
getMax(double) - Method in class org.expasy.mzjava.core.ms.AbsoluteTolerance
 
getMax(double) - Method in class org.expasy.mzjava.core.ms.PpmTolerance
 
getMax(double) - Method in class org.expasy.mzjava.core.ms.Tolerance
 
getMax(int) - Method in class org.expasy.mzjava.stats.FrequencyTable

Return the max value of the bin at index binId

getMaxBinId() - Method in class org.expasy.mzjava.stats.FrequencyTable

Return the id of the largest bin that contains a value

getMaxNumInternalCleavages() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint

Gets the value of the maxNumInternalCleavages property.

getMaxRetentionTime() - Method in interface org.expasy.mzjava.core.ms.spectrum.RetentionTime

Returns the largest retention time, the units of the time is seconds

getMaxRetentionTime() - Method in class org.expasy.mzjava.core.ms.spectrum.RetentionTimeDiscrete
 
getMaxRetentionTime() - Method in class org.expasy.mzjava.core.ms.spectrum.RetentionTimeInterval
 
getMaxScanNumber() - Method in interface org.expasy.mzjava.core.ms.spectrum.ScanNumber

Return the largest scan number

getMaxScanNumber() - Method in class org.expasy.mzjava.core.ms.spectrum.ScanNumberDiscrete
 
getMaxScanNumber() - Method in class org.expasy.mzjava.core.ms.spectrum.ScanNumberInterval
 
getMaxSimScore() - Method in class org.expasy.mzjava.core.ms.cluster.SpectrumClusterEvaluator
 
getMaxVal() - Method in class org.expasy.mzjava.utils.IntervalList
 
getMean() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioResult

Gets the value of the mean property.

getMeanSimScore() - Method in class org.expasy.mzjava.core.ms.cluster.SpectrumClusterEvaluator
 
getMeasure() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FragmentationTableType

Gets the value of the measure property.

getMeasureRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FragmentArrayType

Gets the value of the measureRef property.

getMemberIds() - Method in class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum
 
getMergedPeakCount() - Method in class org.expasy.mzjava.core.ms.spectrum.LibPeakAnnotation
 
getMidInitials() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PersonType

Gets the value of the midInitials property.

getMids(double[]) - Method in interface org.expasy.mzjava.stats.Histogram

Get the n cell midpoints

getMids(double[]) - Method in class org.expasy.mzjava.stats.HistogramImpl
 
getMin(double) - Method in class org.expasy.mzjava.core.ms.AbsoluteTolerance
 
getMin(double) - Method in class org.expasy.mzjava.core.ms.PpmTolerance
 
getMin(double) - Method in class org.expasy.mzjava.core.ms.Tolerance
 
getMin(int) - Method in class org.expasy.mzjava.stats.FrequencyTable

Return the min value of the bin at index binId

getMinBinId() - Method in class org.expasy.mzjava.stats.FrequencyTable

Return the id of the smallest bin that contains a value

getMinDistance() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymeType

Gets the value of the minDistance property.

getMinNumberTermini() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint

Gets the value of the minNumberTermini property.

getMinNumEnzTerm() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.DatabaseRefreshTimestamp

Gets the value of the minNumEnzTerm property.

getMinorVersion() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.UnimodT

Gets the value of the minorVersion property.

getMinRetentionTime() - Method in interface org.expasy.mzjava.core.ms.spectrum.RetentionTime

Returns the smallest retention time, the units of the time is seconds

getMinRetentionTime() - Method in class org.expasy.mzjava.core.ms.spectrum.RetentionTimeDiscrete
 
getMinRetentionTime() - Method in class org.expasy.mzjava.core.ms.spectrum.RetentionTimeInterval
 
getMinScanNumber() - Method in interface org.expasy.mzjava.core.ms.spectrum.ScanNumber

Return the smallest scan number

getMinScanNumber() - Method in class org.expasy.mzjava.core.ms.spectrum.ScanNumberDiscrete
 
getMinScanNumber() - Method in class org.expasy.mzjava.core.ms.spectrum.ScanNumberInterval
 
getMinSimScore() - Method in class org.expasy.mzjava.core.ms.cluster.SpectrumClusterEvaluator
 
getMinSpacing() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity

Gets the value of the minSpacing property.

getMinVal() - Method in class org.expasy.mzjava.utils.IntervalList
 
getMiscNotes() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT

Gets the value of the miscNotes property.

getMiscNotes() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.SpecificityT

Gets the value of the miscNotes property.

getMissedCleavages() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymeType

Gets the value of the missedCleavages property.

getMod() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModificationsT

Gets the value of the mod property.

getModAminoacidMass() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo

Gets the value of the modAminoacidMass property.

getModAttachment() - Method in class org.expasy.mzjava.proteomics.ms.ident.ModificationMatch
 
getModCtermMass() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo

Gets the value of the modCtermMass property.

getModification() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideType

Gets the value of the modification property.

getModification(String) - Static method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodManager
 
getModificationCandidate(int) - Method in class org.expasy.mzjava.proteomics.ms.ident.ModificationMatch
 
getModificationCount() - Method in class org.expasy.mzjava.proteomics.mol.AminoAcidSequence

Return the number of modifications that this peptide has.

getModificationCount(ModAttachment) - Method in class org.expasy.mzjava.proteomics.mol.AminoAcidSequence

Returns the number of modifications that are attached to the given attachment

getModificationCount() - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Returns the number of modifications that theis peptide match has.

getModificationIndexes(Set<ModAttachment>) - Method in class org.expasy.mzjava.proteomics.mol.AminoAcidSequence

Returns a sorted Array containing the indexes of the modified amino acids

getModificationInfo() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Gets the value of the modificationInfo property.

getModificationList() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodManager

Return an unmodifiable list containing all the modifications that are managed by this

getModificationParams() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType

Gets the value of the modificationParams property.

getModifications(Set<ModAttachment>) - Method in class org.expasy.mzjava.proteomics.mol.AminoAcidSequence

Returns a ModificationList containing all the modifications for the given attachments.

getModifications() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.UnimodT

Gets the value of the modifications property.

getModifications(double, Tolerance) - Static method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodManager
 
getModifications(double, Tolerance, Set<String>) - Static method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodManager
 
getModifications(Set<ModAttachment>) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Return a list containing all ModificationMatch for ModAttachment's in the attachments
 set.

getModifications(int, Set<ModAttachment>) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Returns a list containing all ModificationMatch for the residue at index that are attached
 by a ModAttachment contained in the attachments set.

getModificationsAt(int, Set<ModAttachment>) - Method in class org.expasy.mzjava.proteomics.mol.AminoAcidSequence

Returns a ModificationList containing all the modifications for the given index and attachments.

getModifiedPeptide() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo

Gets the value of the modifiedPeptide property.

getModifiedResidueCount() - Method in class org.expasy.mzjava.proteomics.mol.AminoAcidSequence

Returns the number of residues that have a modification

getModMass() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader.PeptideInfoParser
 
getModNtermMass() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo

Gets the value of the modNtermMass property.

getMolecularMass() - Method in class org.expasy.mzjava.core.mol.Composition

Returns the monoisotopic molecular mass of this composition.

getMolecularMass() - Method in class org.expasy.mzjava.core.mol.NumericMass
 
getMolecularMass() - Method in interface org.expasy.mzjava.core.mol.Weighable

Return the molecular mass

getMolecularMass() - Method in class org.expasy.mzjava.glycomics.mol.GlycanNode
 
getMolecularMass() - Method in class org.expasy.mzjava.glycomics.mol.GlycosidicLinkage

Return the molecular mass of hte composition change due to the linkage.

getMolecularMass() - Method in class org.expasy.mzjava.glycomics.mol.Substituent
 
getMolecularMass() - Method in class org.expasy.mzjava.glycomics.mol.SubstituentLinkage

Return the molecular mass of the composition change due to the linkage.

getMolecularMass() - Method in class org.expasy.mzjava.proteomics.mol.modification.Modification
 
getMolecularMass() - Method in class org.expasy.mzjava.proteomics.mol.Peptide

Returns the mass of this peptide

getMolecularMass() - Method in class org.expasy.mzjava.proteomics.ms.dbsearch.Digest
 
getMonoisotopicMassDelta() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ModificationType

Gets the value of the monoisotopicMassDelta property.

getMonoisotopicMassDelta() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SubstitutionModificationType

Gets the value of the monoisotopicMassDelta property.

getMonoMass() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.CompositionT

Gets the value of the monoMass property.

getMonosaccharide(String) - Method in class org.expasy.mzjava.glycomics.io.mol.glycoct.DefaultGlycoCtResolver

Search for the monosaccharide that resolves the GlycoCT code in input.

getMonosaccharide(String) - Method in class org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCTReader
 
getMonosaccharide(String) - Method in interface org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCtResolver
 
getMonosaccharide() - Method in class org.expasy.mzjava.glycomics.mol.CleavedMonosaccharide
 
getMonosaccharideChildren(Monosaccharide) - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph

Returns all children of parent that are Monosaccharides

getMonosaccharideClass() - Method in class org.expasy.mzjava.glycomics.mol.Monosaccharide

Return the class of the Monosaccharide

getMonosaccharideSuperclass() - Method in class org.expasy.mzjava.glycomics.mol.Monosaccharide

Return the superclass of the Monosaccharide

getMostIntenseBinIndex() - Method in interface org.expasy.mzjava.stats.Histogram

Get the most intense bin index

getMostIntenseBinIndex() - Method in class org.expasy.mzjava.stats.HistogramImpl
 
getMostIntenseIndex(double, double) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList

Returns the index of the most intense peak in the range minMz to maxMz.

getMostIntenseIndex() - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList
 
getMostIntenseIndex(double, double) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleFloatPeakList

Returns the index of the most intense peak in the range minMz to maxMz.

getMostIntenseIndex() - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleFloatPeakList
 
getMostIntenseIndex(double, double) - Method in class org.expasy.mzjava.core.ms.peaklist.DoublePeakList

Returns the index of the most intense peak in the range minMz to maxMz.

getMostIntenseIndex() - Method in class org.expasy.mzjava.core.ms.peaklist.DoublePeakList
 
getMostIntenseIndex(double, double) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList
 
getMostIntenseIndex() - Method in class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList
 
getMostIntenseIndex(double, double) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatPeakList

Returns the index of the most intense peak in the range minMz to maxMz.

getMostIntenseIndex() - Method in class org.expasy.mzjava.core.ms.peaklist.FloatPeakList
 
getMostIntenseIndex(double, double) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Returns te index of the peak that is most intense in the specified region.

getMostIntenseIndex() - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Returns the index of the most intense peak in the peak list or -1 if there are no peaks in this peak list.

getMostIntenseIndex(double, double) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
getMostIntenseIndex() - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
getMsDetector() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary

Gets the value of the msDetector property.

getMsIonization() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary

Gets the value of the msIonization property.

getMsLevel() - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum

Returns the ms level that this peak list was measured at

getMsLevel() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MassTableType

Gets the value of the msLevel property.

getMsManufacturer() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary

Gets the value of the msManufacturer property.

getMsMassAnalyzer() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary

Gets the value of the msMassAnalyzer property.

getMsModel() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary

Gets the value of the msModel property.

getMsmsRunSummary() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis

Gets the value of the msmsRunSummary property.

getMz(int) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList.AbstractMergePeakSink
 
getMz(int) - Method in class org.expasy.mzjava.core.ms.peaklist.ArrayCursor
 
getMz(int) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList

Returns the mz of the peak at index

getMz(int) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleFloatPeakList

Returns the mz of the peak at index

getMz(int) - Method in class org.expasy.mzjava.core.ms.peaklist.DoublePeakList

Returns the mz of the peak at index

getMz(int) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList

Returns the mz of the peak at index

getMz(int) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatPeakList

Returns the mz of the peak at index

getMz() - Method in class org.expasy.mzjava.core.ms.peaklist.Peak

Return the m/z of the peak

getMz(int) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakCursor

Returns the m/z of the peak at index

getMz(int) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Returns the mz of the peak at index

getMz(int) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
getMz() - Method in class org.expasy.mzjava.hadoop.io.SpectrumKey
 
getMz() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.FragmentMasses

Gets the value of the mz property.

getMzFormat() - Method in interface org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfWriter.Parameters
 
getMzFormat() - Method in class org.expasy.mzjava.core.io.ms.spectrum.MgfParameters
 
getMzFormat(PeakList.Precision) - Static method in class org.expasy.mzjava.core.io.ms.spectrum.PeakListPrecisionFormat
 
getMzs(double[]) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList

Copies an the mzs from this peak list, beginning at 0,
 to the destination array.

getMzs(double[], int) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList

Copies an the mzs from this peak list, beginning at 0,
 to the specified position of the destination array.

getMzs(int, double[], int, int) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList

Copies an the mzs from this peak list, beginning at the specified position,
 to the specified position of the destination array.

getMzs(double[]) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleFloatPeakList

Copies an the mzs from this peak list, beginning at 0,
 to the destination array.

getMzs(double[], int) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleFloatPeakList

Copies an the mzs from this peak list, beginning at 0,
 to the specified position of the destination array.

getMzs(int, double[], int, int) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleFloatPeakList

Copies an the mzs from this peak list, beginning at the specified position,
 to the specified position of the destination array.

getMzs(double[]) - Method in class org.expasy.mzjava.core.ms.peaklist.DoublePeakList

Copies an the mzs from this peak list, beginning at 0,
 to the destination array.

getMzs(double[], int) - Method in class org.expasy.mzjava.core.ms.peaklist.DoublePeakList

Copies an the mzs from this peak list, beginning at 0,
 to the specified position of the destination array.

getMzs(int, double[], int, int) - Method in class org.expasy.mzjava.core.ms.peaklist.DoublePeakList

Copies an the mzs from this peak list, beginning at the specified position,
 to the specified position of the destination array.

getMzs(double[]) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList

Copies an the mzs from this peak list, beginning at 0,
 to the destination array.

getMzs(double[], int) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList

Copies an the mzs from this peak list, beginning at 0,
 to the specified position of the destination array.

getMzs(int, double[], int, int) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList

Copies an the mzs from this peak list, beginning at the specified position,
 to the specified position of the destination array.

getMzs(double[]) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatPeakList

Copies an the mzs from this peak list, beginning at 0,
 to the destination array.

getMzs(double[], int) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatPeakList

Copies an the mzs from this peak list, beginning at 0,
 to the specified position of the destination array.

getMzs(int, double[], int, int) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatPeakList

Copies an the mzs from this peak list, beginning at the specified position,
 to the specified position of the destination array.

getMzs(double[]) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Copies an the mzs from this peak list, beginning at 0,
 to the destination array.

getMzs(double[], int) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Copies an the mzs from this peak list, beginning at 0,
 to the specified position of the destination array.

getMzs(int, double[], int, int) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Copies an the mzs from this peak list, beginning at the specified position,
 to the specified position of the destination array.

getMzs(double[]) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
getMzs(double[], int) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
getMzs(int, double[], int, int) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
getMzStd() - Method in class org.expasy.mzjava.core.ms.spectrum.LibPeakAnnotation
 
getName() - Method in class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum
 
getName() - Method in class org.expasy.mzjava.glycomics.mol.GlycanNode

Return the name of the GlycanNode

getName() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AbstractParamType

Gets the value of the name property.

getName() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.IdentifiableType

Gets the value of the name property.

getName() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.InteractSummary.Inputfile

Gets the value of the name property.

getName() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis

Gets the value of the name property.

getName() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme

Gets the value of the name property.

getName() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.NameValueType

Gets the value of the name property.

getName() - Method in class org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
 
getName() - Method in class org.expasy.mzjava.stats.FrequencyTable

Return the name of this FrequencyTable

getName() - Method in interface org.expasy.mzjava.stats.Histogram

Get its name

getName() - Method in class org.expasy.mzjava.stats.HistogramImpl
 
getNamespaceURI() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader.NamespaceRewriteDelegate
 
getNeighbors(V) - Method in class org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph
 
getNeighbors(V) - Method in class org.expasy.mzjava.core.ms.cluster.JungSimGraphWrapper
 
getNeighbors(V) - Method in interface org.expasy.mzjava.core.ms.cluster.SimilarityGraph

Return an Iterable that iterates over the neighbours of vertex.

getNeighbors(V) - Method in class org.expasy.mzjava.core.ms.cluster.SparseSimilarityGraph
 
getNeutralLoss() - Method in class org.expasy.mzjava.glycomics.ms.spectrum.GlycanFragAnnotation

Return the mass shift that is associated with this annotation

getNeutralLoss() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.SpecificityT

Gets the value of the neutralLoss property.

getNeutralLoss() - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation

Return the mass shift that is associated with this annotation

getNeutralLosses() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodMod

Return an unmodifiable list containing the neutral losses.

getNeutralPeptideMass() - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch
 
getNew(String) - Method in class org.expasy.mzjava.glycomics.mol.DefaultMonosaccharideLookup

Search for a monosaccharide with the input name the list of known monosaccharides.

getNew(String) - Method in class org.expasy.mzjava.glycomics.mol.DefaultSubstituentLookup

Search for a substituent with the input name the list of known substituents.

getNew(String) - Method in interface org.expasy.mzjava.glycomics.mol.MonosaccharideLookup

Search for a monosaccharide with the input name the list of known monosaccharides.

getNew(String) - Method in interface org.expasy.mzjava.glycomics.mol.SubstituentLookup

Search for a substituent with the input name the list of known substituents.

getNextAA() - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideProteinMatch

Returns the amino acid that occurs after the end of the peptide.

getNoCut() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity

Gets the value of the noCut property.

getNode(int) - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph.AbstractBuilder

Return the nodeId'th node that was added

getNode(int) - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph

Returns the nodeId'th node that was added to this SaccharideGraph.

getNonEmptyBinIndices() - Method in interface org.expasy.mzjava.stats.Histogram

Get the set of non-empty bins

getNonEmptyBinIndices() - Method in class org.expasy.mzjava.stats.HistogramImpl
 
getNormalization() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary

Gets the value of the normalization property.

getNormalized() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraResult.Intensity

Gets the value of the normalized property.

getNrDecoyScores(float) - Method in class org.expasy.mzjava.stats.statscores.ScoreStatistics
 
getNrMembersCleaned() - Method in class org.expasy.mzjava.core.ms.cluster.SpectrumClusterEvaluator
 
getNrMembersOrg() - Method in class org.expasy.mzjava.core.ms.cluster.SpectrumClusterEvaluator
 
getNrTargetScores(float) - Method in class org.expasy.mzjava.stats.statscores.ScoreStatistics
 
getNTermGain() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymeType

Gets the value of the nTermGain property.

getNterminalModification() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.ModificationMap
 
getNtermMod() - Method in class org.expasy.mzjava.proteomics.mol.digest.CleavageSiteMatcher
 
getNtuples() - Method in class org.expasy.mzjava.utils.MixedRadixNtupleGenerator.NtupleContainer
 
getNumber() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.DatasetDerivation.DataFilter

Gets the value of the number property.

getNumber() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ElemRefT

Gets the value of the number property.

getNumberOfCut() - Method in class org.expasy.mzjava.glycomics.mol.CutDescriptor

Return the actual number of cuts in the CutDescriptor.

getNumberOfParsedEntry() - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader.ParseContext
 
getNumberOfPeaksToRetain() - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.TopNList

Return the number of peaks that will be retained.

getNumDatabaseSequences() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchDatabaseType

Gets the value of the numDatabaseSequences property.

getNumericValue(String, int) - Method in class org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCTReader
 
getNumMatchedIons() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Gets the value of the numMatchedIons property.

getNumMatchedIons() - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Return the number of ions that are were matched

getNumMissedCleavages() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Gets the value of the numMissedCleavages property.

getNumMissedCleavages() - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Return the number of missed cleavages that the Peptide contains

getNumResidues() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchDatabaseType

Gets the value of the numResidues property.

getNumSequencesSearched() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationListType

Gets the value of the numSequencesSearched property.

getNumTolTerm() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein

Gets the value of the numTolTerm property.

getNumTolTerm() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Gets the value of the numTolTerm property.

getNumTotProteins() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Gets the value of the numTotProteins property.

getObjectClass() - Method in interface org.expasy.mzjava.avro.io.AvroExternalizable
 
getObjectClass() - Method in class org.expasy.mzjava.avro.io.CompositionReader
 
getObjectClass() - Method in class org.expasy.mzjava.avro.io.CompositionWriter
 
getObjectClass() - Method in class org.expasy.mzjava.avro.io.LibPeakAnnotationReader
 
getObjectClass() - Method in class org.expasy.mzjava.avro.io.LibPeakAnnotationWriter
 
getObjectClass() - Method in class org.expasy.mzjava.avro.io.MsnSpectrumReader
 
getObjectClass() - Method in class org.expasy.mzjava.avro.io.MsnSpectrumWriter
 
getObjectClass() - Method in class org.expasy.mzjava.avro.io.NumericMassReader
 
getObjectClass() - Method in class org.expasy.mzjava.avro.io.NumericMassWriter
 
getObjectClass() - Method in class org.expasy.mzjava.avro.io.PeakListReader
 
getObjectClass() - Method in class org.expasy.mzjava.avro.io.PeakListWriter
 
getObjectClass() - Method in class org.expasy.mzjava.avro.io.PeakReader
 
getObjectClass() - Method in class org.expasy.mzjava.avro.io.PeakWriter
 
getObjectClass() - Method in class org.expasy.mzjava.avro.io.RetentionTimeDiscreteReader
 
getObjectClass() - Method in class org.expasy.mzjava.avro.io.RetentionTimeDiscreteWriter
 
getObjectClass() - Method in class org.expasy.mzjava.avro.io.RetentionTimeIntervalReader
 
getObjectClass() - Method in class org.expasy.mzjava.avro.io.RetentionTimeIntervalWriter
 
getObjectClass() - Method in class org.expasy.mzjava.avro.io.RetentionTimeListReader
 
getObjectClass() - Method in class org.expasy.mzjava.avro.io.RetentionTimeListWriter
 
getObjectClass() - Method in class org.expasy.mzjava.avro.io.ScanNumberDiscreteReader
 
getObjectClass() - Method in class org.expasy.mzjava.avro.io.ScanNumberDiscreteWriter
 
getObjectClass() - Method in class org.expasy.mzjava.avro.io.ScanNumberIntervalReader
 
getObjectClass() - Method in class org.expasy.mzjava.avro.io.ScanNumberIntervalWriter
 
getObjectClass() - Method in class org.expasy.mzjava.avro.io.ScanNumberListReader
 
getObjectClass() - Method in class org.expasy.mzjava.avro.io.ScanNumberListWriter
 
getObjectClass() - Method in class org.expasy.mzjava.avro.io.UUIDReader
 
getObjectClass() - Method in class org.expasy.mzjava.avro.io.UUIDWriter
 
getObjectClass() - Method in class org.expasy.mzjava.proteomics.avro.io.ModificationReader
 
getObjectClass() - Method in class org.expasy.mzjava.proteomics.avro.io.ModificationWriter
 
getObjectClass() - Method in class org.expasy.mzjava.proteomics.avro.io.PepFragAnnotationReader
 
getObjectClass() - Method in class org.expasy.mzjava.proteomics.avro.io.PepFragAnnotationWriter
 
getObjectClass() - Method in class org.expasy.mzjava.proteomics.avro.io.PepLibPeakAnnotationReader
 
getObjectClass() - Method in class org.expasy.mzjava.proteomics.avro.io.PepLibPeakAnnotationWriter
 
getObjectClass() - Method in class org.expasy.mzjava.proteomics.avro.io.PeptideConsensusSpectrumReader
 
getObjectClass() - Method in class org.expasy.mzjava.proteomics.avro.io.PeptideConsensusSpectrumWriter
 
getObjectClass() - Method in class org.expasy.mzjava.proteomics.avro.io.PeptideFragmentReader
 
getObjectClass() - Method in class org.expasy.mzjava.proteomics.avro.io.PeptideFragmentWriter
 
getObjectClass() - Method in class org.expasy.mzjava.proteomics.avro.io.PeptideReader
 
getObjectClass() - Method in class org.expasy.mzjava.proteomics.avro.io.PeptideSpectrumReader
 
getObjectClass() - Method in class org.expasy.mzjava.proteomics.avro.io.PeptideSpectrumWriter
 
getObjectClass() - Method in class org.expasy.mzjava.proteomics.avro.io.PeptideWriter
 
getObservedValue(MsnSpectrum) - Method in interface org.expasy.mzjava.external.io.ms.spectrum.ConsistencyCheck

Get observed value from an MsnSpectrum

getObservedValue(MsnSpectrum) - Method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.FirstMzCheck
 
getObservedValue(MsnSpectrum) - Method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.LastMzCheck
 
getObservedValue(MsnSpectrum) - Method in enum org.expasy.mzjava.external.io.ms.spectrum.mzml.MzmlConsistencyCheck
 
getObservedValue(MsnSpectrum) - Method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.TicCheck
 
getOffset() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.FragmentMasses

Gets the value of the offset property.

getOffset() - Method in exception org.expasy.mzjava.proteomics.mol.digest.CleavageSiteParseException
 
getOptFragmentAnnotation() - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PepLibPeakAnnotation
 
getOptionalAttribute(StartElement, String) - Static method in class org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader.XMLEventUtils
 
getOptionalCharacter(Character) - Method in class org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCTReader
 
getOptionalInteger(Integer) - Method in class org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCTReader
 
getOrganizationRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AffiliationType

Gets the value of the organizationRef property.

getOrganizationRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ParentOrganizationType

Gets the value of the organizationRef property.

getOrigDatabaseUrl() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase

Gets the value of the origDatabaseUrl property.

getOriginalResidue() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SubstitutionModificationType

Gets the value of the originalResidue property.

getOther(V) - Method in class org.expasy.mzjava.core.ms.cluster.SimEdge
 
getOutData() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary

Gets the value of the outData property.

getOutDataType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary

Gets the value of the outDataType property.

getOutEdges(V) - Method in class org.expasy.mzjava.core.ms.cluster.JungSimGraphWrapper
 
getOutputType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary

Gets the value of the outputType property.

getPages() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType

Gets the value of the pages property.

getParameter() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary

Gets the value of the parameter property.

getParameter() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Gets the value of the parameter property.

getParameter() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.PeptideprophetResult.SearchScoreSummary

Gets the value of the parameter property.

getParamGroup() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AbstractContactType

Attributes of this contact such as address, email, telephone etc.Gets the value of the paramGroup property.

getParamGroup() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AmbiguousResidueType

Parameters for capturing e.g.

getParamGroup() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DBSequenceType

Additional descriptors for the sequence, such as taxon, description line etc.Gets the value of the paramGroup property.

getParamGroup() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MassTableType

Additional parameters or descriptors for the MassTable.Gets the value of the paramGroup property.

getParamGroup() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ParamListType

Gets the value of the paramGroup property.

getParamGroup() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType

Additional parameters or descriptors for the PeptideEvidence.Gets the value of the paramGroup property.

getParamGroup() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideType

Additional descriptors of this peptide sequence Gets the value of the paramGroup property.

getParamGroup() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinAmbiguityGroupType

Scores or parameters associated with the ProteinAmbiguityGroup.Gets the value of the paramGroup property.

getParamGroup() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionHypothesisType

Scores or parameters associated with this ProteinDetectionHypothesis e.g.

getParamGroup() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionListType

Scores or output parameters associated with the whole ProteinDetectionList Gets the value of the paramGroup property.

getParamGroup() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SampleType

The characteristics of a
 Material.Gets the value of the paramGroup property.

getParamGroup() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SourceFileType

Any additional parameters description the source
                                                                file.Gets the value of the paramGroup property.

getParamGroup() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType

Scores or attributes associated with the SpectrumIdentificationItem e.g.

getParamGroup() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationListType

Scores or output parameters associated with the SpectrumIdentificationList.Gets the value of the paramGroup property.

getParamGroup() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationResultType

Scores or parameters associated with the SpectrumIdentificationResult (i.e the set of SpectrumIdentificationItems derived from one spectrum) e.g.

getParent(A) - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph

Calculate the parent of a node.

getParent() - Method in class org.expasy.mzjava.glycomics.mol.SEdge
 
getParent() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.OrganizationType

Gets the value of the parent property.

getParentFile() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.DatasetDerivation.DataFilter

Gets the value of the parentFile property.

getParents() - Method in class org.expasy.mzjava.glycomics.mol.SEdge
 
getParentScanNumber() - Method in class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum

Returns the scan number of the parent scan.

getParentTolerance() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType

Gets the value of the parentTolerance property.

getPeakCount() - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.CentroidFilter.PeakIntensityInfo
 
getPeakIndex() - Method in exception org.expasy.mzjava.core.ms.peaklist.UnsortedPeakListException
 
getPepNeutralLoss() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.SpecificityT

Gets the value of the pepNeutralLoss property.

getPeptide() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SequenceCollectionType

Gets the value of the peptide property.

getPeptide() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Gets the value of the peptide property.

getPeptide() - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum

Return the peptide

getPeptide() - Method in class org.expasy.mzjava.proteomics.ms.dbsearch.Digest

Return the peptide.

getPeptide() - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PeptideSpectrum
 
getPeptideBuilder(int, int) - Method in class org.expasy.mzjava.proteomics.mol.Protein

Create a PeptideBuilder that has the sequence initialised by copying this Protein's amino acids starting at
 fromInclusive to toExclusive.

getPeptideEvidence() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SequenceCollectionType

Gets the value of the peptideEvidence property.

getPeptideEvidenceRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceRefType

Gets the value of the peptideEvidenceRef property.

getPeptideEvidenceRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideHypothesisType

Gets the value of the peptideEvidenceRef property.

getPeptideEvidenceRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType

Gets the value of the peptideEvidenceRef property.

getPeptideHypothesis() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionHypothesisType

Gets the value of the peptideHypothesis property.

getPeptideNextAa() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein

Gets the value of the peptideNextAa property.

getPeptideNextAa() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Gets the value of the peptideNextAa property.

getPeptidePrevAa() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein

Gets the value of the peptidePrevAa property.

getPeptidePrevAa() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Gets the value of the peptidePrevAa property.

getPeptideRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType

Gets the value of the peptideRef property.

getPeptideRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType

Gets the value of the peptideRef property.

getPeptides(double, Tolerance) - Method in class org.expasy.mzjava.proteomics.ms.dbsearch.ArrayDigestDB
 
getPeptides(double, Tolerance, Collection<Digest>) - Method in class org.expasy.mzjava.proteomics.ms.dbsearch.ArrayDigestDB
 
getPeptides(double, Tolerance) - Method in interface org.expasy.mzjava.proteomics.ms.dbsearch.DigestDB

Retrieves all the peptides that have a mass that is within
 tolerance of targetMass

getPeptides(double, Tolerance, Collection<Digest>) - Method in interface org.expasy.mzjava.proteomics.ms.dbsearch.DigestDB

Add all the peptides that have a mass that is within tolerance of targetMass to
 the peptides collection

getPeptideSequence() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideType

Gets the value of the peptideSequence property.

getPeptideTerminus() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification

Gets the value of the peptideTerminus property.

getPersonOrOrganization() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AuditCollectionType

Gets the value of the personOrOrganization property.

getPolarity() - Method in class org.expasy.mzjava.core.ms.peaklist.Peak

Return the charge polarity.

getPolarity(int) - Static method in enum org.expasy.mzjava.core.ms.peaklist.Polarity
 
getPosition() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo.ModAminoacidMass

Gets the value of the position property.

getPosition() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.SpecificityT

Gets the value of the position property.

getPosition() - Method in class org.expasy.mzjava.proteomics.ms.ident.ModificationMatch
 
getPost() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType

Gets the value of the post property.

getPre() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType

Gets the value of the pre property.

getPrecision() - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList
 
getPrecision() - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleFloatPeakList
 
getPrecision() - Method in class org.expasy.mzjava.core.ms.peaklist.DoublePeakList
 
getPrecision() - Method in class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList
 
getPrecision() - Method in class org.expasy.mzjava.core.ms.peaklist.FloatPeakList
 
getPrecision() - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Return the precision that this PeakList uses to store the peak and intensity values

getPrecision() - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
getPrecursor() - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
 
getPrecursor() - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Returns the precursor peak of this peak list

getPrecursor() - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
getPrecursorIntensity() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery

Gets the value of the precursorIntensity property.

getPrecursorIntensity() - Method in class org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
 
getPrecursorMassType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary

Gets the value of the precursorMassType property.

getPrecursorMz() - Method in class org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
 
getPrecursorMzMean() - Method in class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum
 
getPrecursorMzStdev() - Method in class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum
 
getPrecursorNeutralLosses() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodMod

Returns an unmodifiable list containing the precursor neutral losses.

getPrecursorNeutralMass() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery

Gets the value of the precursorNeutralMass property.

getPrecursorNeutralMass() - Method in class org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
 
getPredecessors(V) - Method in class org.expasy.mzjava.core.ms.cluster.JungSimGraphWrapper
 
getPreviousAA() - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideProteinMatch

Returns the amino acid that occurs before the start of the peptide.

getPrintStream() - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar.View
 
getProbability() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.PeptideprophetResult

Gets the value of the probability property.

getProtein() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein

Gets the value of the protein property.

getProtein() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Gets the value of the protein property.

getProteinAccessionNumbers() - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum

Return an unmodifiable list containing the protein accession numbers associated with the peptide
 tha this LibrarySpectrum represents.

getProteinAccessionNumbers() - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PeptideSpectrum
 
getProteinAmbiguityGroup() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionListType

Gets the value of the proteinAmbiguityGroup property.

getProteinDescr() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein

Gets the value of the proteinDescr property.

getProteinDescr() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Gets the value of the proteinDescr property.

getProteinDetection() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisCollectionType

Gets the value of the proteinDetection property.

getProteinDetectionHypothesis() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinAmbiguityGroupType

Gets the value of the proteinDetectionHypothesis property.

getProteinDetectionList() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisDataType

Gets the value of the proteinDetectionList property.

getProteinDetectionListRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionType

Gets the value of the proteinDetectionListRef property.

getProteinDetectionProtocol() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisProtocolCollectionType

Gets the value of the proteinDetectionProtocol property.

getProteinDetectionProtocolRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionType

Gets the value of the proteinDetectionProtocolRef property.

getProteinIds() - Method in class org.expasy.mzjava.proteomics.ms.dbsearch.Digest

Returns an Immutable set containing the protein ids

getProteinMatches() - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Return a reference to the protein accession list

getProteinMw() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein

Gets the value of the proteinMw property.

getProteinMw() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Gets the value of the proteinMw property.

getProteinTerminus() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification

Gets the value of the proteinTerminus property.

getProvider() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType

Gets the value of the provider property.

getPsiMsMsName() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodMod

Returns the psi ms ms name

getPublication() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType

Gets the value of the publication property.

getPublisher() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType

Gets the value of the publisher property.

getQuantLabelMasses() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioTimestamp

Gets the value of the quantLabelMasses property.

getQValue(float) - Method in class org.expasy.mzjava.stats.statscores.ScoreStatistics
 
getRange() - Method in interface org.expasy.mzjava.stats.Histogram

Get the range of defined values (first to last bin)

getRange() - Method in class org.expasy.mzjava.stats.HistogramImpl
 
getRank() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType

Gets the value of the rank property.

getRank() - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Return the rank of this PeptideMatch

getRatio() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioContribution

Gets the value of the ratio property.

getRatio() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult

Gets the value of the ratio property.

getRawData() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary

Gets the value of the rawData property.

getRawDataType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary

Gets the value of the rawDataType property.

getRecordDoc() - Method in class org.expasy.mzjava.avro.io.AvroIO

Returns the documentation for this record

 Default is to have no documentation, subclasses can override this to provide doc

getRecordDoc() - Method in class org.expasy.mzjava.avro.io.RetentionTimeDiscreteReader
 
getRecordDoc() - Method in class org.expasy.mzjava.avro.io.RetentionTimeDiscreteWriter
 
getRecordDoc() - Method in class org.expasy.mzjava.avro.io.RetentionTimeIntervalReader
 
getRecordDoc() - Method in class org.expasy.mzjava.avro.io.RetentionTimeIntervalWriter
 
getRecordId() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT

Gets the value of the recordId property.

getRecordId() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodMod

Returns the UniMod record id.

getRecordName() - Method in class org.expasy.mzjava.avro.io.AbstractAvroReader
 
getRecordName() - Method in class org.expasy.mzjava.avro.io.AbstractAvroWriter
 
getRecordName() - Method in class org.expasy.mzjava.avro.io.AvroIO

Return the name of this record

getRecordNameSpace() - Method in class org.expasy.mzjava.avro.io.AbstractAvroReader
 
getRecordNameSpace() - Method in class org.expasy.mzjava.avro.io.AbstractAvroWriter
 
getRecordNameSpace() - Method in class org.expasy.mzjava.avro.io.AvroIO

Return the namespace of this record

getReducingEndAnomericity() - Method in class org.expasy.mzjava.glycomics.mol.Glycan
 
getRegex() - Method in class org.expasy.mzjava.proteomics.mol.digest.CleavageSiteMatcher
 
getRelativeBinFreq(int) - Method in interface org.expasy.mzjava.stats.Histogram

Get the relative (normalized by the cumulative weights) weighted frequencies at given bin

getRelativeBinFreq(int, int) - Method in interface org.expasy.mzjava.stats.Histogram

Get the relative (normalized by the cumulative weights) weighted frequencies between bins

getRelativeBinFreq(int) - Method in class org.expasy.mzjava.stats.HistogramImpl
 
getRelativeBinFreq(int, int) - Method in class org.expasy.mzjava.stats.HistogramImpl
 
getReleaseDate() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchDatabaseType

Gets the value of the releaseDate property.

getReplacementResidue() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SubstitutionModificationType

Gets the value of the replacementResidue property.

getResidue() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MassTableType

Gets the value of the residue property.

getResidue() - Method in class org.expasy.mzjava.proteomics.ms.ident.ModificationMatch
 
getResidues() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ModificationType

Gets the value of the residues property.

getResidues() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchModificationType

Gets the value of the residues property.

getResults(MsnSpectrum) - Method in class org.expasy.mzjava.proteomics.ms.ident.ScanNumberIndexSearchResultMap
 
getResults(MsnSpectrum) - Method in class org.expasy.mzjava.proteomics.ms.ident.ScanNumberSearchResultMap
 
getResults(MsnSpectrum) - Method in class org.expasy.mzjava.proteomics.ms.ident.SearchResultMap
 
getResults(MsnSpectrum) - Method in class org.expasy.mzjava.proteomics.ms.ident.TitleSearchResultMap
 
getRetentionTime() - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum
 
getRetentionTimeFormat() - Method in interface org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfWriter.Parameters
 
getRetentionTimeFormat() - Method in class org.expasy.mzjava.core.io.ms.spectrum.MgfParameters
 
getRetentionTimes() - Method in class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum

Return this MsnSpectrum's retention time list.

getRetentionTimes() - Method in class org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
 
getRetentionTimeSec() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery

Gets the value of the retentionTimeSec property.

getRightValley() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak

Gets the value of the rightValley property.

getRightValley() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak

Gets the value of the rightValley property.

getRing() - Method in class org.expasy.mzjava.glycomics.mol.Monosaccharide

Return the ring type of the Monosaccharide

getRingType(char) - Static method in enum org.expasy.mzjava.glycomics.mol.RingType
 
getRole() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ContactRoleType

Gets the value of the role property.

getRoot() - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph

Return the root of this SaccharideGraph

getSameScanRange() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioSummary

Gets the value of the sameScanRange property.

getSample() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisSampleCollectionType

Gets the value of the sample property.

getSampleEnzyme() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary

Gets the value of the sampleEnzyme property.

getSampleRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType

Gets the value of the sampleRef property.

getSampleRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SubSampleType

Gets the value of the sampleRef property.

getScanNumbers() - Method in class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum

Returns the scan number of this MsnSpectrum

getScanNumbers() - Method in class org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
 
getScore() - Method in class org.expasy.mzjava.core.ms.cluster.SimEdge
 
getScore(String) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Return the score that is associtaed with scoreName

getScoreForQValue(float) - Method in class org.expasy.mzjava.stats.statscores.ScoreStatistics
 
getScoreMap() - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Returns a reference to the score map

getSdSimScore() - Method in class org.expasy.mzjava.core.ms.cluster.SpectrumClusterEvaluator
 
getSearchDatabase() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.InputsType

Gets the value of the searchDatabase property.

getSearchDatabase() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary

Gets the value of the searchDatabase property.

getSearchDatabase() - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideProteinMatch

Returns the search database contains this match.

getSearchDatabaseRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DBSequenceType

Gets the value of the searchDatabaseRef property.

getSearchDatabaseRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchDatabaseRefType

Gets the value of the searchDatabaseRef property.

getSearchDatabaseRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationType

Gets the value of the searchDatabaseRef property.

getSearchEngine() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary

Gets the value of the searchEngine property.

getSearchHit() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult

Gets the value of the searchHit property.

getSearchId() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary

Gets the value of the searchId property.

getSearchId() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult

Gets the value of the searchId property.

getSearchModification() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ModificationParamsType

Gets the value of the searchModification property.

getSearchResult() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery

Gets the value of the searchResult property.

getSearchScore() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Gets the value of the searchScore property.

getSearchScoreSummary() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.PeptideprophetResult

Gets the value of the searchScoreSummary property.

getSearchSpecification() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery

Gets the value of the searchSpecification property.

getSearchSummary() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary

Gets the value of the searchSummary property.

getSearchType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType

Gets the value of the searchType property.

getSecondIndex() - Method in class org.expasy.mzjava.glycomics.mol.CutIndexes

Return the second index of the cleavage

getSense() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity

Gets the value of the sense property.

getSeq() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DBSequenceType

Gets the value of the seq property.

getSequence() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader.PeptideInfoParser
 
getSequence() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SequenceSearchConstraint

Gets the value of the sequence property.

getSequenceCollection() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType

Gets the value of the sequenceCollection property.

getSequenceSearchConstraint() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary

Gets the value of the sequenceSearchConstraint property.

getSerializer(Class<Object>) - Method in class org.expasy.mzjava.hadoop.io.MzJavaSerialization
 
getSimScoreMean() - Method in class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum
 
getSimScoreStdev() - Method in class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum
 
getSite() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.SpecificityT

Gets the value of the site property.

getSiteRegexp() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymeType

Gets the value of the siteRegexp property.

getSites() - Method in class org.expasy.mzjava.proteomics.mol.modification.NeutralLoss
 
getSites() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodMod

Return the list of modification sites

getSizeInDbEntries() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase

Gets the value of the sizeInDbEntries property.

getSizeOfResidues() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase

Gets the value of the sizeOfResidues property.

getSoftwareName() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisSoftwareType

Gets the value of the softwareName property.

getSource() - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader.ParseContext
 
getSource(SimEdge<V>) - Method in class org.expasy.mzjava.core.ms.cluster.JungSimGraphWrapper
 
getSource() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.XrefT

Gets the value of the source property.

getSourceFile() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.InputsType

Gets the value of the sourceFile property.

getSpecGroup() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.SpecificityT

Gets the value of the specGroup property.

getSpecificity() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme

Gets the value of the specificity property.

getSpecificity() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT

Gets the value of the specificity property.

getSpecificityRules() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchModificationType

Gets the value of the specificityRules property.

getSpectra(Peak) - Method in class org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumDB

Collect all peptide spectra with mass closed to the given precursor peak

getSpectra(Peak, Collection<PeptideSpectrum>) - Method in class org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumDB

Add all peptide spectra contained in this database that are within tolerance of the precursor to spectrumCollection

getSpectraData() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.InputsType

Gets the value of the spectraData property.

getSpectraDataRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.InputSpectraType

Gets the value of the spectraDataRef property.

getSpectraDataRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationResultType

Gets the value of the spectraDataRef property.

getSpectrum() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery

Gets the value of the spectrum property.

getSpectrum() - Method in class org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
 
getSpectrumFile() - Method in class org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
 
getSpectrumId(ResultSet) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.AbstractPsmCsvReader

Create a new SpectrumIdentifier from a given ResultSet

getSpectrumId(ResultSet) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.MaxQuantPsmReader
 
getSpectrumID() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationResultType

Gets the value of the spectrumID property.

getSpectrumId(ResultSet) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.ProteinPilotPsmReader
 
getSpectrumIdentification() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisCollectionType

Gets the value of the spectrumIdentification property.

getSpectrumIdentificationItem() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationResultType

Gets the value of the spectrumIdentificationItem property.

getSpectrumIdentificationItemRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideHypothesisType

Gets the value of the spectrumIdentificationItemRef property.

getSpectrumIdentificationItemRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemRefType

Gets the value of the spectrumIdentificationItemRef property.

getSpectrumIdentificationList() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisDataType

Gets the value of the spectrumIdentificationList property.

getSpectrumIdentificationListRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.InputSpectrumIdentificationsType

Gets the value of the spectrumIdentificationListRef property.

getSpectrumIdentificationListRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationType

Gets the value of the spectrumIdentificationListRef property.

getSpectrumIdentificationProtocol() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisProtocolCollectionType

Gets the value of the spectrumIdentificationProtocol property.

getSpectrumIdentificationProtocolRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationType

Gets the value of the spectrumIdentificationProtocolRef property.

getSpectrumIdentificationResult() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationListType

Gets the value of the spectrumIdentificationResult property.

getSpectrumIDFormat() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectraDataType

Gets the value of the spectrumIDFormat property.

getSpectrumIndex() - Method in class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum

Return the index of this MsnSpectrum.

getSpectrumQuery() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary

Gets the value of the spectrumQuery property.

getSpectrumSource() - Method in class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum

Return the URI that describes the source of this MsnSpectrum.

getSpectrumSource() - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum
 
getStandardDeviation(double[]) - Method in class org.expasy.mzjava.core.ms.spectrasim.PearsonsSimFunc
 
getStart() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType

Gets the value of the start property.

getStart() - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideProteinMatch

Returns the start position of the peptide within the protein.

getStartIndex(List<String>, String) - Method in class org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCTReader
 
getStartScan() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery

Gets the value of the startScan property.

getStaticQuant() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioSummary

Gets the value of the staticQuant property.

getStaticQuantLabel() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioTimestamp

Gets the value of the staticQuantLabel property.

getStatus() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak

Gets the value of the status property.

getStatus() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak

Gets the value of the status property.

getStatus() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioPeptideData

Gets the value of the status property.

getStatus() - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum

Returns this LibrarySpectrum's status.

getStopIndex(List<String>, String) - Method in class org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCTReader
 
getSubSample() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SampleType

Gets the value of the subSample property.

getSubstituent(String) - Method in class org.expasy.mzjava.glycomics.io.mol.glycoct.DefaultGlycoCtResolver

Search for the substituent that resolves the GlycoCT code in input.

getSubstituent(String) - Method in class org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCTReader
 
getSubstituent(String) - Method in interface org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCtResolver
 
getSubstituentChildren(Monosaccharide) - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph

Returns all children of parent that are Substituents

getSubstituentLinkage(GlycanNode, GlycanNode) - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph

Return the linkage between parentNode and childNode

getSubstitutionModification() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideType

Gets the value of the substitutionModification property.

getSuccessors(V) - Method in class org.expasy.mzjava.core.ms.cluster.JungSimGraphWrapper
 
getSummaryXml() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis

Gets the value of the summaryXml property.

getSymbol() - Method in class org.expasy.mzjava.core.mol.Atom
 
getSymbol() - Method in enum org.expasy.mzjava.core.mol.AtomicSymbol
 
getSymbol() - Method in interface org.expasy.mzjava.core.mol.Symbol
 
getSymbol(int) - Method in interface org.expasy.mzjava.core.mol.SymbolSequence

Returns the symbol at the specified position in this symbol sequence.

getSymbol() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification

Gets the value of the symbol property.

getSymbol() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification

Gets the value of the symbol property.

getSymbol() - Method in enum org.expasy.mzjava.proteomics.mol.AminoAcid
 
getSymbol(int) - Method in class org.expasy.mzjava.proteomics.mol.AminoAcidSequence
 
getSymbol() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ElemRefT

Gets the value of the symbol property.

getSymbol(int) - Method in class org.expasy.mzjava.proteomics.mol.Protein
 
getSymbol(int) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch
 
getSymbolIndexes(AminoAcid) - Method in class org.expasy.mzjava.proteomics.mol.AminoAcidSequence

Returns an array containing the indexes of where symbol is found in this
 sequence.

getTabValues(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader
 
getTargetDecoyRatio() - Method in class org.expasy.mzjava.stats.statscores.FitDecoyScoreStatistics
 
getTargetMass() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraResult.Intensity

Gets the value of the targetMass property.

getTargetScores() - Method in class org.expasy.mzjava.stats.statscores.ScoreStatistics
 
getTerminalModification() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary

Gets the value of the terminalModification property.

getTerminus() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification

Gets the value of the terminus property.

getText() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.XrefT

Gets the value of the text property.

getTheoreticalMz() - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation

Returns the theoretical m/z for this annotation.

getThreshold() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionProtocolType

Gets the value of the threshold property.

getThreshold() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType

Gets the value of the threshold property.

getThreshold(int) - Method in class org.expasy.mzjava.stats.ROCTable
 
getTime() - Method in interface org.expasy.mzjava.core.ms.spectrum.RetentionTime

Returns the retention time the units of the time is seconds

getTime() - Method in class org.expasy.mzjava.core.ms.spectrum.RetentionTimeDiscrete
 
getTime() - Method in class org.expasy.mzjava.core.ms.spectrum.RetentionTimeInterval

Returns the time in the middle of the interval in seconds

getTime() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak

Gets the value of the time property.

getTime() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak

Gets the value of the time property.

getTime() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.AnalysisSummary

Gets the value of the time property.

getTime() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp

Gets the value of the time property.

getTimeWidth() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak

Gets the value of the timeWidth property.

getTimeWidth() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak

Gets the value of the timeWidth property.

getTitle() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType

Gets the value of the title property.

getTitle() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT

Gets the value of the title property.

getTotal() - Method in class org.expasy.mzjava.stats.FrequencyTable

Return the total number of values in this table.

getTotalIntensity() - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.CentroidFilter.PeakIntensityInfo
 
getTotalIonCurrent() - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList

Returns the sum of all intensities

getTotalIonCurrent() - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList
 
getTotalIonCurrent() - Method in class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList
 
getTotalIonCurrent() - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Returns the sum of all intensities

getTotalIonCurrent() - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
getTotalNumIons() - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Return the total number of ions that were generated for the Peptide

getTotalPeakCount() - Method in class org.expasy.mzjava.core.ms.spectrasim.DpSimFunc
 
getTotalPeakCount() - Method in class org.expasy.mzjava.core.ms.spectrasim.McNdpSimFunc
 
getTotalPeakCount() - Method in class org.expasy.mzjava.core.ms.spectrasim.NdpSimFunc
 
getTotalPeakCount() - Method in class org.expasy.mzjava.core.ms.spectrasim.PearsonsSimFunc
 
getTotalPeakCount() - Method in class org.expasy.mzjava.core.ms.spectrasim.PspcSimFunc
 
getTotalPeakCount() - Method in class org.expasy.mzjava.core.ms.spectrasim.SharedPeakSimFunc
 
getTotalPeakCount() - Method in interface org.expasy.mzjava.core.ms.spectrasim.SimFunc

Returns the total number peaks in plX and plY from the last call to calcSimilarity

getTotalPeakCount() - Method in class org.expasy.mzjava.core.ms.spectrasim.WeightedPearsonsSimFunc
 
getTotNumIons() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Gets the value of the totNumIons property.

getTranslationTable() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DatabaseTranslationType

Gets the value of the translationTable property.

getTranslationTableRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType

Gets the value of the translationTableRef property.

getTrueNegative(int) - Method in class org.expasy.mzjava.stats.ROCTable
 
getTruePositive(int) - Method in class org.expasy.mzjava.stats.ROCTable
 
getTruePositiveRate(int) - Method in class org.expasy.mzjava.stats.ROCTable
 
getType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.UserParamType

Gets the value of the type property.

getType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase

Gets the value of the type property.

getType() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.NameValueType

Gets the value of the type property.

getType() - Method in class org.expasy.mzjava.stats.Histogram.Normalization
 
getUnion(Class) - Method in class org.expasy.mzjava.avro.io.AvroIO

Return the readers or writers for the union of the recordSuperclass

getUnitAccession() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AbstractParamType

Gets the value of the unitAccession property.

getUnitCvRef() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AbstractParamType

Gets the value of the unitCvRef property.

getUnitName() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AbstractParamType

Gets the value of the unitName property.

getUpperBound() - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.AbstractMergePeakFilter

Return the current upper bound peak index

getUri() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisSoftwareType

Gets the value of the uri property.

getUri() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.CvType

Gets the value of the uri property.

getURL() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase

Gets the value of the url property.

getUrl() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.XrefT

Gets the value of the url property.

getUse() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioContribution

Gets the value of the use property.

getUsernameOfPoster() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT

Gets the value of the usernameOfPoster property.

getUserParam() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ParamType

Gets the value of the userParam property.

getValue() - Method in class org.expasy.mzjava.app.io.MonitoredIterativeReader
 
getValue() - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar
 
getValue() - Method in interface org.expasy.mzjava.core.ms.spectrum.ScanNumber

Return the scan number.

getValue() - Method in class org.expasy.mzjava.core.ms.spectrum.ScanNumberDiscrete
 
getValue() - Method in class org.expasy.mzjava.core.ms.spectrum.ScanNumberInterval
 
getValue() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AbstractParamType

Gets the value of the value property.

getValue() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.NameValueType

Gets the value of the value property.

getValue() - Method in class org.expasy.mzjava.stats.Histogram.Normalization
 
getValueAttribute() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.NameValueType

Gets the value of the valueAttribute property.

getValues() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FragmentArrayType

Gets the value of the values property.

getVariable() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification

Gets the value of the variable property.

getVariable() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification

Gets the value of the variable property.

getVersion() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisSoftwareType

Gets the value of the version property.

getVersion() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.CvType

Gets the value of the version property.

getVersion() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType

Gets the value of the version property.

getVersion() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchDatabaseType

Gets the value of the version property.

getVersion() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioSummary

Gets the value of the version property.

getVersion() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.AnalysisSummary

Gets the value of the version property.

getVersion() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioSummary

Gets the value of the version property.

getVertex1() - Method in class org.expasy.mzjava.core.ms.cluster.SimEdge
 
getVertex2() - Method in class org.expasy.mzjava.core.ms.cluster.SimEdge
 
getVertexCount() - Method in class org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph
 
getVertexCount() - Method in class org.expasy.mzjava.core.ms.cluster.JungSimGraphWrapper
 
getVertexCount() - Method in interface org.expasy.mzjava.core.ms.cluster.SimilarityGraph

Return the number of vertexes in this graph.

getVertexCount() - Method in class org.expasy.mzjava.core.ms.cluster.SparseSimilarityGraph
 
getVertices() - Method in class org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph
 
getVertices() - Method in class org.expasy.mzjava.core.ms.cluster.JungSimGraphWrapper
 
getVertices() - Method in interface org.expasy.mzjava.core.ms.cluster.SimilarityGraph

Return an Iterable that iterates over the vertices in this graph.

getVertices() - Method in class org.expasy.mzjava.core.ms.cluster.SparseSimilarityGraph
 
getVolume() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType

Gets the value of the volume property.

getWindowsParent() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.DatasetDerivation.DataFilter

Gets the value of the windowsParent property.

getWorstScore() - Method in class org.expasy.mzjava.core.ms.spectrasim.DpSimFunc
 
getWorstScore() - Method in class org.expasy.mzjava.core.ms.spectrasim.McNdpSimFunc
 
getWorstScore() - Method in class org.expasy.mzjava.core.ms.spectrasim.NdpSimFunc
 
getWorstScore() - Method in class org.expasy.mzjava.core.ms.spectrasim.PearsonsSimFunc
 
getWorstScore() - Method in class org.expasy.mzjava.core.ms.spectrasim.PspcSimFunc
 
getWorstScore() - Method in class org.expasy.mzjava.core.ms.spectrasim.SharedPeakSimFunc
 
getWorstScore() - Method in interface org.expasy.mzjava.core.ms.spectrasim.SimFunc

Return the worst the score that can be returned by calls to calcSimilarity.

getWorstScore() - Method in class org.expasy.mzjava.core.ms.spectrasim.WeightedPearsonsSimFunc
 
getXpressLight() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioSummary

Gets the value of the xpressLight property.

getXpressLight() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioTimestamp

Gets the value of the xpressLight property.

getXref() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT

Gets the value of the xref property.

getYear() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType

Gets the value of the year property.

GlobalThresholdClusterBuilder<V> - Class in org.expasy.mzjava.core.ms.cluster
 
GlobalThresholdClusterBuilder(double) - Constructor for class org.expasy.mzjava.core.ms.cluster.GlobalThresholdClusterBuilder
 
Glycan - Class in org.expasy.mzjava.glycomics.mol

Data structure to represent a Glycan.

Glycan(Monosaccharide, Optional<Anomericity>, String, Composition) - Constructor for class org.expasy.mzjava.glycomics.mol.Glycan
 
Glycan.Builder - Class in org.expasy.mzjava.glycomics.mol

A builder to build Glycans.

Glycan.Builder() - Constructor for class org.expasy.mzjava.glycomics.mol.Glycan.Builder
 
GlycanFragAnnotation - Class in org.expasy.mzjava.glycomics.ms.spectrum
 
GlycanFragAnnotation(int, GlycanFragment) - Constructor for class org.expasy.mzjava.glycomics.ms.spectrum.GlycanFragAnnotation

Construct a GlycanFragAnnotation

GlycanFragAnnotation(int, GlycanFragment, Composition, Mass) - Constructor for class org.expasy.mzjava.glycomics.ms.spectrum.GlycanFragAnnotation
 
GlycanFragAnnotation(GlycanFragAnnotation) - Constructor for class org.expasy.mzjava.glycomics.ms.spectrum.GlycanFragAnnotation

Copy constructor

GlycanFragAnnotation.FragBuilder - Class in org.expasy.mzjava.glycomics.ms.spectrum

GlycanFragAnnotation Builder

GlycanFragAnnotation.FragBuilder(int, GlycanFragment) - Constructor for class org.expasy.mzjava.glycomics.ms.spectrum.GlycanFragAnnotation.FragBuilder

Construct a new FragBuilder

GlycanFragAnnotation.FragBuilder(GlycanFragAnnotation) - Constructor for class org.expasy.mzjava.glycomics.ms.spectrum.GlycanFragAnnotation.FragBuilder

Copy constructor

GlycanFragment - Class in org.expasy.mzjava.glycomics.mol
 
GlycanFragment(Monosaccharide, FragmentType, List<GlycanNode>, List<SEdge>, IdentityEdgeMultimap<Monosaccharide, Monosaccharide, GlycosidicEdge>, IdentityEdgeMultimap<Monosaccharide, Substituent, SubstituentEdge>, Composition, Map<CleavedMonosaccharide, IonType>, Map<SEdge, IonType>) - Constructor for class org.expasy.mzjava.glycomics.mol.GlycanFragment
 
GlycanFragment(Monosaccharide, FragmentType, Composition) - Constructor for class org.expasy.mzjava.glycomics.mol.GlycanFragment
 
GlycanFragment.Builder - Class in org.expasy.mzjava.glycomics.mol

A builder to build Glycosidic Fragments.

GlycanFragment.Builder() - Constructor for class org.expasy.mzjava.glycomics.mol.GlycanFragment.Builder
 
GlycanFragmenter - Class in org.expasy.mzjava.glycomics.ms.fragment
 
GlycanFragmenter(List<GlycanPeakGenerator<GlycanFragAnnotation>>, PeakList.Precision, int, int) - Constructor for class org.expasy.mzjava.glycomics.ms.fragment.GlycanFragmenter

Constructs a glycan fragmenter that generates peaks using the supplied peak generators.

GlycanFragmenter(Set<IonType>, boolean, boolean, PeakList.Precision, int, int) - Constructor for class org.expasy.mzjava.glycomics.ms.fragment.GlycanFragmenter

Construct a glycan fragmenter that generates peaks for the supplied ion types.

GlycanFragmentPeakGenerator - Class in org.expasy.mzjava.glycomics.ms.fragment
 
GlycanFragmentPeakGenerator(Set<FragmentType>, Set<IonType>, int) - Constructor for class org.expasy.mzjava.glycomics.ms.fragment.GlycanFragmentPeakGenerator
 
GlycanMassCalculator - Interface in org.expasy.mzjava.glycomics.mol
 
GlycanNode - Class in org.expasy.mzjava.glycomics.mol
 
GlycanNode(String, Composition) - Constructor for class org.expasy.mzjava.glycomics.mol.GlycanNode
 
GlycanNode(GlycanNode) - Constructor for class org.expasy.mzjava.glycomics.mol.GlycanNode
 
GlycanPeakGenerator<A extends PeakAnnotation> - Interface in org.expasy.mzjava.glycomics.ms.fragment
 
GlycanSpectrum - Class in org.expasy.mzjava.glycomics.ms.spectrum
 
GlycanSpectrum(Glycan, int) - Constructor for class org.expasy.mzjava.glycomics.ms.spectrum.GlycanSpectrum

Constructor for GlycanSpectrum.

GlycanSpectrum(Spectrum<GlycanFragAnnotation>, Glycan, int) - Constructor for class org.expasy.mzjava.glycomics.ms.spectrum.GlycanSpectrum

Constructor for GlycanSpectrum.

GlycanSpectrum(Glycan, int, PeakList.Precision) - Constructor for class org.expasy.mzjava.glycomics.ms.spectrum.GlycanSpectrum

Constructor for GlycanSpectrum.

GlycanSpectrum(Glycan, int, int, PeakList.Precision) - Constructor for class org.expasy.mzjava.glycomics.ms.spectrum.GlycanSpectrum

Constructor for GlycanSpectrum.

GlycanSpectrum(Glycan, int, int, double, PeakList.Precision) - Constructor for class org.expasy.mzjava.glycomics.ms.spectrum.GlycanSpectrum

Constructor for GlycanSpectrum.

GlycanSpectrum(GlycanSpectrum, PeakProcessor<GlycanFragAnnotation, GlycanFragAnnotation>) - Constructor for class org.expasy.mzjava.glycomics.ms.spectrum.GlycanSpectrum

Copy constructor

GlycanSpectrum(GlycanSpectrum, PeakProcessorChain<GlycanFragAnnotation>) - Constructor for class org.expasy.mzjava.glycomics.ms.spectrum.GlycanSpectrum

Copy constructor

glycoctListsToSugar(String, List<String>, List<String>) - Method in class org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCTReader
 
glycoctListToMap(List<String>) - Method in class org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCTReader
 
GlycoCTReader - Class in org.expasy.mzjava.glycomics.io.mol.glycoct

Created with IntelliJ IDEA.

GlycoCTReader() - Constructor for class org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCTReader
 
GlycoCtResolver - Interface in org.expasy.mzjava.glycomics.io.mol.glycoct
 
glycoctToList(String) - Method in class org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCTReader
 
GlycosidicLinkage - Class in org.expasy.mzjava.glycomics.mol
 
GlycosidicLinkage(Anomericity, Integer, Integer, Composition, Composition) - Constructor for class org.expasy.mzjava.glycomics.mol.GlycosidicLinkage
 
GlycosidicLinkage(Optional<Anomericity>, Optional<Integer>, Optional<Integer>, Optional<Composition>, Optional<Composition>) - Constructor for class org.expasy.mzjava.glycomics.mol.GlycosidicLinkage
 
graph - Variable in class org.expasy.mzjava.glycomics.mol.SaccharideGraph.AbstractBuilder
 
groupOfPoster - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT
 
grow() - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList

Grow the backing if the array is full.

grow(double[], int) - Static method in class org.expasy.mzjava.utils.PrimitiveArrayUtils

Grow the array arr by loadFactor

grow(float[], int) - Static method in class org.expasy.mzjava.utils.PrimitiveArrayUtils

Grow the array arr by loadFactor

GWPWriter - Class in org.expasy.mzjava.glycomics.io.ms.gwp

A writer to write peak lists in the glycoworkbench gwp format

GWPWriter(Writer, PeakList.Precision) - Constructor for class org.expasy.mzjava.glycomics.io.ms.gwp.GWPWriter
 




H

H - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
H_MASS - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
hackRatioConfidenceInterval95(int, int) - Static method in class org.expasy.mzjava.stats.PoissonUtils
 
HadoopSpectraReader<A extends PeakAnnotation,S extends Spectrum<A>> - Class in org.expasy.mzjava.hadoop.io
 
HadoopSpectraReader(Configuration, Path, AbstractPeakListValue<S>) - Constructor for class org.expasy.mzjava.hadoop.io.HadoopSpectraReader
 
HadoopSpectraReader(String, String, AbstractPeakListValue<S>) - Constructor for class org.expasy.mzjava.hadoop.io.HadoopSpectraReader
 
HadoopSpectraReader(String, String, SpectrumKey, AbstractPeakListValue<S>) - Constructor for class org.expasy.mzjava.hadoop.io.HadoopSpectraReader
 
HadoopSpectraReader(FileSystem, Path, AbstractPeakListValue<S>) - Constructor for class org.expasy.mzjava.hadoop.io.HadoopSpectraReader
 
HadoopSpectraReader(Configuration, Path, SpectrumKey, AbstractPeakListValue<S>) - Constructor for class org.expasy.mzjava.hadoop.io.HadoopSpectraReader
 
HadoopSpectraWriter<S extends Spectrum> - Class in org.expasy.mzjava.hadoop.io
 
HadoopSpectraWriter(String, String, AbstractPeakListValue<S>) - Constructor for class org.expasy.mzjava.hadoop.io.HadoopSpectraWriter
 
HadoopSpectraWriter(String, String, AbstractPeakListValue<S>, Configuration, SequenceFile.CompressionType) - Constructor for class org.expasy.mzjava.hadoop.io.HadoopSpectraWriter
 
handle(int[]) - Method in interface org.expasy.mzjava.utils.MixedRadixNtupleGenerator.Handler
 
handle(int[]) - Method in class org.expasy.mzjava.utils.MixedRadixNtupleGenerator.NtupleContainer
 
handleAnnotations - Variable in class org.expasy.mzjava.avro.io.AbstractPeakListReader
 
handleBeginIonLine(S, String) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfReader

Handle Begin Ion line

handleComment(S, String) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfReader

Handle comment line.

handleEndIonLine(S, String) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfReader

Handle end ion line, which is a line that starts with "END IONS".

handleIntermediaryLine(String) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfReader

Allows subclasses to handle lines that occur between BEGIN IONS and END IONS tags.

handleIsolationWindow(double, double, double, S) - Method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.EbiMzmlReader

Handle isolation window parameters.

handleMsLevelAtLeast(Spectrum, S) - Method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.EbiMzmlReader

Extract information from mzml spectrum to msn spectrum.

handlePeakLine(S, String, AbstractMsReader.ParseContext) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfReader

Handle peak line, which is any line that starts with a digit

handlePeakLine(LibrarySpectrumBuilder, String) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.MsLibReader

Handle peak line, which is any line that starts with a digit

handleTagLine(String, String, S) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfReader

Handle tag value line.

handleTagLine(String, String, LibrarySpectrumBuilder) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.MsLibReader

Handle tag value line.

handleUnknownLine(S, String) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfReader

Handle line that is not a comment, begin ion, tag, peak or end ion.

handleUnknownLine(LibrarySpectrumBuilder, String) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.MsLibReader

Handle line that is not a comment, begin ion, tag, peak or end ion

handleUnknownMod(String, String, int) - Method in interface org.expasy.mzjava.proteomics.io.ms.ident.UnknownModListener

Callback method that delegate to the implementer the handling of the unknown
 modification parsed by the reader

hasAmbiguousAminoAcids() - Method in class org.expasy.mzjava.proteomics.mol.AminoAcidSequence

Returns true if this AminoAcidSequence has amino acids that are ambiguous such as X or B.

hasAnnotations() - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
 
hasAnnotations() - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Returns true if the spectrum has annotations

hasAnnotations() - Method in class org.expasy.mzjava.core.ms.spectrum.AnnotatedPeak

Returns true this peak has annotations, false otherwise.

hasAnnotations() - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
hasAnnotationsAt(int) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
 
hasAnnotationsAt(int) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Returns true if the spectrum has annotations at peak index

hasAnnotationsAt(int) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
hasCtermMod() - Method in class org.expasy.mzjava.proteomics.mol.digest.CleavageSiteMatcher
 
hashCode() - Method in class org.expasy.mzjava.core.mol.Atom
 
hashCode() - Method in class org.expasy.mzjava.core.mol.Composition
 
hashCode() - Method in class org.expasy.mzjava.core.mol.NumericMass
 
hashCode() - Method in class org.expasy.mzjava.core.ms.cluster.SimEdge
 
hashCode() - Method in class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum
 
hashCode() - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
 
hashCode() - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList
 
hashCode() - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleFloatPeakList
 
hashCode() - Method in class org.expasy.mzjava.core.ms.peaklist.DoublePeakList
 
hashCode() - Method in class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList
 
hashCode() - Method in class org.expasy.mzjava.core.ms.peaklist.FloatPeakList
 
hashCode() - Method in class org.expasy.mzjava.core.ms.peaklist.Peak
 
hashCode() - Method in class org.expasy.mzjava.core.ms.spectrum.AnnotatedPeak
 
hashCode() - Method in class org.expasy.mzjava.core.ms.spectrum.LibPeakAnnotation
 
hashCode() - Method in class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum
 
hashCode() - Method in class org.expasy.mzjava.core.ms.spectrum.RetentionTimeDiscrete
 
hashCode() - Method in class org.expasy.mzjava.core.ms.spectrum.RetentionTimeInterval
 
hashCode() - Method in class org.expasy.mzjava.core.ms.spectrum.ScanNumberDiscrete
 
hashCode() - Method in class org.expasy.mzjava.core.ms.spectrum.ScanNumberInterval
 
hashCode() - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
hashCode() - Method in class org.expasy.mzjava.glycomics.mol.CleavedMonosaccharide
 
hashCode() - Method in class org.expasy.mzjava.glycomics.mol.CutDescriptor
 
hashCode() - Method in class org.expasy.mzjava.glycomics.mol.CutIndexes
 
hashCode() - Method in class org.expasy.mzjava.glycomics.mol.Glycan
 
hashCode() - Method in class org.expasy.mzjava.glycomics.mol.GlycanFragment
 
hashCode() - Method in class org.expasy.mzjava.glycomics.mol.GlycosidicLinkage
 
hashCode() - Method in class org.expasy.mzjava.glycomics.mol.Monosaccharide
 
hashCode() - Method in class org.expasy.mzjava.glycomics.mol.NodeSet
 
hashCode() - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph
 
hashCode() - Method in class org.expasy.mzjava.glycomics.mol.SEdge
 
hashCode() - Method in class org.expasy.mzjava.glycomics.mol.SNode
 
hashCode() - Method in class org.expasy.mzjava.glycomics.mol.Substituent
 
hashCode() - Method in class org.expasy.mzjava.glycomics.mol.SubstituentLinkage
 
hashCode() - Method in class org.expasy.mzjava.glycomics.ms.spectrum.GlycanFragAnnotation
 
hashCode() - Method in class org.expasy.mzjava.glycomics.ms.spectrum.GlycanSpectrum
 
hashCode() - Method in class org.expasy.mzjava.hadoop.io.AbstractPeakListValue
 
hashCode() - Method in class org.expasy.mzjava.hadoop.io.SpectrumKey
 
hashCode() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.AminoacidModificationHashable
 
hashCode() - Method in class org.expasy.mzjava.proteomics.mol.AminoAcidSequence
 
hashCode() - Method in class org.expasy.mzjava.proteomics.mol.modification.Modification
 
hashCode() - Method in class org.expasy.mzjava.proteomics.mol.modification.NeutralLoss
 
hashCode() - Method in class org.expasy.mzjava.proteomics.mol.PeptideFragment
 
hashCode() - Method in class org.expasy.mzjava.proteomics.mol.Protein
 
hashCode() - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum
 
hashCode() - Method in class org.expasy.mzjava.proteomics.ms.dbsearch.Digest
 
hashCode() - Method in class org.expasy.mzjava.proteomics.ms.ident.ModificationMatch
 
hashCode() - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch
 
hashCode() - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideProteinMatch
 
hashCode() - Method in class org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
 
hashCode() - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation
 
hashCode() - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PepLibPeakAnnotation
 
hashCode() - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PeptideSpectrum
 
hashCode() - Method in class org.expasy.mzjava.stats.Histogram.Normalization
 
hashCode() - Method in class org.expasy.mzjava.stats.HistogramImpl
 
hashCode() - Method in class org.expasy.mzjava.utils.Counter
 
hasHyperEdges() - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph

Returns true if the glycan has hyperedges.

hasModificationAt(int) - Method in class org.expasy.mzjava.proteomics.mol.AminoAcidSequence

Returns true if the residue at index has a modification.

hasModificationAt(int, Set<ModAttachment>) - Method in class org.expasy.mzjava.proteomics.mol.AminoAcidSequence

Returns true if the residue at index has a modification attached by modAttachment.

hasModificationAt(ModAttachment) - Method in class org.expasy.mzjava.proteomics.mol.AminoAcidSequence

Returns true if there are modifications attached via the given modAttachment

hasModificationAt(Set<ModAttachment>) - Method in class org.expasy.mzjava.proteomics.mol.AminoAcidSequence

Returns true if there are modifications attached via any of the ModAttachments in modAttachments

hasModifications() - Method in class org.expasy.mzjava.proteomics.mol.AminoAcidSequence

Returns true if this AminoAcidSequence has modifications.

hasNeutralLoss() - Method in class org.expasy.mzjava.glycomics.ms.spectrum.GlycanFragAnnotation

Returns true if this annotation annotates a peak with a neutral loss, false otherwise

hasNeutralLoss() - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation

Returns true if this annotation annotates a peak with a neutral loss, false otherwise

hasNext() - Method in class org.expasy.mzjava.app.io.MonitoredIterativeReader
 
hasNext() - Method in class org.expasy.mzjava.core.io.ConcatIterativeReader
 
hasNext() - Method in interface org.expasy.mzjava.core.io.IterativeReader

Returns true if the reader has more elements.

hasNext() - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader
 
hasNext() - Method in class org.expasy.mzjava.core.mol.polymer.prot.BioJavaFastaProteinReader
 
hasNext() - Method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.EbiMzmlReader
 
hasNext() - Method in class org.expasy.mzjava.hadoop.io.HadoopSpectraReader
 
hasNext() - Method in class org.expasy.mzjava.proteomics.io.mol.FastaProteinReader
 
hasNtermMod() - Method in class org.expasy.mzjava.proteomics.mol.digest.CleavageSiteMatcher
 
hasSameSequence(AminoAcidSequence) - Method in class org.expasy.mzjava.proteomics.mol.AminoAcidSequence

Returns true if this and sequence have the same AA sequence even if
 the two sequences have different modifications.

hasSameSequence(SymbolSequence<AminoAcid>) - Method in class org.expasy.mzjava.proteomics.mol.AminoAcidSequence

Returns true if this and sequence have the same AA sequence.

hasScore(String) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Returns true if there is a score for scoreName

hasSetCarbon() - Method in class org.expasy.mzjava.glycomics.mol.GlycosidicLinkage

Check if the linkage has the anomeric and the linked carbons already set.

hasSetCarbon() - Method in interface org.expasy.mzjava.glycomics.mol.Linkage

Check if the linkage has the anomeric and the linked carbons already set.

hasSetCarbon() - Method in class org.expasy.mzjava.glycomics.mol.SubstituentLinkage

Check if the linkage has the anomeric carbon already set.

heavy2LightError - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioResult
 
heavy2LightMean - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioResult
 
heavy2LightRatio - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult
 
heavyArea - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult
 
heavyFirstscan - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult
 
heavyLastscan - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult
 
heavyMass - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioPeptideData
 
heavyMass - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult
 
hidden - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.SpecificityT
 
HighestPeakPerBinNormalizer<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist.peaktransformer

Normalises a PeakList by dividing the PeakList into bins and scaling the peaks in each bin so that
 the most intense peak has intensity = maxBinIntensity

HighestPeakPerBinNormalizer(double, double) - Constructor for class org.expasy.mzjava.core.ms.peaklist.peaktransformer.HighestPeakPerBinNormalizer

Construct a HighestPeakPerBinNormalizer.

Histogram - Interface in org.expasy.mzjava.stats

Histogram groups numbers into bins (class intervals) of same width.

Histogram.Normalization - Class in org.expasy.mzjava.stats

Type of Histogram Normalization

Histogram.Normalization(Histogram.Normalization.NormType, double) - Constructor for class org.expasy.mzjava.stats.Histogram.Normalization
 
Histogram.Normalization.NormType - Enum in org.expasy.mzjava.stats
 
HistogramImpl - Class in org.expasy.mzjava.stats

The default implementation of Histogram

HistogramImpl() - Constructor for class org.expasy.mzjava.stats.HistogramImpl
 
HistogramImpl(double, double, double) - Constructor for class org.expasy.mzjava.stats.HistogramImpl

Remark:

HistogramImpl(int, double, double) - Constructor for class org.expasy.mzjava.stats.HistogramImpl
 
hitRank - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 




I

I - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
I_MASS - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
id - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.CvType
 
id - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.IdentifiableType
 
id - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp
 
id - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult
 
IdentifiableType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

Other classes in the model can be specified as sub-classes, inheriting from Identifiable.

IdentifiableType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.IdentifiableType
 
IdentityPeakProcessor<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist.peaktransformer

Data processor that does not change the mz, intensity or annotations

IdentityPeakProcessor() - Constructor for class org.expasy.mzjava.core.ms.peaklist.peaktransformer.IdentityPeakProcessor
 
ignore - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT
 
include - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FilterType
 
includeProteinPattern - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader
 
increment() - Method in class org.expasy.mzjava.utils.Counter

Increment counter by 1.

increment(int) - Method in class org.expasy.mzjava.utils.Counter

Increment counter by inc.

incrementValue() - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar
 
independent - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymesType
 
independent - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme
 
indeterminate() - Static method in class org.expasy.mzjava.app.pb.ConsoleProgressBar
 
indeterminate(ConsoleProgressBar.View) - Static method in class org.expasy.mzjava.app.pb.ConsoleProgressBar
 
index - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.IonTypeType
 
index - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
 
indexEqualOrLarger(double, int, double[]) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList

Finds the index that has of the peak that has an mz which is equal to or larger than mz

indexEqualOrLarger(float, int, float[]) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList

Finds the index that has of the peak that has an mz which is equal to or larger than mz

indexMax(double[]) - Static method in class org.expasy.mzjava.utils.PrimitiveArrayUtils

Get the index of the maximum value

indexOf(double) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
 
indexOf(int, int, double) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList
 
indexOf(int, int, double) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleFloatPeakList
 
indexOf(int, int, double) - Method in class org.expasy.mzjava.core.ms.peaklist.DoublePeakList
 
indexOf(int, int, double) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList
 
indexOf(int, int, double) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatPeakList
 
indexOf(double) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Returns the index of the first occurrence of the specified mzKey
 in this peak list, or (-(insertion point) - 1) if this
 peak list does not contain the exact mzKey.

indexOf(int, int, double) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Returns the index of the first occurrence of the specified mzKey
 in the specified range within this peak list, or (-(insertion point) - 1)
 if this peak list does not contain the exact mzKey.

indexOf(double) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
indexOf(int, int, double) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
init(AbstractMsReader.ParseContext) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader
 
init(AbstractMsReader.ParseContext) - Method in class org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader
 
initBins(int) - Method in class org.expasy.mzjava.stats.HistogramImpl
 
initialCapacity - Variable in class org.expasy.mzjava.core.ms.consensus.AbstractConsensusSpectrumBuilder
 
initialCapacity(int) - Method in class org.expasy.mzjava.core.ms.consensus.AbstractConsensusSpectrumBuilder
 
inputfile - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.InteractSummary
 
inputs - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DataCollectionType
 
inputSpectra - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationType
 
InputSpectraType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

The attribute referencing an identifier within the SpectraData section.

InputSpectraType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.InputSpectraType
 
inputSpectrumIdentifications - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionType
 
InputSpectrumIdentificationsType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

The lists of spectrum identifications that are input to the protein detection process.

InputSpectrumIdentificationsType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.InputSpectrumIdentificationsType
 
InputsType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

The inputs to the analyses including the databases searched, the spectral data and the source file converted to mzIdentML.

InputsType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.InputsType
 
insert(double, int, double[], int) - Static method in class org.expasy.mzjava.utils.PrimitiveArrayUtils

Insert the value into the array at index.

insert(float, int, float[], int) - Static method in class org.expasy.mzjava.utils.PrimitiveArrayUtils

Insert the value into the array at index.

INT_PRECISION - Static variable in class org.expasy.mzjava.utils.NumberFormatFactory
 
intCombMeth - Variable in class org.expasy.mzjava.core.ms.consensus.AbstractConsensusSpectrumBuilder
 
INTEGER - Static variable in class org.expasy.mzjava.utils.RegexConstants

integer expression

intensity - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraResult
 
intensityCombMethod(AbstractMergePeakFilter.IntensityMode) - Method in class org.expasy.mzjava.core.ms.consensus.AbstractConsensusSpectrumBuilder
 
intensityList - Variable in class org.expasy.mzjava.core.ms.peaklist.ArrayCursor
 
intensityMode - Variable in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.Builder
 
InteractSummary - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

InteractSummary() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.InteractSummary
 
InteractSummary.Inputfile - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

InteractSummary.Inputfile() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.InteractSummary.Inputfile
 
interruptDigestion(Protein, int, int, int) - Method in class org.expasy.mzjava.proteomics.mol.digest.AcceptAllDigestionController

Control digestion flow given the potential digest bounds

interruptDigestion(Protein, int, int, int) - Method in interface org.expasy.mzjava.proteomics.mol.digest.DigestionController

Control digestion flow given the potential digest bounds

interruptDigestion(Protein, int, int, int) - Method in class org.expasy.mzjava.proteomics.mol.digest.LengthDigestionController
 
intersect(Set<E>, Set<E>) - Static method in class org.expasy.mzjava.core.ms.cluster.FMeasure
 
IntervalList - Class in org.expasy.mzjava.utils

This class manages a list of intervals and implements a method to quickly check whether a given value lies within
 the list of intervals or not.

IntervalList() - Constructor for class org.expasy.mzjava.utils.IntervalList
 
IntervalList(double, double, double) - Constructor for class org.expasy.mzjava.utils.IntervalList

The binned array indexing the intervals goes from minVal to maxVal with bin size binWidth.

IntervalSpectrumLibrary<S extends PeakList> - Class in org.expasy.mzjava.core.ms.library
 
IntervalSpectrumLibrary(double, double, Collection<S>) - Constructor for class org.expasy.mzjava.core.ms.library.IntervalSpectrumLibrary
 
intValue(BigInteger, int) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader
 
InverseArcsinhTransformer<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist.peaktransformer

Following Huber et al.

InverseArcsinhTransformer(double, double, double) - Constructor for class org.expasy.mzjava.core.ms.peaklist.peaktransformer.InverseArcsinhTransformer

Constructor

IonCurrentNormalizer<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist.peaktransformer
 
IonCurrentNormalizer() - Constructor for class org.expasy.mzjava.core.ms.peaklist.peaktransformer.IonCurrentNormalizer
 
IonType - Enum in org.expasy.mzjava.core.ms.spectrum
 
ionType - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FragmentationType
 
IonTypeType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

IonType defines the index of fragmentation ions being reported, importing a CV term for the type of ion e.g.

IonTypeType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.IonTypeType
 
isApproved() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT

Gets the value of the approved property.

isApproved() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodMod

Returns the approved flag.

isCTerm() - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideProteinMatch

Returns true if the peptide in on the C-Term of the protein, false otherwise

isDecoy - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType
 
isDefaultIsotope() - Method in class org.expasy.mzjava.core.mol.Atom
 
isDest(V, SimEdge<V>) - Method in class org.expasy.mzjava.core.ms.cluster.JungSimGraphWrapper
 
isEmpty() - Method in class org.expasy.mzjava.core.mol.Composition.Builder

Returns true if there are no atoms in this builder and the charge is 0

isEmpty() - Method in class org.expasy.mzjava.core.mol.Composition

Returns true if this composition contains no atoms or charge, false otherwise.

isEmpty() - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
 
isEmpty() - Method in class org.expasy.mzjava.core.ms.peaklist.ArrayCursor
 
isEmpty() - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakCursor

Returns true if this cursor contains no peaks.

isEmpty() - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.TopNList

Returns true if this contains no peaks.

isEmpty() - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Returns true if this peak list contains no peaks.

isEmpty() - Method in class org.expasy.mzjava.core.ms.peaklist.PeakProcessorChain
 
isEmpty() - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
isEmpty() - Method in class org.expasy.mzjava.glycomics.mol.CutDescriptor

Return true if the CutDescriptor is empty.

isEmpty() - Method in class org.expasy.mzjava.glycomics.mol.NodeSet
 
isEmpty() - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph

Check if there is no nodes in the glycan.

isEmpty() - Method in class org.expasy.mzjava.proteomics.mol.AminoAcidSequence

Returns true if this AminoAcidSequence contains no residues.

isEmpty() - Method in interface org.expasy.mzjava.proteomics.mol.modification.ModificationList
 
isEmpty() - Method in interface org.expasy.mzjava.stats.Histogram

Return true if no data

isEmpty() - Method in class org.expasy.mzjava.stats.HistogramImpl
 
isEndOfParsing() - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader.ParseContext
 
isFixedMod() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchModificationType

Gets the value of the fixedMod property.

isFlag() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.NeutralLossT

Gets the value of the flag property.

isGlycosidicCut() - Method in class org.expasy.mzjava.glycomics.mol.CutIndexes

Check if the cut is a glycosidic cut

isHeavy - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak
 
isHeavy - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak
 
isHidden() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.SpecificityT

Gets the value of the hidden property.

isHyperEdge() - Method in class org.expasy.mzjava.glycomics.mol.SEdge
 
isIndependent() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymesType

Gets the value of the independent property.

isIndependent() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme

Gets the value of the independent property.

isIndeterminate() - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar
 
isIndeterminate() - Method in interface org.expasy.mzjava.app.pb.ProgressBar

Return true if indeterminate

isIsDecoy() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType

Gets the value of the isDecoy property.

isIsRejected() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraResult

Gets the value of the isRejected property.

isLeaf(Monosaccharide) - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph

Returns true if the specified monosaccharide is a leaf in the saccharide.

isMonosaccharide() - Method in class org.expasy.mzjava.glycomics.mol.SNode
 
isNTerm() - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideProteinMatch

Returns true if the peptide in on the N-Term of the protein, false otherwise

isotopePattern - Static variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModificationTypeAdapter
 
isotopicContributions - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary
 
isPassingFilter(TDoubleArrayList, TDoubleArrayList, int) - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.NPeaksPerSlidingWindowFilter

Selects nrOfPeaks highest peaks within sliding window.

isPassThreshold() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionHypothesisType

Gets the value of the passThreshold property.

isPassThreshold() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType

Gets the value of the passThreshold property.

isReject() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraResult.Intensity

Gets the value of the reject property.

isRejected - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraResult
 
isRejected - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
isRejected() - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Returns true if this PeptideMatch was rejected, false otherwise

isRequired() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.PepNeutralLossT

Gets the value of the required property.

isReusable() - Method in class org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph.AbstractBuilder
 
isReusable() - Method in interface org.expasy.mzjava.core.ms.cluster.SimilarityGraphBuilder

Returns true if build can be called more than once, false otherwise.

isReusable() - Method in class org.expasy.mzjava.core.ms.cluster.SparseSimilarityGraph.Builder
 
isSemiSpecific() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymeType

Gets the value of the semiSpecific property.

isSignificantlyDifferent(double, double, double) - Static method in class org.expasy.mzjava.stats.PoissonUtils
 
isSignificantlyDifferent(double, double, double, double, double) - Static method in class org.expasy.mzjava.stats.PoissonUtils
 
isSource(V, SimEdge<V>) - Method in class org.expasy.mzjava.core.ms.cluster.JungSimGraphWrapper
 
isSubstituent() - Method in class org.expasy.mzjava.glycomics.mol.SNode
 
issue - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType
 
isUnambiguous() - Method in enum org.expasy.mzjava.proteomics.mol.AminoAcid

Returns true if this amino acid symbol unambiguously refers to only one amino acid.

isWithinTolerance(Tolerance) - Method in class org.expasy.mzjava.proteomics.ms.ident.ModificationMatch

Checks whether all modification candidates are within tolerance of the massShift.

IterativeReader<T> - Interface in org.expasy.mzjava.core.io

A reader that can be iterated over

IterativeReaders - Class in org.expasy.mzjava.core.io
 
IterativeReaders() - Constructor for class org.expasy.mzjava.core.io.IterativeReaders
 
iterator() - Method in class org.expasy.mzjava.glycomics.mol.NodeSet
 




J

JungSimGraphWrapper<V> - Class in org.expasy.mzjava.core.ms.cluster

Wraps a SimilarityGraph in a jung.UndirectedGraph so that the JUNG algorithms can be used.

JungSimGraphWrapper(SimilarityGraph<V>) - Constructor for class org.expasy.mzjava.core.ms.cluster.JungSimGraphWrapper
 




K

K - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
k - Variable in class org.expasy.mzjava.core.ms.spectrasim.SharedPeakSimFunc
 
K_MASS - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
KMeansPlusPlusClusterBuilder<V> - Class in org.expasy.mzjava.core.ms.cluster

KMeans cluster builder that uses the algorithm provided by commons math KMeansPlusPlusClusterer.

KMeansPlusPlusClusterBuilder(int) - Constructor for class org.expasy.mzjava.core.ms.cluster.KMeansPlusPlusClusterBuilder
 
KMeansPlusPlusClusterBuilder(int, Optional<Long>) - Constructor for class org.expasy.mzjava.core.ms.cluster.KMeansPlusPlusClusterBuilder
 
KryoAvroSerializer<O> - Class in org.expasy.mzjava.spark
 
KryoAvroSerializer(AvroWriter<O>, AvroReader<O>) - Constructor for class org.expasy.mzjava.spark.KryoAvroSerializer

Build a serializer that fowards the serialization to the writer
 and read





L

labeledResidues - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioSummary
 
labeledResidues - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioSummary
 
lastIntensity() - Method in class org.expasy.mzjava.core.ms.peaklist.ArrayCursor
 
lastIntensity() - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakCursor

Returns the intensity of the last peak

lastMz() - Method in class org.expasy.mzjava.core.ms.peaklist.ArrayCursor
 
lastMz() - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakCursor

Returns the m/z of the last peak

LastMzCheck - Class in org.expasy.mzjava.external.io.ms.spectrum.mzml
 
LastMzCheck() - Constructor for class org.expasy.mzjava.external.io.ms.spectrum.mzml.LastMzCheck
 
lastName - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PersonType
 
leftValley - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak
 
leftValley - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak
 
length - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DBSequenceType
 
LengthDigestionController - Class in org.expasy.mzjava.proteomics.mol.digest

DigestionController that excludes peptides that fall outside the length range.

LengthDigestionController(int, int) - Constructor for class org.expasy.mzjava.proteomics.mol.digest.LengthDigestionController

Create a DigestionController that excludes peptides that have a length < min and > max

LibPeakAnnotation - Class in org.expasy.mzjava.core.ms.spectrum
 
LibPeakAnnotation(int, double, double) - Constructor for class org.expasy.mzjava.core.ms.spectrum.LibPeakAnnotation
 
LibPeakAnnotation(LibPeakAnnotation) - Constructor for class org.expasy.mzjava.core.ms.spectrum.LibPeakAnnotation
 
LibPeakAnnotationReader - Class in org.expasy.mzjava.avro.io
 
LibPeakAnnotationReader() - Constructor for class org.expasy.mzjava.avro.io.LibPeakAnnotationReader
 
LibPeakAnnotationWriter - Class in org.expasy.mzjava.avro.io
 
LibPeakAnnotationWriter() - Constructor for class org.expasy.mzjava.avro.io.LibPeakAnnotationWriter
 
LibraResult - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

LibraResult() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraResult
 
LibraResult.Intensity - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

LibraResult.Intensity() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraResult.Intensity
 
LibraryMergePeakFilter<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist.peakfilter
 
LibraryMergePeakFilter(double, double, AbstractMergePeakFilter.IntensityMode, int) - Constructor for class org.expasy.mzjava.core.ms.peaklist.peakfilter.LibraryMergePeakFilter
 
LibrarySpectrumBuilder - Class in org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt
 
LibrarySpectrumBuilder() - Constructor for class org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.LibrarySpectrumBuilder
 
LibraSummary - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

LibraSummary() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary
 
LibraSummary.FragmentMasses - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

LibraSummary.FragmentMasses() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.FragmentMasses
 
LibraSummary.IsotopicContributions - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

LibraSummary.IsotopicContributions() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.IsotopicContributions
 
LibraSummary.IsotopicContributions.ContributingChannel - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

LibraSummary.IsotopicContributions.ContributingChannel() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.IsotopicContributions.ContributingChannel
 
LibraSummary.IsotopicContributions.ContributingChannel.AffectedChannel - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

LibraSummary.IsotopicContributions.ContributingChannel.AffectedChannel() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.IsotopicContributions.ContributingChannel.AffectedChannel
 
lightArea - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult
 
lightFirstscan - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult
 
lightLastscan - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult
 
lightMass - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioPeptideData
 
lightMass - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult
 
limit(int) - Method in class org.expasy.mzjava.proteomics.mol.ModifiedPeptideFactory.Builder
 
LINE_DELIMITOR - Static variable in class org.expasy.mzjava.utils.RegexConstants

About new lines, sources at http://en.wikipedia.org/wiki/Newline:
 
 Systems based on ASCII or a compatible character set use either LF (Line
 feed, '\n', 0x0A, 10 in decimal) or CR (Carriage return, '\r', 0x0D, 13
 in decimal) individually, or CR followed by LF (CR+LF, 0x0D 0x0A).

lineNr - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader
 
Linkage - Interface in org.expasy.mzjava.glycomics.mol
 
LinkageAcceptor - Interface in org.expasy.mzjava.glycomics.mol
 
list - Variable in class org.expasy.mzjava.core.ms.peaklist.peakfilter.TopNList
 
listFilePaths(String, String) - Static method in class org.expasy.mzjava.utils.PathUtils
 
loadDoubles(double[], double[]) - Static method in class org.expasy.mzjava.utils.PrimitiveArrayUtils

Load doubles from src to dest arrays.

loadDoubles(double[], double[], int) - Static method in class org.expasy.mzjava.utils.PrimitiveArrayUtils

Load doubles from src to dest arrays.

loadFactor - Variable in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
 
loadModifs(Collection<MsmsPipelineAnalysis.MsmsRunSummary>, Map<URI, ModificationMap>) - Static method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.ModificationMap
 
localPath - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
 
location - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ExternalDataType
 
location - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ModificationType
 
location - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SubstitutionModificationType
 
Log10Transformer<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist.peaktransformer

Performs a base 10 logarithm transform on peak intensities + 1.

Log10Transformer() - Constructor for class org.expasy.mzjava.core.ms.peaklist.peaktransformer.Log10Transformer
 
LogTransformer<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist.peaktransformer

Performs a base e (natural) logarithm transform on peak intensities + 1.

LogTransformer() - Constructor for class org.expasy.mzjava.core.ms.peaklist.peaktransformer.LogTransformer
 




M

m - Variable in class org.expasy.mzjava.core.ms.spectrasim.SharedPeakSimFunc
 
main(String[]) - Static method in class org.expasy.mzjava.proteomics.cookbook.DbSearchPaperExample
 
majorVersion - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.UnimodT
 
makeDigest(Protein, int, int, int) - Method in class org.expasy.mzjava.proteomics.mol.digest.AcceptAllDigestionController

Make a peptide digest from the given protein.

makeDigest(Protein, int, int, int) - Method in interface org.expasy.mzjava.proteomics.mol.digest.DigestionController

Make a peptide digest from the given protein.

makeDigest(Protein, int, int, int) - Method in class org.expasy.mzjava.proteomics.mol.digest.LengthDigestionController
 
makeFormula(TObjectIntMap<Atom>, int) - Static method in class org.expasy.mzjava.core.mol.Composition.Builder

Make the atomic formula given an atomCounterMap and charge

makePeptideMatch(ResultSet) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.AbstractPsmCsvReader

Create a new PeptideMatch from a given ResultSet

makePeptideMatch(ResultSet) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.MaxQuantPsmReader
 
makePeptideMatch(ResultSet) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.ProteinPilotPsmReader
 
maps - Variable in class org.expasy.mzjava.core.ms.library.AbstractMapSpectrumLibrary
 
marshal(UnimodMod) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModificationTypeAdapter
 
Mass - Class in org.expasy.mzjava.core.mol

A class that is both Weighable and Copyable.

Mass() - Constructor for class org.expasy.mzjava.core.mol.Mass
 
mass - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ResidueType
 
mass - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
 
mass - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
 
mass - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo.ModAminoacidMass
 
MassCalculator - Class in org.expasy.mzjava.core.mol
 
MassCalculator() - Constructor for class org.expasy.mzjava.core.mol.MassCalculator
 
massDelta - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchModificationType
 
massdiff - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
 
massdiff - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
 
massdiff - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
massdiff - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioSummary
 
massTable - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType
 
massTableRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType
 
MassTableType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

The masses of residues used in the search.

MassTableType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MassTableType
 
massTol - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult
 
masstol - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioSummary
 
massTolerance - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary
 
MassType - Enum in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for massType.

maxMzClusterWidth - Variable in class org.expasy.mzjava.core.ms.consensus.AbstractConsensusSpectrumBuilder
 
maxMzClusterWidth(double) - Method in class org.expasy.mzjava.core.ms.consensus.AbstractConsensusSpectrumBuilder
 
maxMzClusterWidth - Variable in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.Builder
 
maxMzDiff - Variable in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.Builder
 
maxNumInternalCleavages - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint
 
MaxQuantPsmReader - Class in org.expasy.mzjava.proteomics.io.ms.ident
 
MaxQuantPsmReader() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.MaxQuantPsmReader
 
MaxQuantPsmReader(ModificationResolver) - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.MaxQuantPsmReader
 
maxSimScore - Variable in class org.expasy.mzjava.core.ms.cluster.SpectrumClusterEvaluator
 
McNdpSimFunc<X extends PeakAnnotation,Y extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.spectrasim

Calculates PeakList similarity using the Mean Centered Normalized Dot Product similarity function

 Olson et.al..

McNdpSimFunc(int, Tolerance) - Constructor for class org.expasy.mzjava.core.ms.spectrasim.McNdpSimFunc

Construct a McNdpSimFunc that uses the default peak list aligner.

McNdpSimFunc(int, PeakListAligner<X, Y>, PeakPairProcessor<X, Y>...) - Constructor for class org.expasy.mzjava.core.ms.spectrasim.McNdpSimFunc

Construct a McNdpSimFunc that uses the supplied PeakListAligner and PeakPairProcessor chain to process
 and align the peak lists.

mean - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioResult
 
meanSimScore - Variable in class org.expasy.mzjava.core.ms.cluster.SpectrumClusterEvaluator
 
measure - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FragmentationTableType
 
measureRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FragmentArrayType
 
MeasureType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

References to CV terms defining the measures about product ions to be reported in SpectrumIdentificationItem

MeasureType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MeasureType
 
memberIds - Variable in class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum
 
merge(Collection<? extends PeakList<A>>) - Method in class org.expasy.mzjava.core.ms.peaklist.PeakListMerger
 
merge(PeakCursor<A>, PeakCursor<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.PeakListMerger
 
Mg - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
Mg_MASS - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
MgfParameters - Class in org.expasy.mzjava.core.io.ms.spectrum
 
MgfParameters(PeakList.Precision) - Constructor for class org.expasy.mzjava.core.io.ms.spectrum.MgfParameters
 
MgfParameters(PeakList.Precision, MsnSpectrum) - Constructor for class org.expasy.mzjava.core.io.ms.spectrum.MgfParameters
 
MgfParameters(NumberFormat, NumberFormat, Optional<MsnSpectrum>) - Constructor for class org.expasy.mzjava.core.io.ms.spectrum.MgfParameters
 
MgfReader - Class in org.expasy.mzjava.core.io.ms.spectrum
 
MgfReader(File, PeakList.Precision) - Constructor for class org.expasy.mzjava.core.io.ms.spectrum.MgfReader
 
MgfReader(File, PeakList.Precision, PeakProcessorChain<PeakAnnotation>) - Constructor for class org.expasy.mzjava.core.io.ms.spectrum.MgfReader
 
MgfReader(Reader, URI, PeakList.Precision) - Constructor for class org.expasy.mzjava.core.io.ms.spectrum.MgfReader
 
MgfWriter - Class in org.expasy.mzjava.core.io.ms.spectrum

MGF Writer

MgfWriter(Writer, PeakList.Precision) - Constructor for class org.expasy.mzjava.core.io.ms.spectrum.MgfWriter
 
MgfWriter(File, PeakList.Precision) - Constructor for class org.expasy.mzjava.core.io.ms.spectrum.MgfWriter
 
MgfWriter(Writer, MgfParameters) - Constructor for class org.expasy.mzjava.core.io.ms.spectrum.MgfWriter
 
MgfWriter(File, MgfParameters) - Constructor for class org.expasy.mzjava.core.io.ms.spectrum.MgfWriter
 
midInitials - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PersonType
 
mids - Variable in class org.expasy.mzjava.stats.HistogramImpl
 
minDistance - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymeType
 
minNumberTermini - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint
 
minNumEnzTerm - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.DatabaseRefreshTimestamp
 
minorVersion - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.UnimodT
 
minPeakCount - Variable in class org.expasy.mzjava.core.ms.consensus.AbstractConsensusSpectrumBuilder
 
minPeakCount - Variable in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.Builder
 
minSimScore - Variable in class org.expasy.mzjava.core.ms.cluster.SpectrumClusterEvaluator
 
minSpacing - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity
 
miscNotes - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT
 
miscNotes - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.SpecificityT
 
missedCleavageMax(int) - Method in class org.expasy.mzjava.proteomics.mol.digest.ProteinDigester.Builder
 
missedCleavages - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymeType
 
MixedRadixNtupleGenerator - Class in org.expasy.mzjava.utils

This object generates all tuples of length n (n-tuple) where each element
 belongs to different base numbers bi.

MixedRadixNtupleGenerator(MixedRadixNtupleGenerator.Handler) - Constructor for class org.expasy.mzjava.utils.MixedRadixNtupleGenerator
 
MixedRadixNtupleGenerator.Handler - Interface in org.expasy.mzjava.utils
 
MixedRadixNtupleGenerator.NtupleContainer - Class in org.expasy.mzjava.utils

A reusable container that stores generated n-tuples

MixedRadixNtupleGenerator.NtupleContainer() - Constructor for class org.expasy.mzjava.utils.MixedRadixNtupleGenerator.NtupleContainer
 
MixedRadixNtupleGenerator.NtupleContainer(Predicate<int[]>) - Constructor for class org.expasy.mzjava.utils.MixedRadixNtupleGenerator.NtupleContainer
 
Mn - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
Mn_MASS - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
mod - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModificationsT
 
MODA_PROB - Static variable in class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader
 
MODA_SCORE - Static variable in class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader
 
modAminoacidMass - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo
 
MODaPsmReader - Class in org.expasy.mzjava.proteomics.io.ms.ident
 
MODaPsmReader(List<AminoAcid>, Multimap<Integer, Modification>, Multimap<ModAttachment, Modification>) - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader
 
MODaPsmReader() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader
 
MODaPsmReader.PeptideInfoParser - Class in org.expasy.mzjava.proteomics.io.ms.ident
 
MODaPsmReader.PeptideInfoParser() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader.PeptideInfoParser
 
MODaPsmReader.PSMInfoParser - Class in org.expasy.mzjava.proteomics.io.ms.ident
 
MODaPsmReader.PSMInfoParser() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader.PSMInfoParser
 
MODaPsmReader.SpectrumInfoParser - Class in org.expasy.mzjava.proteomics.io.ms.ident
 
MODaPsmReader.SpectrumInfoParser() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader.SpectrumInfoParser
 
ModAttachment - Enum in org.expasy.mzjava.proteomics.mol.modification
 
modCtermMass - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo
 
ModelDisType - Enum in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for model_dis_type.

modification - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideType
 
Modification - Class in org.expasy.mzjava.proteomics.mol.modification
 
Modification(String, Mass) - Constructor for class org.expasy.mzjava.proteomics.mol.modification.Modification
 
modificationInfo - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
ModificationList - Interface in org.expasy.mzjava.proteomics.mol.modification
 
ModificationLists - Class in org.expasy.mzjava.proteomics.mol.modification
 
ModificationMap - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml
 
ModificationMap() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.ModificationMap
 
ModificationMatch - Class in org.expasy.mzjava.proteomics.ms.ident

Class to hold information on modifications that were found for a PSM.

ModificationMatch(double, AminoAcid, Integer, ModAttachment) - Constructor for class org.expasy.mzjava.proteomics.ms.ident.ModificationMatch

Create a ModificationMatch given a mass shift

ModificationMatch(Modification, AminoAcid, int, ModAttachment) - Constructor for class org.expasy.mzjava.proteomics.ms.ident.ModificationMatch

Create a ModificationMatch given a modification.

ModificationMatchResolver - Interface in org.expasy.mzjava.proteomics.ms.ident
 
modificationParams - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType
 
ModificationParamsType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

The specification of static/variable modifications (e.g.

ModificationParamsType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ModificationParamsType
 
ModificationReader - Class in org.expasy.mzjava.proteomics.avro.io
 
ModificationReader() - Constructor for class org.expasy.mzjava.proteomics.avro.io.ModificationReader
 
ModificationResolver - Interface in org.expasy.mzjava.proteomics.mol.modification

Interface for classes that can create a Modification from a String.

modifications - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.UnimodT
 
ModificationsT - Class in org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb

Java class for modifications_t complex type.

ModificationsT() - Constructor for class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModificationsT
 
ModificationType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

A molecule modification specification.

ModificationType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ModificationType
 
ModificationTypeAdapter - Class in org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb

XmlAdapter to convert ModT objects into UnimodMod objects.

ModificationTypeAdapter() - Constructor for class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModificationTypeAdapter
 
ModificationWriter - Class in org.expasy.mzjava.proteomics.avro.io
 
ModificationWriter() - Constructor for class org.expasy.mzjava.proteomics.avro.io.ModificationWriter
 
modifiedPeptide - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo
 
ModifiedPeptideFactory - Class in org.expasy.mzjava.proteomics.mol

This factory creates modified Peptides given an Peptide source
 and a set of targeted AAs/variable modifications.

ModifiedPeptideFactory(ModifiedPeptideFactory.Builder) - Constructor for class org.expasy.mzjava.proteomics.mol.ModifiedPeptideFactory
 
ModifiedPeptideFactory.Builder - Class in org.expasy.mzjava.proteomics.mol
 
ModifiedPeptideFactory.Builder() - Constructor for class org.expasy.mzjava.proteomics.mol.ModifiedPeptideFactory.Builder
 
ModListModMatchResolver - Class in org.expasy.mzjava.proteomics.ms.ident

Resolves ModificationMatches against the list of Modifications held by this ModListModMatchResolver.

ModListModMatchResolver(Tolerance, Collection<Modification>) - Constructor for class org.expasy.mzjava.proteomics.ms.ident.ModListModMatchResolver
 
ModListModMatchResolver(Tolerance, Modification...) - Constructor for class org.expasy.mzjava.proteomics.ms.ident.ModListModMatchResolver
 
modMassStorage - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader
 
modMatchResolver - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader
 
modNtermMass - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo
 
ModT - Class in org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb

Java class for mod_t complex type.

ModT() - Constructor for class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT
 
MonitoredIterativeReader<T> - Class in org.expasy.mzjava.app.io

MonitoredIterativeReader monitors the progression of IterativeReader reads.

MonitoredIterativeReader(IterativeReader<T>) - Constructor for class org.expasy.mzjava.app.io.MonitoredIterativeReader
 
MonitoredIterativeReader(IterativeReader<T>, ConsoleProgressBar.View) - Constructor for class org.expasy.mzjava.app.io.MonitoredIterativeReader
 
monoisotopicMassDelta - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ModificationType
 
monoisotopicMassDelta - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SubstitutionModificationType
 
monoMass - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.CompositionT
 
Monosaccharide - Class in org.expasy.mzjava.glycomics.mol
 
Monosaccharide(String, Composition, MonosaccharideSuperclass, MonosaccharideClass, RingType, int, int) - Constructor for class org.expasy.mzjava.glycomics.mol.Monosaccharide
 
Monosaccharide(Monosaccharide) - Constructor for class org.expasy.mzjava.glycomics.mol.Monosaccharide
 
MonosaccharideClass - Enum in org.expasy.mzjava.glycomics.mol
 
monosaccharideEdgeMultimap - Variable in class org.expasy.mzjava.glycomics.mol.SaccharideGraph
 
MonosaccharideLookup - Interface in org.expasy.mzjava.glycomics.mol
 
MonosaccharideSuperclass - Enum in org.expasy.mzjava.glycomics.mol
 
moveBefore(double) - Method in class org.expasy.mzjava.core.ms.peaklist.ArrayCursor
 
moveBefore(double) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakCursor

Move the cursor right before mz (peak.mz < mz)

movePast(double) - Method in class org.expasy.mzjava.core.ms.peaklist.ArrayCursor
 
movePast(double) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakCursor

Move the cursor right after mz (peak.mz > mz)

moveToClosest(double) - Method in class org.expasy.mzjava.core.ms.peaklist.ArrayCursor
 
moveToClosest(double) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakCursor

Move the cursor to the m/z that is closest to mz.

msDetector - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary
 
msDetector(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder.Builder

Set the msDetector attribute of element msms_run_summary

msIonization - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary
 
msIonization(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder.Builder

Set the msIonization attribute of element msms_run_summary

msLevel - Variable in class org.expasy.mzjava.core.ms.consensus.AbstractConsensusSpectrumBuilder
 
msLevel(int) - Method in class org.expasy.mzjava.core.ms.consensus.AbstractConsensusSpectrumBuilder
 
msLevel - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MassTableType
 
MsLibReader - Class in org.expasy.mzjava.proteomics.io.ms.spectrum
 
MsLibReader(Reader, URI, PeakList.Precision, SpectraLibCommentParser, AnnotationResolver, PeakProcessorChain<PepLibPeakAnnotation>, ModificationResolver) - Constructor for class org.expasy.mzjava.proteomics.io.ms.spectrum.MsLibReader
 
msManufacturer - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary
 
msManufacturer(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder.Builder

Set the msManufacturer attribute of element msms_run_summary

msMassAnalyzer - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary
 
msMassAnalyzer(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder.Builder

Set the msMassAnalyzer attribute of element msms_run_summary

msModel - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary
 
msModel(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder.Builder

Set the msModel attribute of element msms_run_summary

MsmsPipelineAnalysis - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

MsmsPipelineAnalysis() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis
 
MsmsPipelineAnalysis.AnalysisSummary - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

MsmsPipelineAnalysis.AnalysisSummary() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.AnalysisSummary
 
MsmsPipelineAnalysis.DatasetDerivation - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

MsmsPipelineAnalysis.DatasetDerivation() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.DatasetDerivation
 
MsmsPipelineAnalysis.DatasetDerivation.DataFilter - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

MsmsPipelineAnalysis.DatasetDerivation.DataFilter() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.DatasetDerivation.DataFilter
 
MsmsPipelineAnalysis.MsmsRunSummary - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

MsmsPipelineAnalysis.MsmsRunSummary() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary
 
MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp
 
MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme
 
MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity
 
MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
 
MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
 
MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint
 
MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
 
MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SequenceSearchConstraint - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SequenceSearchConstraint() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SequenceSearchConstraint
 
MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
 
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
 
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult
 
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
 
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult
 
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo
 
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo.ModAminoacidMass - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo.ModAminoacidMass() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo.ModAminoacidMass
 
msmsRunSummary - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis
 
msnReader(File) - Static method in class org.expasy.mzjava.hadoop.io.HadoopSpectraReader
 
msnSpectra(JavaSparkContext, String) - Static method in class org.expasy.mzjava.spark.MzJavaSparkUtils
 
MsnSpectrum - Class in org.expasy.mzjava.core.ms.spectrum
 
MsnSpectrum() - Constructor for class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum

Default constructor

MsnSpectrum(PeakList.Precision) - Constructor for class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum

Construct a MsnSpectrum that stores the peak list at the given precision

MsnSpectrum(int, PeakList.Precision) - Constructor for class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum

Construct a MsnSpectrum that stores the peak list at the given precision and
 has an initial capacity equal to initialCapacity

MsnSpectrum(int, double, PeakList.Precision) - Constructor for class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum

Construct a MsnSpectrum that has a constant intensity.

MsnSpectrum(MsnSpectrum, PeakProcessor<PeakAnnotation, PeakAnnotation>) - Constructor for class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum

Copy constructor

MsnSpectrum(MsnSpectrum, PeakProcessor<PeakAnnotation, PeakAnnotation>, Function<Double, Double>) - Constructor for class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum

Copy constructor

MsnSpectrum(MsnSpectrum, PeakProcessorChain<PeakAnnotation>) - Constructor for class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum

Copy constructor

MsnSpectrum(MsnSpectrum, PeakProcessorChain<PeakAnnotation>, Function<Double, Double>) - Constructor for class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum

Copy constructor

MsnSpectrumMetaDataReader - Class in org.expasy.mzjava.avro.io
 
MsnSpectrumMetaDataReader(AbstractAvroReader<? extends MsnSpectrum>) - Constructor for class org.expasy.mzjava.avro.io.MsnSpectrumMetaDataReader
 
MsnSpectrumMetaDataWriter - Class in org.expasy.mzjava.avro.io
 
MsnSpectrumMetaDataWriter(MsnSpectrumWriter) - Constructor for class org.expasy.mzjava.avro.io.MsnSpectrumMetaDataWriter
 
MsnSpectrumReader - Class in org.expasy.mzjava.avro.io
 
MsnSpectrumReader() - Constructor for class org.expasy.mzjava.avro.io.MsnSpectrumReader
 
MsnSpectrumReader(AbstractAvroReader<PeakAnnotation>, Optional<PeakList.Precision>, List<PeakProcessor<PeakAnnotation, PeakAnnotation>>) - Constructor for class org.expasy.mzjava.avro.io.MsnSpectrumReader
 
MsnSpectrumReader(AbstractAvroReader<? extends PeakAnnotation>[]) - Constructor for class org.expasy.mzjava.avro.io.MsnSpectrumReader
 
MsnSpectrumReader(AbstractAvroReader<? extends PeakAnnotation>[], Optional<PeakList.Precision>, List<PeakProcessor<PeakAnnotation, PeakAnnotation>>) - Constructor for class org.expasy.mzjava.avro.io.MsnSpectrumReader
 
MsnSpectrumValue - Class in org.expasy.mzjava.hadoop.io
 
MsnSpectrumValue() - Constructor for class org.expasy.mzjava.hadoop.io.MsnSpectrumValue
 
MsnSpectrumValue(Optional<PeakList.Precision>, List<PeakProcessor<PeakAnnotation, PeakAnnotation>>) - Constructor for class org.expasy.mzjava.hadoop.io.MsnSpectrumValue
 
MsnSpectrumWriter - Class in org.expasy.mzjava.avro.io
 
MsnSpectrumWriter() - Constructor for class org.expasy.mzjava.avro.io.MsnSpectrumWriter
 
MsnSpectrumWriter(Optional<PeakList.Precision>) - Constructor for class org.expasy.mzjava.avro.io.MsnSpectrumWriter
 
msnWriter(File) - Static method in class org.expasy.mzjava.hadoop.io.HadoopSpectraWriter
 
MspAnnotationResolver - Class in org.expasy.mzjava.proteomics.io.ms.spectrum.msp

Parses annotations from Msp files.

MspAnnotationResolver() - Constructor for class org.expasy.mzjava.proteomics.io.ms.spectrum.msp.MspAnnotationResolver
 
MspCommentParser - Class in org.expasy.mzjava.proteomics.io.ms.spectrum.msp
 
MspCommentParser() - Constructor for class org.expasy.mzjava.proteomics.io.ms.spectrum.msp.MspCommentParser
 
MspReader - Class in org.expasy.mzjava.proteomics.io.ms.spectrum

An IterativeReader that can read nist msp files.

MspReader.Builder - Class in org.expasy.mzjava.proteomics.io.ms.spectrum
 
MspReader.Builder(Reader, URI, PeakList.Precision) - Constructor for class org.expasy.mzjava.proteomics.io.ms.spectrum.MspReader.Builder
 
MsReaderFactory - Class in org.expasy.mzjava.proteomics.io.ms.spectrum

This class is a MS reader factory that provides new instance of MsReaders.

MsReaderFactory() - Constructor for class org.expasy.mzjava.proteomics.io.ms.spectrum.MsReaderFactory
 
MSTClusterBuilder<V> - Class in org.expasy.mzjava.core.ms.cluster
 
MSTClusterBuilder(double) - Constructor for class org.expasy.mzjava.core.ms.cluster.MSTClusterBuilder
 
MSTClusterBuilder(double, DoubleFunction<SimEdge<V>>) - Constructor for class org.expasy.mzjava.core.ms.cluster.MSTClusterBuilder
 
mz - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.FragmentMasses
 
MzAffineTransformer<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist.peaktransformer

Performs affine transformation (slope*mz+offset) on peak m/z.

MzAffineTransformer(double, double) - Constructor for class org.expasy.mzjava.core.ms.peaklist.peaktransformer.MzAffineTransformer

Make an instance of affine transformer (slope*mz+offset) on peak intensities.

MzIdentMlReader - Class in org.expasy.mzjava.proteomics.io.ms.ident
 
MzIdentMlReader() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.MzIdentMlReader
 
MzIdentMlReader(ModificationResolver) - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.MzIdentMlReader
 
MzIdentMLType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

The upper-most hierarchy level of mzIdentML with sub-containers for example describing software, protocols and search results (spectrum identifications or protein detection results).

MzIdentMLType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType
 
MzJavaKryoRegistrator - Class in org.expasy.mzjava.spark
 
MzJavaKryoRegistrator() - Constructor for class org.expasy.mzjava.spark.MzJavaKryoRegistrator
 
MzJavaSerialization - Class in org.expasy.mzjava.hadoop.io
 
MzJavaSerialization() - Constructor for class org.expasy.mzjava.hadoop.io.MzJavaSerialization
 
MzJavaSparkUtils - Class in org.expasy.mzjava.spark
 
mzList - Variable in class org.expasy.mzjava.core.ms.peaklist.ArrayCursor
 
MzmlConsistencyCheck - Enum in org.expasy.mzjava.external.io.ms.spectrum.mzml

An enumeration of all consistency to check in mzml.

MzmlSpectrumCheck - Class in org.expasy.mzjava.external.io.ms.spectrum.mzml

The base object to define a consistency check between a MsnSpectrum
 and a ebi mzml Spectrum for a specific target value.

MzmlSpectrumCheck() - Constructor for class org.expasy.mzjava.external.io.ms.spectrum.mzml.MzmlSpectrumCheck
 
MzRangeFilter<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist.peakfilter

Class to select or exclude peaks in certain mz ranges.

MzRangeFilter(IntervalList, boolean) - Constructor for class org.expasy.mzjava.core.ms.peaklist.peakfilter.MzRangeFilter
 
MzxmlReader - Class in org.expasy.mzjava.core.io.ms.spectrum
 
MzxmlReader(File, PeakList.Precision) - Constructor for class org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader
 
MzxmlReader(File, PeakList.Precision, PeakProcessorChain<PeakAnnotation>) - Constructor for class org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader
 
MzxmlReader.ConsistencyCheck - Enum in org.expasy.mzjava.core.io.ms.spectrum
 
MzxmlReader.ConsistencyCheckException - Exception in org.expasy.mzjava.core.io.ms.spectrum
 
MzxmlReader.XMLEventUtils - Class in org.expasy.mzjava.core.io.ms.spectrum
 
MzxmlReader.XMLEventUtils() - Constructor for class org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader.XMLEventUtils
 




N

N - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
n - Variable in class org.expasy.mzjava.core.ms.spectrasim.SharedPeakSimFunc
 
N_MASS - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
Na - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
Na_MASS - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
name - Variable in class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum
 
name - Variable in class org.expasy.mzjava.glycomics.mol.GlycanNode
 
name - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AbstractParamType
 
name - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.IdentifiableType
 
name - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.InteractSummary.Inputfile
 
name - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme
 
name - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis
 
name - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.NameValueType
 
NamespaceFilterXMLReader - Class in org.expasy.mzjava.proteomics.io.ms.ident

Used to add a default namespace for xml files that do not have a xmlns defined

NamespaceFilterXMLReader(String) - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.NamespaceFilterXMLReader
 
NameValueType - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for nameValueType complex type.

NameValueType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.NameValueType
 
NdpSimFunc<X extends PeakAnnotation,Y extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.spectrasim

Calculates the similarity between two PeakLists using the normalized dot product (ndp).

NdpSimFunc(int, Tolerance) - Constructor for class org.expasy.mzjava.core.ms.spectrasim.NdpSimFunc

Construct a NdpSimFunc that uses the default peak list aligner.

NdpSimFunc(int, PeakListAligner<X, Y>, PeakPairProcessor<X, Y>...) - Constructor for class org.expasy.mzjava.core.ms.spectrasim.NdpSimFunc

Construct a NdpSimFunc that uses the supplied PeakListAligner and PeakPairProcessor chain to process
 and align the peak lists.

NeutralLoss - Class in org.expasy.mzjava.proteomics.mol.modification
 
NeutralLoss(TObjectIntMap<Atom>, int, Set<String>) - Constructor for class org.expasy.mzjava.proteomics.mol.modification.NeutralLoss
 
neutralLoss - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.SpecificityT
 
NeutralLossT - Class in org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb

Java class for NeutralLoss_t complex type.

NeutralLossT() - Constructor for class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.NeutralLossT
 
newAmmoniaLossGenerator(Set<IonType>, double) - Static method in class org.expasy.mzjava.proteomics.ms.fragment.PeptideNeutralLossPeakGenerator
 
newBuilder(File, PeakList.Precision) - Static method in class org.expasy.mzjava.proteomics.io.ms.spectrum.MspReader

Factory method to create a Builder for creating a MspReader to read an msp file from file

newBuilder(Reader, URI, PeakList.Precision) - Static method in class org.expasy.mzjava.proteomics.io.ms.spectrum.MspReader

Factory method to create a Builder for creating a MspReader to read an msp file from the reader

newBuilder(File, PeakList.Precision) - Static method in class org.expasy.mzjava.proteomics.io.ms.spectrum.SptxtReader

Factory method to create a Builder for creating a SptxtReader to read an sptxt file from file

newBuilder(Reader, URI, PeakList.Precision) - Static method in class org.expasy.mzjava.proteomics.io.ms.spectrum.SptxtReader

Factory method to create a Builder for creating a SptxtReader to read an sptxt file from the reader

newBuilder() - Static method in class org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumDB

Factory method for creating a builder that can be used to configure and build an in memory PeptideSpectrumDB.

newFromPeak(double, int) - Method in class org.expasy.mzjava.core.ms.library.AbstractIntervalSpectrumLibrary
 
newFromPeak(double, int) - Method in class org.expasy.mzjava.core.ms.library.DefaultSpectrumLibrary
 
newFromPeak(double, int) - Method in class org.expasy.mzjava.core.ms.library.IntervalSpectrumLibrary
 
newInstance(int) - Static method in class org.expasy.mzjava.app.pb.ConsoleProgressBar
 
newInstance(int, ConsoleProgressBar.View) - Static method in class org.expasy.mzjava.app.pb.ConsoleProgressBar
 
newInstance(int, int) - Static method in class org.expasy.mzjava.app.pb.ConsoleProgressBar
 
newInstance(int, int, ConsoleProgressBar.View) - Static method in class org.expasy.mzjava.app.pb.ConsoleProgressBar
 
newLibrarySpectraReader(File, PeakList.Precision) - Static method in class org.expasy.mzjava.proteomics.io.ms.spectrum.MsReaderFactory
 
newMergeSink() - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList
 
newMergeSink() - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleFloatPeakList
 
newMergeSink() - Method in class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList
 
newMergeSink() - Method in class org.expasy.mzjava.core.ms.peaklist.FloatPeakList
 
newModificationLossGenerator(Mass, Set<AminoAcid>, Set<Modification>, Set<ModAttachment>, Set<IonType>, double) - Static method in class org.expasy.mzjava.proteomics.ms.fragment.PeptideNeutralLossPeakGenerator
 
newMsnSpectraReader(File, PeakList.Precision) - Static method in class org.expasy.mzjava.proteomics.io.ms.spectrum.MsReaderFactory
 
newPeakList(PeakList.Precision, double) - Method in class org.expasy.mzjava.avro.io.AbstractPeakListReader
 
newPeakList(PeakList.Precision, double) - Method in class org.expasy.mzjava.avro.io.MsnSpectrumReader
 
newPeakList(PeakList.Precision, double) - Method in class org.expasy.mzjava.avro.io.PeakListReader
 
newPeakList(PeakList.Precision) - Static method in class org.expasy.mzjava.core.ms.peaklist.PeakListFactory
 
newPeakList(PeakList.Precision, int) - Static method in class org.expasy.mzjava.core.ms.peaklist.PeakListFactory
 
newPeakList(PeakList.Precision, double[], double[]) - Static method in class org.expasy.mzjava.core.ms.peaklist.PeakListFactory
 
newPeakList(PeakList.Precision, double[], double[], int) - Static method in class org.expasy.mzjava.core.ms.peaklist.PeakListFactory
 
newPeakList(PeakList.Precision, double) - Method in class org.expasy.mzjava.proteomics.avro.io.PeptideConsensusSpectrumReader
 
newPeakList(PeakList.Precision, double) - Method in class org.expasy.mzjava.proteomics.avro.io.PeptideSpectrumReader
 
newPhosphateLossGenerator(Set<IonType>, double) - Static method in class org.expasy.mzjava.proteomics.ms.fragment.PeptideNeutralLossPeakGenerator
 
newPhosphoricAcidLossGenerator(Set<IonType>, double) - Static method in class org.expasy.mzjava.proteomics.ms.fragment.PeptideNeutralLossPeakGenerator
 
newProtein(ProteinSequence) - Static method in class org.expasy.mzjava.core.mol.polymer.prot.ProteinFactory
 
newProtein(String, Sequence<AminoAcidCompound>) - Static method in class org.expasy.mzjava.core.mol.polymer.prot.ProteinFactory
 
newProteinMatch(MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader
 
newProteinMatch(MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader
 
newSequestPeptideFragmenter(PeakList.Precision) - Static method in class org.expasy.mzjava.proteomics.ms.fragment.PeptideFragmenterFactory
 
newSpectrum(AbstractMsReader.ParseContext, PeakList.Precision) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfReader

Create a new spectrum.

newSpectrum(AbstractMsReader.ParseContext, PeakList.Precision) - Method in class org.expasy.mzjava.core.io.ms.spectrum.MgfReader
 
newSpectrum(StartElement, AbstractMsReader.ParseContext) - Method in class org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader

Create a spectrum

newSpectrum(PeakList.Precision) - Method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.EbiMzmlReader

Override this method to make an instance of S (MsnSpectrum by default)


newStrictReader(File, PeakList.Precision) - Static method in class org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader

Create an instance of MzxmlReader that strictly checks that the decoded spectrum is consistent with xml  attributes
 (see also addConsistencyChecks()/removeConsistencyChecks() method)

newStrictReader(File, PeakList.Precision, PeakProcessorChain<PeakAnnotation>) - Static method in class org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader

Create an instance of MzxmlReader that strictly checks that the decoded spectrum is consistent with xml  attributes
 (see also addConsistencyChecks()/removeConsistencyChecks() method)

newStrictReader(MzMLUnmarshaller, PeakList.Precision) - Static method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.EbiMzmlReader
 
newStrictReader(MzMLUnmarshaller, PeakList.Precision, PeakProcessorChain<PeakAnnotation>) - Static method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.EbiMzmlReader
 
newStrictWriter(EngineType, Comparator<PeptideMatch>) - Static method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriter

Create an instance of PepXmlWriter that strictly checks for inconsistencies

newStrictWriter(EngineType, String) - Static method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriter

Create an instance of PepXmlWriter that strictly checks for inconsistencies

newTolerantReader(File, PeakList.Precision) - Static method in class org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader

Create an instance of MzxmlReader that does not check for inconsistencies

newTolerantReader(MzMLUnmarshaller, PeakList.Precision) - Static method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.EbiMzmlReader
 
newTolerantReader(MzMLUnmarshaller, PeakList.Precision, PeakProcessorChain<PeakAnnotation>) - Static method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.EbiMzmlReader
 
newTolerantWriter(EngineType, Comparator<PeptideMatch>) - Static method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriter

Create an instance of PepXmlWriter that does not check for inconsistencies

newTolerantWriter(EngineType, String) - Static method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriter

Create an instance of PepXmlWriter that does not check for inconsistencies

newToPeak(double, int) - Method in class org.expasy.mzjava.core.ms.library.AbstractIntervalSpectrumLibrary
 
newToPeak(double, int) - Method in class org.expasy.mzjava.core.ms.library.DefaultSpectrumLibrary
 
newToPeak(double, int) - Method in class org.expasy.mzjava.core.ms.library.IntervalSpectrumLibrary
 
newUniprotProtein(String) - Static method in class org.expasy.mzjava.core.mol.polymer.prot.ProteinFactory
 
newWaterLossGenerator(Set<IonType>, double) - Static method in class org.expasy.mzjava.proteomics.ms.fragment.PeptideNeutralLossPeakGenerator
 
next() - Method in class org.expasy.mzjava.app.io.MonitoredIterativeReader
 
next() - Method in class org.expasy.mzjava.core.io.ConcatIterativeReader
 
next() - Method in interface org.expasy.mzjava.core.io.IterativeReader

Returns the next element in the reader.

next() - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader
 
next() - Method in class org.expasy.mzjava.core.io.ms.spectrum.MgfReader

Overridden so that the compiler knows that MsnSpectra are returned by next().

next() - Method in class org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader
 
next() - Method in class org.expasy.mzjava.core.mol.polymer.prot.BioJavaFastaProteinReader
 
next() - Method in class org.expasy.mzjava.core.ms.peaklist.ArrayCursor
 
next(double) - Method in class org.expasy.mzjava.core.ms.peaklist.ArrayCursor
 
next() - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakCursor

Moves the cursor to the next peak if there are more peaks.

next(double) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakCursor

Moves the cursor to the next peak only if peak.mz <= mz.

next() - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.TopNList

Advance the cursor to the next peak

next() - Method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.EbiMzmlReader
 
next() - Method in class org.expasy.mzjava.hadoop.io.HadoopSpectraReader
 
next() - Method in class org.expasy.mzjava.proteomics.io.mol.FastaProteinReader
 
next() - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.DtaReader

Overridden so that the compiler knows that MsnSpectra are returned by next().

nextCharacters(XMLEventReader) - Static method in class org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader.XMLEventUtils
 
nextStartElementIf(XMLEventReader, String) - Static method in class org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader.XMLEventUtils

Return the next start element only if match tagName.

NHighestPeaksNormalizer - Class in org.expasy.mzjava.core.ms.peaklist.peaktransformer

Each peak intensity is divided by the summed up intensity of the k most intense peaks and multiplied by a
 normalization factor (targetIntensity)

NHighestPeaksNormalizer(int, double) - Constructor for class org.expasy.mzjava.core.ms.peaklist.peaktransformer.NHighestPeaksNormalizer
 
noCut - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity
 
noCut(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder.SpecificityBuilder
 
nodes - Variable in class org.expasy.mzjava.glycomics.mol.SaccharideGraph
 
NodeSet<E> - Class in org.expasy.mzjava.glycomics.mol

This class implements the Set interface with a IdentityHashMap, using
 reference-equality in place of object-equality when comparing entries.

NodeSet(int) - Constructor for class org.expasy.mzjava.glycomics.mol.NodeSet

Constructs a new, empty set with the specified expected maximum size.

NodeSet(Collection<E>) - Constructor for class org.expasy.mzjava.glycomics.mol.NodeSet
 
noIntensity(double, int...) - Static method in class org.expasy.mzjava.core.ms.peaklist.Peak

Factory method to construct a Peak that has an intensity of 0

normalization - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary
 
normalize(Histogram.Normalization) - Method in interface org.expasy.mzjava.stats.Histogram

Normalize histogram (weighted) frequencies

normalize(Histogram.Normalization) - Method in class org.expasy.mzjava.stats.HistogramImpl
 
normalized - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraResult.Intensity
 
NormalizedDotProduct - Class in org.expasy.mzjava.stats

Static methods to calculate the normalized dot product

NPeaksFilter<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist.peakfilter

Extracts the top (most intense) numberOfPeaks peaks that are pushed to this PeakProcessor.

NPeaksFilter(int) - Constructor for class org.expasy.mzjava.core.ms.peaklist.peakfilter.NPeaksFilter
 
NPeaksPerBinFilter<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist.peakfilter

Filter that retains the top k peaks per fixed mz range

NPeaksPerBinFilter(int, double) - Constructor for class org.expasy.mzjava.core.ms.peaklist.peakfilter.NPeaksPerBinFilter
 
NPeaksPerSlidingWindowFilter<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist.peakfilter

This filters applies a sliding window and keeps a peak only if it is among the N-highest peaks in this window.

NPeaksPerSlidingWindowFilter(int, double, double) - Constructor for class org.expasy.mzjava.core.ms.peaklist.peakfilter.NPeaksPerSlidingWindowFilter
 
NPeaksPerSlidingWindowFilter(int, double) - Constructor for class org.expasy.mzjava.core.ms.peaklist.peakfilter.NPeaksPerSlidingWindowFilter
 
nrMembersCleaned - Variable in class org.expasy.mzjava.core.ms.cluster.SpectrumClusterEvaluator
 
nrMembersOrg - Variable in class org.expasy.mzjava.core.ms.cluster.SpectrumClusterEvaluator
 
nrOfMembers() - Method in class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum
 
nTermGain - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymeType
 
nTermSet - Static variable in enum org.expasy.mzjava.proteomics.mol.modification.ModAttachment
 
NthPeakNormalizer<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist.peaktransformer

Rescales the intensity to the nth most intense peak in the spectrum

NthPeakNormalizer(int) - Constructor for class org.expasy.mzjava.core.ms.peaklist.peaktransformer.NthPeakNormalizer

Creates a NthPeakNormalizer that scales the intensities to the nthPeak most
 intense peak.

ntuples - Variable in class org.expasy.mzjava.utils.MixedRadixNtupleGenerator.NtupleContainer
 
number - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.DatasetDerivation.DataFilter
 
number - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ElemRefT
 
NumberFormatFactory - Class in org.expasy.mzjava.utils

A factory to create Locale.US NumberFormats.

numDatabaseSequences - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchDatabaseType
 
NumericMass - Class in org.expasy.mzjava.core.mol
 
NumericMass(double) - Constructor for class org.expasy.mzjava.core.mol.NumericMass
 
NumericMassReader - Class in org.expasy.mzjava.avro.io
 
NumericMassReader() - Constructor for class org.expasy.mzjava.avro.io.NumericMassReader
 
NumericMassWriter - Class in org.expasy.mzjava.avro.io
 
NumericMassWriter() - Constructor for class org.expasy.mzjava.avro.io.NumericMassWriter
 
NumericModificationResolver - Class in org.expasy.mzjava.proteomics.mol.modification
 
NumericModificationResolver() - Constructor for class org.expasy.mzjava.proteomics.mol.modification.NumericModificationResolver
 
numMatchedIons - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
numMissedCleavages - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
numResidues - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchDatabaseType
 
numSequencesSearched - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationListType
 
numTolTerm - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
 
numTolTerm - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
numTotProteins - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 




O

O - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
O_MASS - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
ObjectFactory - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

This object contains factory methods for each 
 Java content interface and Java element interface 
 generated in the org.expasy.mzjava.proteomics.io.ms.liberator.mzidentml.v110 package.

ObjectFactory() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: org.expasy.mzjava.proteomics.io.ms.liberator.mzidentml.v110

ObjectFactory - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

This object contains factory methods for each 
 Java content interface and Java element interface 
 generated in the org.expasy.mzjava.proteomics.io.ms.liberator.pepxml.v117 package.

ObjectFactory() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: org.expasy.mzjava.proteomics.io.ms.liberator.pepxml.v117

ObjectFactory - Class in org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb

This object contains factory methods for each 
 Java content interface and Java element interface 
 generated in the org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb package.

ObjectFactory() - Constructor for class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb

octetsToDoubles(byte[], double[]) - Static method in class org.expasy.mzjava.core.io.ms.spectrum.BytesUtils
 
octetToDouble(byte...) - Static method in class org.expasy.mzjava.core.io.ms.spectrum.BytesUtils

Convert eight bytes into one double

of(N...) - Static method in class org.expasy.mzjava.glycomics.mol.NodeSet

Create a new NodeSet that contains the nodes

offset - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.FragmentMasses
 
onAmbiguousAminoAcid(DigestDB.AmbiguousAminoAcidAction) - Method in interface org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumDB.DigestDSL

Set what happens when an ambiguous amino acid is found.

onFailSendWarning(MsnSpectrum, Spectrum) - Method in interface org.expasy.mzjava.external.io.ms.spectrum.ConsistencyCheck

Send warning when check fails

onFailSendWarning(MsnSpectrum, Spectrum) - Method in enum org.expasy.mzjava.external.io.ms.spectrum.mzml.MzmlConsistencyCheck
 
onFailSendWarning(MsnSpectrum, Spectrum) - Method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.MzmlSpectrumCheck
 
onFailThrowException(MsnSpectrum, Spectrum) - Method in interface org.expasy.mzjava.external.io.ms.spectrum.ConsistencyCheck

Throw a ConsistencyCheckException when check fails

onFailThrowException(MsnSpectrum, Spectrum) - Method in enum org.expasy.mzjava.external.io.ms.spectrum.mzml.MzmlConsistencyCheck
 
onFailThrowException(MsnSpectrum, Spectrum) - Method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.MzmlSpectrumCheck
 
order() - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph

Return the number of monosaccharides and substituents in this glycan

org.expasy.mzjava.app.io - package org.expasy.mzjava.app.io
 
org.expasy.mzjava.app.pb - package org.expasy.mzjava.app.pb
 
org.expasy.mzjava.avro.io - package org.expasy.mzjava.avro.io
 
org.expasy.mzjava.core.io - package org.expasy.mzjava.core.io
 
org.expasy.mzjava.core.io.ms.spectrum - package org.expasy.mzjava.core.io.ms.spectrum
 
org.expasy.mzjava.core.io.ms.spectrum.mgf - package org.expasy.mzjava.core.io.ms.spectrum.mgf
 
org.expasy.mzjava.core.mol - package org.expasy.mzjava.core.mol
 
org.expasy.mzjava.core.mol.polymer.prot - package org.expasy.mzjava.core.mol.polymer.prot
 
org.expasy.mzjava.core.ms - package org.expasy.mzjava.core.ms
 
org.expasy.mzjava.core.ms.cluster - package org.expasy.mzjava.core.ms.cluster
 
org.expasy.mzjava.core.ms.consensus - package org.expasy.mzjava.core.ms.consensus
 
org.expasy.mzjava.core.ms.library - package org.expasy.mzjava.core.ms.library
 
org.expasy.mzjava.core.ms.peaklist - package org.expasy.mzjava.core.ms.peaklist
 
org.expasy.mzjava.core.ms.peaklist.peakfilter - package org.expasy.mzjava.core.ms.peaklist.peakfilter
 
org.expasy.mzjava.core.ms.peaklist.peaktransformer - package org.expasy.mzjava.core.ms.peaklist.peaktransformer
 
org.expasy.mzjava.core.ms.spectrasim - package org.expasy.mzjava.core.ms.spectrasim
 
org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor - package org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor
 
org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.filter - package org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.filter
 
org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer - package org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer
 
org.expasy.mzjava.core.ms.spectrum - package org.expasy.mzjava.core.ms.spectrum
 
org.expasy.mzjava.external.io.ms.spectrum - package org.expasy.mzjava.external.io.ms.spectrum
 
org.expasy.mzjava.external.io.ms.spectrum.mzml - package org.expasy.mzjava.external.io.ms.spectrum.mzml
 
org.expasy.mzjava.glycomics.io.mol.glycoct - package org.expasy.mzjava.glycomics.io.mol.glycoct
 
org.expasy.mzjava.glycomics.io.ms.gwp - package org.expasy.mzjava.glycomics.io.ms.gwp
 
org.expasy.mzjava.glycomics.mol - package org.expasy.mzjava.glycomics.mol
 
org.expasy.mzjava.glycomics.ms.fragment - package org.expasy.mzjava.glycomics.ms.fragment
 
org.expasy.mzjava.glycomics.ms.spectrum - package org.expasy.mzjava.glycomics.ms.spectrum
 
org.expasy.mzjava.hadoop.io - package org.expasy.mzjava.hadoop.io
 
org.expasy.mzjava.proteomics.avro.io - package org.expasy.mzjava.proteomics.avro.io
 
org.expasy.mzjava.proteomics.cookbook - package org.expasy.mzjava.proteomics.cookbook
 
org.expasy.mzjava.proteomics.hadoop.io - package org.expasy.mzjava.proteomics.hadoop.io
 
org.expasy.mzjava.proteomics.io.mol - package org.expasy.mzjava.proteomics.io.mol
 
org.expasy.mzjava.proteomics.io.mol.fasta - package org.expasy.mzjava.proteomics.io.mol.fasta
 
org.expasy.mzjava.proteomics.io.ms.ident - package org.expasy.mzjava.proteomics.io.ms.ident
 
org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110 - package org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110
 
org.expasy.mzjava.proteomics.io.ms.ident.pepxml - package org.expasy.mzjava.proteomics.io.ms.ident.pepxml
 
org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117 - package org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117
 
org.expasy.mzjava.proteomics.io.ms.spectrum - package org.expasy.mzjava.proteomics.io.ms.spectrum
 
org.expasy.mzjava.proteomics.io.ms.spectrum.msp - package org.expasy.mzjava.proteomics.io.ms.spectrum.msp
 
org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt - package org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt
 
org.expasy.mzjava.proteomics.mol - package org.expasy.mzjava.proteomics.mol
 
org.expasy.mzjava.proteomics.mol.digest - package org.expasy.mzjava.proteomics.mol.digest
 
org.expasy.mzjava.proteomics.mol.modification - package org.expasy.mzjava.proteomics.mol.modification
 
org.expasy.mzjava.proteomics.mol.modification.unimod - package org.expasy.mzjava.proteomics.mol.modification.unimod
 
org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb - package org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb
 
org.expasy.mzjava.proteomics.ms.consensus - package org.expasy.mzjava.proteomics.ms.consensus
 
org.expasy.mzjava.proteomics.ms.dbsearch - package org.expasy.mzjava.proteomics.ms.dbsearch
 
org.expasy.mzjava.proteomics.ms.fragment - package org.expasy.mzjava.proteomics.ms.fragment
 
org.expasy.mzjava.proteomics.ms.ident - package org.expasy.mzjava.proteomics.ms.ident
 
org.expasy.mzjava.proteomics.ms.spectrum - package org.expasy.mzjava.proteomics.ms.spectrum
 
org.expasy.mzjava.script - package org.expasy.mzjava.script
 
org.expasy.mzjava.spark - package org.expasy.mzjava.spark
 
org.expasy.mzjava.stats - package org.expasy.mzjava.stats
 
org.expasy.mzjava.stats.statscores - package org.expasy.mzjava.stats.statscores
 
org.expasy.mzjava.utils - package org.expasy.mzjava.utils
 
org.expasy.mzjava.utils.function - package org.expasy.mzjava.utils.function
 
organizationRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AffiliationType
 
organizationRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ParentOrganizationType
 
OrganizationType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

Organizations are entities like companies, universities, government agencies.

OrganizationType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.OrganizationType
 
origDatabaseUrl - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
 
originalResidue - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SubstitutionModificationType
 
outData - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
 
outDataType - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
 
outputType - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary
 
overlap() - Method in interface org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.DefaultPeakListAligner.OverlapListener
 




P

P - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
P_MASS - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
pages - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType
 
param(String, String) - Method in class org.expasy.mzjava.utils.URIBuilder
 
parameter - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
 
parameter - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
parameter - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.PeptideprophetResult.SearchScoreSummary
 
parameter(String, String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder.Builder

Add a parameter element in element search_summary

paramGroup - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AbstractContactType
 
paramGroup - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AmbiguousResidueType
 
paramGroup - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DBSequenceType
 
paramGroup - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MassTableType
 
paramGroup - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ParamListType
 
paramGroup - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType
 
paramGroup - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideType
 
paramGroup - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinAmbiguityGroupType
 
paramGroup - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionHypothesisType
 
paramGroup - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionListType
 
paramGroup - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SampleType
 
paramGroup - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SourceFileType
 
paramGroup - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType
 
paramGroup - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationListType
 
paramGroup - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationResultType
 
ParamListType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

Helper type to allow multiple cvParams or userParams to be given for an element.

ParamListType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ParamListType
 
ParamType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

Helper type to allow either a cvParam or a userParam to be provided for an element.

ParamType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ParamType
 
parent - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.OrganizationType
 
parentFile - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.DatasetDerivation.DataFilter
 
ParentOrganizationType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

The containing organization (the university or business which a lab belongs to, etc.)

ParentOrganizationType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ParentOrganizationType
 
parentTolerance - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType
 
parse(String, TObjectIntMap<Atom>) - Method in class org.expasy.mzjava.core.mol.AtomicCompositionParser

Parses the given string content and transmit data to builder.

parse(Reader, Map<String, Monosaccharide>) - Method in class org.expasy.mzjava.glycomics.mol.DefaultMonosaccharideLookup

Parser for the Monosaccharide Lookup file

parse(Reader, Map<String, Substituent>) - Method in class org.expasy.mzjava.glycomics.mol.DefaultSubstituentLookup

Parser for the Substituent Lookup file

parse(File, PSMReaderCallback) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.AbstractPsmCsvReader
 
parse(InputStream, PSMReaderCallback) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.AbstractPsmCsvReader
 
parse(Reader, PSMReaderCallback) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.AbstractPsmCsvReader
 
parse(File, String, PSMReaderCallback) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.AbstractPsmCsvReader
 
parse(File, PSMReaderCallback) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader
 
parse(InputStream, PSMReaderCallback) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader
 
parse(Reader, PSMReaderCallback) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader
 
parse(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader.PeptideInfoParser
 
parse(String, SpectrumIdentifier) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader.PSMInfoParser
 
parse(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader.SpectrumInfoParser
 
parse(File, PSMReaderCallback) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.MzIdentMlReader
 
parse(Reader, PSMReaderCallback) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.MzIdentMlReader
 
parse(InputStream, PSMReaderCallback) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.MzIdentMlReader
 
parse(InputSource, PSMReaderCallback) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.MzIdentMlReader
 
parse(File, PSMReaderCallback) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader
 
parse(InputStream, PSMReaderCallback) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader
 
parse(Reader, PSMReaderCallback) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader
 
parse(XMLStreamReader, Optional<String>, PSMReaderCallback) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader
 
parse(File, PSMReaderCallback) - Method in interface org.expasy.mzjava.proteomics.io.ms.ident.PsmReader

Parse file and call back PSMReaderCallback on each found PSM

parse(InputStream, PSMReaderCallback) - Method in interface org.expasy.mzjava.proteomics.io.ms.ident.PsmReader

Parse inputStream and call back PSMReaderCallback on each found PSM

parse(Reader, PSMReaderCallback) - Method in interface org.expasy.mzjava.proteomics.io.ms.ident.PsmReader

Parse reader and call back PSMReaderCallback on each found PSM

parse(String) - Static method in class org.expasy.mzjava.proteomics.mol.Peptide

Parse s to build a Peptide.

parse(String, ModificationResolver) - Static method in class org.expasy.mzjava.proteomics.mol.Peptide

Parse s to build a Peptide using the modResolver to convert modification strings to
 Modification

parse(String, FragmentType) - Static method in class org.expasy.mzjava.proteomics.mol.PeptideFragment

Parse s to build a PeptideFragment.

parse(String, FragmentType, ModificationResolver) - Static method in class org.expasy.mzjava.proteomics.mol.PeptideFragment

Parse s to build a PeptideFragment using the modResolver to convert modification strings to
 Modification

parseAndAdd(String) - Method in class org.expasy.mzjava.proteomics.mol.PeptideBuilder

Parse the peptideSequence string and add the sequence and modifications to this builder

parseBackboneAnnotation(String, Peptide) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.msp.MspAnnotationResolver

Parses annotations like
 

parseBackboneAnnotation(String, Peptide) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.SpectraStAnnotationResolver

Parses annotations like
 

parseBoolean(BigInteger) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader
 
parseChargeTag(String, S) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfReader

Parse the line that starts with CHARGE

parseComment(String, LibrarySpectrumBuilder) - Method in interface org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.SpectraLibCommentParser
 
parseComment(String, LibrarySpectrumBuilder) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.SpectraStCommentParser
 
parseComposition(String) - Static method in class org.expasy.mzjava.core.mol.Composition

Creates a Composition by parsing the given string.

parseDouble(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader
 
parseHeader(AbstractMsReader.ParseContext) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfReader
 
parseHeader(AbstractMsReader.ParseContext) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader

This is called on reader initialization.

parseHeader(AbstractMsReader.ParseContext) - Method in class org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader
 
parseHeader(String, Protein.Builder) - Method in interface org.expasy.mzjava.proteomics.io.mol.fasta.FastaHeaderParser
 
parseHeader(String, Protein.Builder) - Method in class org.expasy.mzjava.proteomics.io.mol.fasta.PirPrfFastaHeaderParser
 
parseHeader(String, Protein.Builder) - Method in class org.expasy.mzjava.proteomics.io.mol.fasta.UniprotFastaHeaderParser
 
parseHeader(String, Protein.Builder) - Method in class org.expasy.mzjava.proteomics.io.mol.FastaProteinReader
 
parseHeader(AbstractMsReader.ParseContext) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.DtaReader
 
parseHeader(AbstractMsReader.ParseContext) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.MsLibReader
 
parseInternalAnnotation(String) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.msp.MspAnnotationResolver
 
parseInternalAnnotation(String) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.SpectraStAnnotationResolver
 
parseModification(String) - Static method in class org.expasy.mzjava.proteomics.mol.modification.Modification

Parse a modification.

parseModsComment(String, LibrarySpectrumBuilder) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.SpectraStCommentParser
 
parseNextEntry(AbstractMsReader.ParseContext) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfReader
 
parseNextEntry(AbstractMsReader.ParseContext) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader
 
parseNextEntry(AbstractMsReader.ParseContext) - Method in class org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader
 
parseNextEntry(AbstractMsReader.ParseContext) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.DtaReader
 
parseNextEntry(AbstractMsReader.ParseContext) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.MsLibReader
 
parseNextMs1Entry(S, AbstractMsReader.ParseContext) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfReader

Parse all the lines that belong to one MS1 spectrum and the metadata and peaks to the spectrum.

parseNextMs2Entry(S, AbstractMsReader.ParseContext) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfReader

Parse all lines that correspond to the next MS2 entry and the metadata and peaks to the spectrum.

parsePattern - Static variable in class org.expasy.mzjava.proteomics.mol.modification.Modification
 
parsePepMassTag(String, S) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfReader

Parse the line that starts with PEPMASS

parsePrecursorAnnotation(String, Peptide) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.msp.MspAnnotationResolver

Parses annotations like
 

parsePrecursorAnnotation(String, Peptide) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.SpectraStAnnotationResolver

Parses annotations like
 

parseProteinComment(String, LibrarySpectrumBuilder) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.SpectraStCommentParser
 
parseRetentionTimeTag(String, S) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfReader

Parse the line that starts with RTINSECONDS

parseScanNumbers(String) - Method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.ScanNumberIncrementer
 
parseScanNumbers(String) - Method in interface org.expasy.mzjava.external.io.ms.spectrum.mzml.SpectrumIdParser
 
parseScanTag(String, S) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfReader

Parse the line that starts with CHARGE

parseTitle(String, MsnSpectrum) - Method in class org.expasy.mzjava.core.io.ms.spectrum.mgf.AnalystTitleParser
 
parseTitle(String, MsnSpectrum) - Method in class org.expasy.mzjava.core.io.ms.spectrum.mgf.DelegatingRegexTitleParser
 
parseTitle(String, MsnSpectrum) - Method in class org.expasy.mzjava.core.io.ms.spectrum.mgf.RegexScanNumTitleParser
 
parseTitle(String, MsnSpectrum) - Method in class org.expasy.mzjava.core.io.ms.spectrum.mgf.ThermoFisherOrbitrapTitleParser
 
parseTitle(String, MsnSpectrum) - Method in interface org.expasy.mzjava.core.io.ms.spectrum.mgf.TitleParser
 
parseTitleTag(String, S) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfReader

Parse the line that starts with a TITLE tag.

parseTitleTag(String, MsnSpectrum) - Method in class org.expasy.mzjava.core.io.ms.spectrum.MgfReader
 
parseUnknownCommentTag(String, String, LibrarySpectrumBuilder) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.msp.MspCommentParser
 
parseUnknownCommentTag(String, String, LibrarySpectrumBuilder) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.SpectraStCommentParser
 
parseUnknownTag(String, String, S) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfReader

Called if there are any tags that are not handled by MgfReader
 
 This is meant to be over ridden by subclasses that want to
 parse tags that the MgfReader does not know about

parseUnknownTag(String, String, LibrarySpectrumBuilder) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.MsLibReader

Called if there are any tags that are not handled by SptxtReader2

 This is meant to be over ridden by subclasses that want to
 parse tags that the SptxtReader2 does not know about

passThreshold - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionHypothesisType
 
passThreshold - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType
 
pathExists(String) - Static method in class org.expasy.mzjava.utils.PathUtils
 
PathUtils - Class in org.expasy.mzjava.utils
 
Peak - Class in org.expasy.mzjava.core.ms.peaklist

A peak in a mass spectrometer-typed spectrum must be an ion with a mass
 value.

Peak() - Constructor for class org.expasy.mzjava.core.ms.peaklist.Peak

Default constructor.

Peak(double, double, int...) - Constructor for class org.expasy.mzjava.core.ms.peaklist.Peak

Constructs a Peak.

Peak(Peak) - Constructor for class org.expasy.mzjava.core.ms.peaklist.Peak

Copy constructor

PeakAnnotation - Interface in org.expasy.mzjava.core.ms.peaklist

Tagging interface for an annotation of a peak in a PeakList

PeakCollectorSink<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist

Sink that adds peaks to a peak list

PeakCollectorSink() - Constructor for class org.expasy.mzjava.core.ms.peaklist.PeakCollectorSink
 
PeakCollectorSink(PeakList<A>) - Constructor for class org.expasy.mzjava.core.ms.peaklist.PeakCollectorSink
 
peakCount - Variable in class org.expasy.mzjava.core.ms.spectrasim.SharedPeakSimFunc
 
PeakCountEqualizer<X extends PeakAnnotation,Y extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer

Processor that equalizes the number of peaks such that peak lists x and y have the same number of peaks

PeakCountEqualizer() - Constructor for class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.PeakCountEqualizer
 
PeakCursor<A extends PeakAnnotation> - Interface in org.expasy.mzjava.core.ms.peaklist

A cursor for traversing a PeakList

peakFraction - Variable in class org.expasy.mzjava.core.ms.consensus.AbstractConsensusSpectrumBuilder
 
peakFraction - Variable in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.Builder
 
peakList - Variable in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList.AbstractMergePeakSink
 
PeakList<A extends PeakAnnotation> - Interface in org.expasy.mzjava.core.ms.peaklist

A list of mz/intensity values.

PeakList.Precision - Enum in org.expasy.mzjava.core.ms.peaklist
 
PeakListAligner<X extends PeakAnnotation,Y extends PeakAnnotation> - Interface in org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor

Interface to be implemented by classes that can align two PeakLists

PeakListComparator - Class in org.expasy.mzjava.core.ms.peaklist
 
PeakListComparator() - Constructor for class org.expasy.mzjava.core.ms.peaklist.PeakListComparator
 
PeakListFactory - Class in org.expasy.mzjava.core.ms.peaklist
 
PeakListMerger<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist
 
PeakListMerger() - Constructor for class org.expasy.mzjava.core.ms.peaklist.PeakListMerger
 
PeakListPrecisionFormat - Class in org.expasy.mzjava.core.io.ms.spectrum
 
PeakListReader - Class in org.expasy.mzjava.avro.io
 
PeakListReader() - Constructor for class org.expasy.mzjava.avro.io.PeakListReader
 
PeakListReader(Optional<PeakList.Precision>, List<PeakProcessor<PeakAnnotation, PeakAnnotation>>) - Constructor for class org.expasy.mzjava.avro.io.PeakListReader
 
PeakListSimGraphFactory - Class in org.expasy.mzjava.core.ms.cluster

A factory for building similarity graphs given a list of PeakLists that are sorted by charge and m/z.

PeakListUtils - Class in org.expasy.mzjava.core.ms.peaklist
 
PeakListValue - Class in org.expasy.mzjava.hadoop.io
 
PeakListValue() - Constructor for class org.expasy.mzjava.hadoop.io.PeakListValue
 
PeakListValue(Optional<PeakList.Precision>, List<PeakProcessor<PeakAnnotation, PeakAnnotation>>) - Constructor for class org.expasy.mzjava.hadoop.io.PeakListValue
 
PeakListWriter - Class in org.expasy.mzjava.avro.io
 
PeakListWriter() - Constructor for class org.expasy.mzjava.avro.io.PeakListWriter
 
PeakListWriter(Optional<PeakList.Precision>) - Constructor for class org.expasy.mzjava.avro.io.PeakListWriter
 
PeakPairIntensityLog10Transformer<X extends PeakAnnotation,Y extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer

Peak pair processor transforms the intensities of the peaks using base 10 logarithm.

PeakPairIntensityLog10Transformer() - Constructor for class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.PeakPairIntensityLog10Transformer
 
PeakPairIntensityLogETransformer<X extends PeakAnnotation,Y extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer

Peak pair processor transforms the intensities of the peaks using natural (base e) logarithm.

PeakPairIntensityLogETransformer() - Constructor for class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.PeakPairIntensityLogETransformer
 
PeakPairIntensitySqrtTransformer<X extends PeakAnnotation,Y extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer

Peak pair processor that transforms the intensities of the peaks using square root.

PeakPairIntensitySqrtTransformer() - Constructor for class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.PeakPairIntensitySqrtTransformer
 
PeakPairIonCurrentNormalizer<X extends PeakAnnotation,Y extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer

Processor that scales down the peak list that has the larger ion current so that it has the same current as the
 other peak list.

PeakPairIonCurrentNormalizer(double) - Constructor for class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.PeakPairIonCurrentNormalizer
 
PeakPairProcessor<X extends PeakAnnotation,Y extends PeakAnnotation> - Interface in org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor

Interface to be implemented by any class that processes peak pairs and
 acts as an element in a peak pair processor chain.

PeakPairProcessorChain<X extends PeakAnnotation,Y extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor
 
PeakPairProcessorChain(PeakListAligner<X, Y>) - Constructor for class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.PeakPairProcessorChain
 
PeakPairProcessorChain(PeakListAligner<X, Y>, PeakPairProcessor<X, Y>...) - Constructor for class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.PeakPairProcessorChain
 
PeakPairSink<X extends PeakAnnotation,Y extends PeakAnnotation> - Interface in org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor

Interface to be implemented by any class that is a sink for peak pairs

PeakPairSource<X extends PeakAnnotation,Y extends PeakAnnotation> - Interface in org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor

A peak pair source that can push peak pairs to a sink

PeakProcessor<IN extends PeakAnnotation,OUT extends PeakAnnotation> - Interface in org.expasy.mzjava.core.ms.peaklist

A peak sink that is one element in a peak processor chain.

PeakProcessorChain<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist

A list of peak processors.

PeakProcessorChain() - Constructor for class org.expasy.mzjava.core.ms.peaklist.PeakProcessorChain
 
PeakProcessorChain(PeakProcessor<A, A>) - Constructor for class org.expasy.mzjava.core.ms.peaklist.PeakProcessorChain
 
peakProcessorList - Variable in class org.expasy.mzjava.avro.io.AbstractPeakListReader
 
PeakReader - Class in org.expasy.mzjava.avro.io
 
PeakReader() - Constructor for class org.expasy.mzjava.avro.io.PeakReader
 
PeakSink<A extends PeakAnnotation> - Interface in org.expasy.mzjava.core.ms.peaklist

Interface to be implemented by any class that is a sink for peaks

 Before a PeakList is processed start is called, then processPeak is called for every peak and finally
 the end method is called.

PeakSource<A extends PeakAnnotation> - Interface in org.expasy.mzjava.core.ms.peaklist
 
PeakWriter - Class in org.expasy.mzjava.avro.io
 
PeakWriter() - Constructor for class org.expasy.mzjava.avro.io.PeakWriter
 
peakWriter - Variable in class org.expasy.mzjava.proteomics.avro.io.PeptideConsensusSpectrumWriter
 
PearsonsCorrelationCoeff - Class in org.expasy.mzjava.stats

Static methods to calculate the Pearson's correlation coefficient

PearsonsSimFunc<X extends PeakAnnotation,Y extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.spectrasim

Calculates PeakList similarity using the Pearson's correlation coefficient.

PearsonsSimFunc(int, Tolerance) - Constructor for class org.expasy.mzjava.core.ms.spectrasim.PearsonsSimFunc

Construct a PearsonsSimFunc that uses the default peak list aligner.

PearsonsSimFunc(int, PeakListAligner<X, Y>, PeakPairProcessor<X, Y>...) - Constructor for class org.expasy.mzjava.core.ms.spectrasim.PearsonsSimFunc

Construct a PearsonsSimFunc that uses the supplied PeakListAligner and PeakPairProcessor chain to process
 and align the peak lists.

peekIntensity(int) - Method in class org.expasy.mzjava.core.ms.peaklist.ArrayCursor
 
peekIntensity(int) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakCursor

Returns the intensity of the peak that is n positions removed from the peak that this cursor is currently pointing at

peekMz(int) - Method in class org.expasy.mzjava.core.ms.peaklist.ArrayCursor
 
peekMz(int) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakCursor

Returns the m/z of the peak that is n positions removed from the peak that this cursor is currently pointing at

PepFragAnnotation - Class in org.expasy.mzjava.proteomics.ms.spectrum

This class is used to annotate peptide fragment peaks in a PeakList.

PepFragAnnotation(PepFragAnnotation) - Constructor for class org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation

Copy constructor

PepFragAnnotation(IonType, int, AminoAcidSequence) - Constructor for class org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation

Construct a PepFragAnnotation

PepFragAnnotation.Builder - Class in org.expasy.mzjava.proteomics.ms.spectrum

PepFragAnnotation Builder

PepFragAnnotation.Builder(IonType, int, AminoAcidSequence) - Constructor for class org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation.Builder

Construct a new Builder

PepFragAnnotation.Builder(PepFragAnnotation) - Constructor for class org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation.Builder

Copy constructor

PepFragAnnotationReader - Class in org.expasy.mzjava.proteomics.avro.io
 
PepFragAnnotationReader() - Constructor for class org.expasy.mzjava.proteomics.avro.io.PepFragAnnotationReader
 
PepFragAnnotationWriter - Class in org.expasy.mzjava.proteomics.avro.io
 
PepFragAnnotationWriter() - Constructor for class org.expasy.mzjava.proteomics.avro.io.PepFragAnnotationWriter
 
PepLibPeakAnnotation - Class in org.expasy.mzjava.proteomics.ms.spectrum

Class to store annotations of consensus peaks.

PepLibPeakAnnotation(PepLibPeakAnnotation) - Constructor for class org.expasy.mzjava.proteomics.ms.spectrum.PepLibPeakAnnotation

Copy constructor

PepLibPeakAnnotation(int, double, double) - Constructor for class org.expasy.mzjava.proteomics.ms.spectrum.PepLibPeakAnnotation

Constructor

PepLibPeakAnnotation(int, double, double, Optional<PepFragAnnotation>) - Constructor for class org.expasy.mzjava.proteomics.ms.spectrum.PepLibPeakAnnotation
 
PepLibPeakAnnotationReader - Class in org.expasy.mzjava.proteomics.avro.io
 
PepLibPeakAnnotationReader() - Constructor for class org.expasy.mzjava.proteomics.avro.io.PepLibPeakAnnotationReader
 
PepLibPeakAnnotationWriter - Class in org.expasy.mzjava.proteomics.avro.io
 
PepLibPeakAnnotationWriter() - Constructor for class org.expasy.mzjava.proteomics.avro.io.PepLibPeakAnnotationWriter
 
pepNeutralLoss - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.SpecificityT
 
PepNeutralLossT - Class in org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb

Java class for PepNeutralLoss_t complex type.

PepNeutralLossT() - Constructor for class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.PepNeutralLossT
 
peptide - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SequenceCollectionType
 
peptide - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
Peptide - Class in org.expasy.mzjava.proteomics.mol
 
Peptide(AminoAcid, AminoAcid...) - Constructor for class org.expasy.mzjava.proteomics.mol.Peptide

Construct an Peptide by copying the residues.

Peptide(List<AminoAcid>) - Constructor for class org.expasy.mzjava.proteomics.mol.Peptide

Constructs an Peptide by copying the residues.

Peptide(AminoAcidSequence) - Constructor for class org.expasy.mzjava.proteomics.mol.Peptide

Copy constructor.

Peptide(AminoAcidSequence, int, int) - Constructor for class org.expasy.mzjava.proteomics.mol.Peptide

Constructs a Peptide by copying the residues and modifications from src.

Peptide(List<AminoAcid>, Multimap<Integer, Modification>, Multimap<ModAttachment, Modification>) - Constructor for class org.expasy.mzjava.proteomics.mol.Peptide

Constructs an Peptide from the list of residues with the modifications contained in
 side chain and term mod map.

Peptide(Peptide, Set<AminoAcid>, AminoAcid) - Constructor for class org.expasy.mzjava.proteomics.mol.Peptide
 
peptide(Peptide) - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.BuilderOld
 
PeptideBuilder - Class in org.expasy.mzjava.proteomics.mol

A builder for constructing Peptides

PeptideBuilder(String) - Constructor for class org.expasy.mzjava.proteomics.mol.PeptideBuilder

Construct a peptide builder initialised by parsing the peptide string

PeptideBuilder(List<AminoAcid>) - Constructor for class org.expasy.mzjava.proteomics.mol.PeptideBuilder

Construct a PeptideBuilder initialised to contain the amino acids from sequence

PeptideBuilder(AminoAcid...) - Constructor for class org.expasy.mzjava.proteomics.mol.PeptideBuilder

Construct a PeptideBuilder initialised to contain the amino acids from seq

PeptideBuilder(AminoAcid[], int, int) - Constructor for class org.expasy.mzjava.proteomics.mol.PeptideBuilder

Constructs an PeptideBuilder by copying the residues from residues starting at
 fromInclusive to toExclusive.

PeptideBuilder(Peptide) - Constructor for class org.expasy.mzjava.proteomics.mol.PeptideBuilder

Construct a PeptideBuilder initialised to contain the amino acids sequence and modifications
 copied from the peptide

PeptideConsensusPeakSink - Class in org.expasy.mzjava.proteomics.ms.consensus

Peak filter that retains peaks that are within tolerance of a peak in the theoretical spectrum or peaks
 that have a mergedPeakCount that is >= absoluteMinPeakCount && >= peakFraction*consensusSize.

PeptideConsensusPeakSink(PeptideConsensusSpectrum, double, int) - Constructor for class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusPeakSink
 
PeptideConsensusSpectrum - Class in org.expasy.mzjava.proteomics.ms.consensus
 
PeptideConsensusSpectrum(Peptide) - Constructor for class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum

Construct a LibrarySpectrum for the peptide

PeptideConsensusSpectrum(Peptide, Set<UUID>) - Constructor for class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum

Construct a LibrarySpectrum for the peptide

PeptideConsensusSpectrum(Peptide, PeakList.Precision, Set<UUID>) - Constructor for class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum

Construct a Spectrum that has a precision of precision

PeptideConsensusSpectrum(Peptide, PeakList.Precision) - Constructor for class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum

Construct a Spectrum that has a precision of precision

PeptideConsensusSpectrum(Peptide, int, PeakList.Precision, Set<UUID>) - Constructor for class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum

Construct a Spectrum that has an initial capacity of initialCapacity and a precision
 of precision

PeptideConsensusSpectrum(Peptide, PeakList.Precision, Set<UUID>, Set<String>) - Constructor for class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum
 
PeptideConsensusSpectrum(Peptide, PeakList.Precision, Set<UUID>, Set<String>, RetentionTimeDiscrete) - Constructor for class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum
 
PeptideConsensusSpectrum(Peptide, int, PeakList.Precision) - Constructor for class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum

Construct a Spectrum that has an initial capacity of initialCapacity and a precision
 of precision

PeptideConsensusSpectrum(PeptideConsensusSpectrum, PeakProcessor<PepLibPeakAnnotation, PepLibPeakAnnotation>) - Constructor for class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum

Copy constructor

PeptideConsensusSpectrum(PeptideConsensusSpectrum, PeakProcessorChain<PepLibPeakAnnotation>) - Constructor for class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum
 
PeptideConsensusSpectrum.AnnotationParametersSetter - Interface in org.expasy.mzjava.proteomics.ms.consensus
 
PeptideConsensusSpectrum.Builder - Class in org.expasy.mzjava.proteomics.ms.consensus
 
PeptideConsensusSpectrum.Builder(PeakList.Precision, URI) - Constructor for class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.Builder
 
PeptideConsensusSpectrum.BuilderOld - Class in org.expasy.mzjava.proteomics.ms.consensus
 
PeptideConsensusSpectrum.BuilderOld() - Constructor for class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.BuilderOld
 
PeptideConsensusSpectrum.ConsensusParametersSetter - Interface in org.expasy.mzjava.proteomics.ms.consensus
 
PeptideConsensusSpectrum.FilterParametersSetter - Interface in org.expasy.mzjava.proteomics.ms.consensus
 
PeptideConsensusSpectrum.Status - Enum in org.expasy.mzjava.proteomics.ms.consensus
 
PeptideConsensusSpectrumReader - Class in org.expasy.mzjava.proteomics.avro.io
 
PeptideConsensusSpectrumReader() - Constructor for class org.expasy.mzjava.proteomics.avro.io.PeptideConsensusSpectrumReader
 
PeptideConsensusSpectrumReader(Optional<PeakList.Precision>, List<PeakProcessor<PepLibPeakAnnotation, PepLibPeakAnnotation>>) - Constructor for class org.expasy.mzjava.proteomics.avro.io.PeptideConsensusSpectrumReader
 
PeptideConsensusSpectrumValue - Class in org.expasy.mzjava.proteomics.hadoop.io
 
PeptideConsensusSpectrumValue() - Constructor for class org.expasy.mzjava.proteomics.hadoop.io.PeptideConsensusSpectrumValue
 
PeptideConsensusSpectrumValue(Optional<PeakList.Precision>, List<PeakProcessor<PepLibPeakAnnotation, PepLibPeakAnnotation>>) - Constructor for class org.expasy.mzjava.proteomics.hadoop.io.PeptideConsensusSpectrumValue
 
PeptideConsensusSpectrumWriter - Class in org.expasy.mzjava.proteomics.avro.io
 
PeptideConsensusSpectrumWriter() - Constructor for class org.expasy.mzjava.proteomics.avro.io.PeptideConsensusSpectrumWriter
 
PeptideConsensusSpectrumWriter(Optional<PeakList.Precision>) - Constructor for class org.expasy.mzjava.proteomics.avro.io.PeptideConsensusSpectrumWriter
 
peptideEvidence - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SequenceCollectionType
 
peptideEvidenceRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceRefType
 
peptideEvidenceRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideHypothesisType
 
peptideEvidenceRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType
 
PeptideEvidenceRefType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

Reference to the PeptideEvidence element identified.

PeptideEvidenceRefType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceRefType
 
PeptideEvidenceType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

PeptideEvidence links a specific Peptide element to a specific position in a DBSequence.

PeptideEvidenceType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType
 
PeptideFragment - Class in org.expasy.mzjava.proteomics.mol
 
PeptideFragment(FragmentType, AminoAcid, AminoAcid...) - Constructor for class org.expasy.mzjava.proteomics.mol.PeptideFragment

Construct an PeptideFragment by copying the residues

PeptideFragment(FragmentType, AminoAcidSequence, int, int) - Constructor for class org.expasy.mzjava.proteomics.mol.PeptideFragment

Constructor that copies the residues and modifications from src.

PeptideFragment(FragmentType, List<AminoAcid>, Multimap<Integer, Modification>, Multimap<ModAttachment, Modification>) - Constructor for class org.expasy.mzjava.proteomics.mol.PeptideFragment

Constructs an PeptideFragment from the list of residues with the modifications contained in
 side chain and term mod map.

PeptideFragmentAnnotator - Class in org.expasy.mzjava.proteomics.ms.consensus

Peak sink that collects the peaks into a LibrarySpectrum and annotates the peaks

PeptideFragmentAnnotator(Tolerance, PeptideSpectrum) - Constructor for class org.expasy.mzjava.proteomics.ms.consensus.PeptideFragmentAnnotator
 
PeptideFragmentAnnotator - Class in org.expasy.mzjava.proteomics.ms.fragment

This facade highly simplifies and hides the complexity of annotated a peakList
 given a peptide as this process implies peptide fragmentation, aligning peaks and reporting
 annotations.

PeptideFragmentAnnotator(PeptideFragmenter, Tolerance) - Constructor for class org.expasy.mzjava.proteomics.ms.fragment.PeptideFragmentAnnotator
 
PeptideFragmentAnnotator(PeptideFragmenter, PeakListAligner<PepFragAnnotation, PepFragAnnotation>) - Constructor for class org.expasy.mzjava.proteomics.ms.fragment.PeptideFragmentAnnotator
 
PeptideFragmenter - Class in org.expasy.mzjava.proteomics.ms.fragment
 
PeptideFragmenter(Set<IonType>, PeakList.Precision) - Constructor for class org.expasy.mzjava.proteomics.ms.fragment.PeptideFragmenter

Construct a CID peptide fragmenter that generates peaks for the supplied ion types.

PeptideFragmenter(List<PeptidePeakGenerator<PepFragAnnotation>>, PeakList.Precision) - Constructor for class org.expasy.mzjava.proteomics.ms.fragment.PeptideFragmenter

Constructs a CID peptide fragmenter that generates peaks using the supplied peak generators

PeptideFragmenterFactory - Class in org.expasy.mzjava.proteomics.ms.fragment

Creates custom made PeptideFragmenter instances

PeptideFragmentReader - Class in org.expasy.mzjava.proteomics.avro.io
 
PeptideFragmentReader() - Constructor for class org.expasy.mzjava.proteomics.avro.io.PeptideFragmentReader
 
PeptideFragmentWriter - Class in org.expasy.mzjava.proteomics.avro.io
 
PeptideFragmentWriter() - Constructor for class org.expasy.mzjava.proteomics.avro.io.PeptideFragmentWriter
 
peptideHypothesis - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionHypothesisType
 
PeptideHypothesisType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

Peptide evidence on which this ProteinHypothesis is based by reference to a PeptideEvidence element.

PeptideHypothesisType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideHypothesisType
 
PeptideMatch - Class in org.expasy.mzjava.proteomics.ms.ident

PeptideMatch stores the match information from a peptide spectrum match

PeptideMatch(AminoAcid...) - Constructor for class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Create a peptide match given an amino acid sequence

PeptideMatch(List<AminoAcid>) - Constructor for class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Create a peptide match given an amino acid sequence

PeptideMatch(String) - Constructor for class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Create a peptide match given an amino acid sequence

PeptideMatch(SymbolSequence<AminoAcid>) - Constructor for class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Create a peptide match given an amino acid esequence

PeptideMatch(PeptideSpectrum, String, double) - Constructor for class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Construct a PeptideMatch from a peptide spectrum and score.

PeptideMatchComparator - Class in org.expasy.mzjava.proteomics.ms.ident
 
PeptideMatchComparator(String) - Constructor for class org.expasy.mzjava.proteomics.ms.ident.PeptideMatchComparator
 
PeptideNeutralLossPeakGenerator - Class in org.expasy.mzjava.proteomics.ms.fragment

Generates a neutral loss for a peptide fragment if the modificationPredicate accepts
 the fragment.

PeptideNeutralLossPeakGenerator(Mass, Set<AminoAcid>, Set<IonType>, double) - Constructor for class org.expasy.mzjava.proteomics.ms.fragment.PeptideNeutralLossPeakGenerator
 
PeptideNeutralLossPeakGenerator(Mass, Predicate<PeptideFragment>, Set<IonType>, double) - Constructor for class org.expasy.mzjava.proteomics.ms.fragment.PeptideNeutralLossPeakGenerator
 
PeptideNeutralLossPeakGenerator.ModifiedAaPresencePredicate - Class in org.expasy.mzjava.proteomics.ms.fragment

Accepts a PeptideFragment if the fragment contains an amino acid in aminoAcids
 that has a modification which is equal to the mass of one modification in modifications.

peptideNextAa - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
 
peptideNextAa - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
PeptideParseException - Exception in org.expasy.mzjava.proteomics.mol
 
PeptideParseException(String) - Constructor for exception org.expasy.mzjava.proteomics.mol.PeptideParseException
 
PeptideParseException(String, Throwable) - Constructor for exception org.expasy.mzjava.proteomics.mol.PeptideParseException
 
PeptidePeakGenerator<A extends PeakAnnotation> - Interface in org.expasy.mzjava.proteomics.ms.fragment
 
peptidePrevAa - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
 
peptidePrevAa - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
PeptideprophetResult - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

PeptideprophetResult() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.PeptideprophetResult
 
PeptideprophetResult.SearchScoreSummary - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

PeptideprophetResult.SearchScoreSummary() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.PeptideprophetResult.SearchScoreSummary
 
PeptideProteinMatch - Class in org.expasy.mzjava.proteomics.ms.ident

Class that stores the information where a peptide matches to a protein.

PeptideProteinMatch(String, Optional<String>, Optional<String>, Optional<String>, PeptideProteinMatch.HitType) - Constructor for class org.expasy.mzjava.proteomics.ms.ident.PeptideProteinMatch

Constructor, none of the parameters can be null.

PeptideProteinMatch(String, Optional<String>, Optional<String>, Optional<String>, int, int, PeptideProteinMatch.HitType) - Constructor for class org.expasy.mzjava.proteomics.ms.ident.PeptideProteinMatch

Constructor, none of the parameters can be null
 
 The previous and next AA are wrapped in com.google.common.base.Optional so that it is possible to differentiate
 between a unknown AA and when the information is not available.

PeptideProteinMatch.HitType - Enum in org.expasy.mzjava.proteomics.ms.ident
 
peptideReader - Variable in class org.expasy.mzjava.proteomics.avro.io.PeptideConsensusSpectrumReader
 
PeptideReader - Class in org.expasy.mzjava.proteomics.avro.io
 
PeptideReader() - Constructor for class org.expasy.mzjava.proteomics.avro.io.PeptideReader
 
peptideRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType
 
peptideRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType
 
peptideSequence - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideType
 
PeptideSpectrum - Class in org.expasy.mzjava.proteomics.ms.spectrum
 
PeptideSpectrum(Peptide, int) - Constructor for class org.expasy.mzjava.proteomics.ms.spectrum.PeptideSpectrum
 
PeptideSpectrum(Peptide, int, PeakList.Precision) - Constructor for class org.expasy.mzjava.proteomics.ms.spectrum.PeptideSpectrum
 
PeptideSpectrum(Peptide, int, int, PeakList.Precision) - Constructor for class org.expasy.mzjava.proteomics.ms.spectrum.PeptideSpectrum
 
PeptideSpectrum(Peptide, int, int, double, PeakList.Precision) - Constructor for class org.expasy.mzjava.proteomics.ms.spectrum.PeptideSpectrum
 
PeptideSpectrum(PeptideSpectrum, PeakProcessor<PepFragAnnotation, PepFragAnnotation>) - Constructor for class org.expasy.mzjava.proteomics.ms.spectrum.PeptideSpectrum
 
PeptideSpectrum(PeptideSpectrum, PeakProcessorChain<PepFragAnnotation>) - Constructor for class org.expasy.mzjava.proteomics.ms.spectrum.PeptideSpectrum
 
PeptideSpectrum(Spectrum<PepFragAnnotation>, Peptide, int) - Constructor for class org.expasy.mzjava.proteomics.ms.spectrum.PeptideSpectrum
 
PeptideSpectrumCache - Interface in org.expasy.mzjava.proteomics.ms.dbsearch
 
PeptideSpectrumDB - Class in org.expasy.mzjava.proteomics.ms.dbsearch

PeptideSpectrumDB is a facade that collects together all the classes that are required by a peptide spectrum
 database.

PeptideSpectrumDB(Tolerance, PeptideFragmenter, DigestDB, PeptideSpectrumCache, PeakProcessorChain<PepFragAnnotation>) - Constructor for class org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumDB

Construct a PeptideSpectrumDB backed by the fragmenter, proteinDB and peptideSpectrumCache.

PeptideSpectrumDB.DigestDSL - Interface in org.expasy.mzjava.proteomics.ms.dbsearch

Fluent interface for configuring the protein digestion and fragmentation.

PeptideSpectrumDB.DigestSourceDSL - Interface in org.expasy.mzjava.proteomics.ms.dbsearch

Fluent interface for configuring the protein source

PeptideSpectrumDB.EndDSL - Interface in org.expasy.mzjava.proteomics.ms.dbsearch
 
PeptideSpectrumDB.FragmentDSL - Interface in org.expasy.mzjava.proteomics.ms.dbsearch

Fluent interface for configuring the protein digestion and fragmentation.

PeptideSpectrumDB.StartDSL - Interface in org.expasy.mzjava.proteomics.ms.dbsearch

Fluent interface that starts the build.

PeptideSpectrumReader - Class in org.expasy.mzjava.proteomics.avro.io
 
PeptideSpectrumReader() - Constructor for class org.expasy.mzjava.proteomics.avro.io.PeptideSpectrumReader
 
PeptideSpectrumReader(Optional<PeakList.Precision>, List<PeakProcessor<PepFragAnnotation, PepFragAnnotation>>) - Constructor for class org.expasy.mzjava.proteomics.avro.io.PeptideSpectrumReader
 
PeptideSpectrumValue - Class in org.expasy.mzjava.proteomics.hadoop.io
 
PeptideSpectrumValue() - Constructor for class org.expasy.mzjava.proteomics.hadoop.io.PeptideSpectrumValue
 
PeptideSpectrumValue(Optional<PeakList.Precision>, List<PeakProcessor<PepFragAnnotation, PepFragAnnotation>>) - Constructor for class org.expasy.mzjava.proteomics.hadoop.io.PeptideSpectrumValue
 
PeptideSpectrumWriter - Class in org.expasy.mzjava.proteomics.avro.io
 
PeptideSpectrumWriter() - Constructor for class org.expasy.mzjava.proteomics.avro.io.PeptideSpectrumWriter
 
PeptideSpectrumWriter(Optional<PeakList.Precision>) - Constructor for class org.expasy.mzjava.proteomics.avro.io.PeptideSpectrumWriter
 
peptideTerminus - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
 
PeptideType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

One (poly)peptide (a sequence with modifications).

PeptideType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideType
 
peptideWriter - Variable in class org.expasy.mzjava.proteomics.avro.io.PeptideConsensusSpectrumWriter
 
PeptideWriter - Class in org.expasy.mzjava.proteomics.avro.io
 
PeptideWriter() - Constructor for class org.expasy.mzjava.proteomics.avro.io.PeptideWriter
 
PepXmlReader - Class in org.expasy.mzjava.proteomics.io.ms.ident
 
PepXmlReader(PepXmlReader.ModMassStorage, boolean) - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader
 
PepXmlReader(PepXmlReader.ModMassStorage, boolean, ModificationMatchResolver) - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader
 
PepXmlReader.ModMassStorage - Enum in org.expasy.mzjava.proteomics.io.ms.ident
 
PepXmlReader.NamespaceRewriteDelegate - Class in org.expasy.mzjava.proteomics.io.ms.ident
 
PepXmlReader.NamespaceRewriteDelegate(XMLStreamReader) - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader.NamespaceRewriteDelegate
 
PepXmlWriter - Class in org.expasy.mzjava.proteomics.io.ms.ident

This Writer writes peptide identifications in PepXML format.

PepXmlWriter(PepXmlWriterBuilder.Builder) - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriter
 
PepXmlWriter.ConsistencyCheck - Enum in org.expasy.mzjava.proteomics.io.ms.ident
 
PepXmlWriterBuilder - Class in org.expasy.mzjava.proteomics.io.ms.ident

This builder Builds PepXmlWriter instances.

PepXmlWriterBuilder() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder
 
PepXmlWriterBuilder.Builder - Class in org.expasy.mzjava.proteomics.io.ms.ident

Build PepXmlWriter

PepXmlWriterBuilder.EnzymeEnd - Interface in org.expasy.mzjava.proteomics.io.ms.ident
 
PepXmlWriterBuilder.SampleEnzymeBuilder - Class in org.expasy.mzjava.proteomics.io.ms.ident
 
PepXmlWriterBuilder.SpecificityBuilder - Class in org.expasy.mzjava.proteomics.io.ms.ident
 
PeriodicTable - Class in org.expasy.mzjava.core.mol

Periodic table of the elements.

personOrOrganization - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AuditCollectionType
 
PersonType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

A person's name and contact details.

PersonType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PersonType
 
PirPrfFastaHeaderParser - Class in org.expasy.mzjava.proteomics.io.mol.fasta
 
PirPrfFastaHeaderParser() - Constructor for class org.expasy.mzjava.proteomics.io.mol.fasta.PirPrfFastaHeaderParser
 
PoissonUtils - Class in org.expasy.mzjava.stats
 
Polarity - Enum in org.expasy.mzjava.core.ms.peaklist
 
populatePrePostOrder(GlycanNode, Counter) - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph

Populate the pre and post order table

position - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo.ModAminoacidMass
 
position - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.SpecificityT
 
PositionT - Enum in org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb

Java class for position_t.

post - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType
 
postOrder - Variable in class org.expasy.mzjava.glycomics.mol.SaccharideGraph
 
PpmTolerance - Class in org.expasy.mzjava.core.ms
 
PpmTolerance(double) - Constructor for class org.expasy.mzjava.core.ms.PpmTolerance
 
pre - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType
 
precision - Variable in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader
 
precision - Variable in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.Builder
 
precision(PeakList.Precision) - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.BuilderOld
 
precisionOverride - Variable in class org.expasy.mzjava.avro.io.AbstractPeakListReader
 
precMassType(MassType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder.Builder

Set the precursor_mass_type attribute of element search_summary

precursorIntensity - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
 
precursorMassType - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
 
precursorMzMean - Variable in class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum
 
precursorMzStdev - Variable in class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum
 
precursorNeutralMass - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
 
precursorReader - Variable in class org.expasy.mzjava.proteomics.avro.io.PeptideConsensusSpectrumReader
 
PrecursorSplitter - Class in org.expasy.mzjava.utils.function

Splits a list of PeakList into sub lists.

PrecursorSplitter(Tolerance) - Constructor for class org.expasy.mzjava.utils.function.PrecursorSplitter
 
preOrder - Variable in class org.expasy.mzjava.glycomics.mol.SaccharideGraph
 
previous() - Method in class org.expasy.mzjava.core.ms.peaklist.ArrayCursor
 
previous() - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakCursor

Moves the cursor to the previous peak if there are any previous peaks.

PrimitiveArrayUtils - Class in org.expasy.mzjava.utils

Provides static generic methods on primitive arrays.

probability - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.PeptideprophetResult
 
Procedure<T> - Interface in org.expasy.mzjava.utils.function

Interface for procedures with one parameter.

process(PeakList<A>, PeakSink<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.PeakProcessorChain
 
process(TDoubleList, TDoubleList, TIntObjectMap<List<A>>, PeakSink<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.PeakProcessorChain
 
process(Number[], Number[], TIntObjectMap<List<A>>, PeakSink<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.PeakProcessorChain
 
process(TDoubleArrayList, TDoubleArrayList, TDoubleArrayList, TIntObjectHashMap<List<X>>, TIntObjectHashMap<List<Y>>) - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.DelayedPeakPairProcessor

Preform the processing

process(PeakPairSink<X, Y>, PeakList<X>, PeakList<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.PeakPairProcessorChain
 
process(TDoubleArrayList, TDoubleArrayList, TDoubleArrayList, TIntObjectHashMap<List<X>>, TIntObjectHashMap<List<Y>>) - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.TopPeakPairTransformer
 
process(TDoubleArrayList, TDoubleArrayList, TDoubleArrayList, TIntObjectHashMap<List<X>>, TIntObjectHashMap<List<Y>>) - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.UnitVectorPeakPairTransformer
 
processCached(TDoubleArrayList, TDoubleArrayList, TIntObjectHashMap<List<IN>>) - Method in class org.expasy.mzjava.core.ms.peaklist.DelayedPeakProcessor

This method is called when all the peaks have been cached

processCached(TDoubleArrayList, TDoubleArrayList, TIntObjectHashMap<List<IN>>) - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.AbstractMergePeakFilter
 
processCached(TDoubleArrayList, TDoubleArrayList, TIntObjectHashMap<List<A>>) - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.BinnedSpectrumFilter
 
processCached(TDoubleArrayList, TDoubleArrayList, TIntObjectHashMap<List<A>>) - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.CentroidFilter
 
processCached(TDoubleArrayList, TDoubleArrayList, TIntObjectHashMap<List<A>>) - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.NPeaksPerSlidingWindowFilter
 
processCached(TDoubleArrayList, TDoubleArrayList, TIntObjectHashMap<List<A>>) - Method in class org.expasy.mzjava.core.ms.peaklist.peaktransformer.AddFlankingPeaksTransformer
 
processCached(TDoubleArrayList, TDoubleArrayList, TIntObjectHashMap<List<A>>) - Method in class org.expasy.mzjava.core.ms.peaklist.peaktransformer.ContrastEnhancingTransformer
 
processCached(TDoubleArrayList, TDoubleArrayList, TIntObjectHashMap<List<A>>) - Method in class org.expasy.mzjava.core.ms.peaklist.peaktransformer.HighestPeakPerBinNormalizer
 
processCached(TDoubleArrayList, TDoubleArrayList, TIntObjectHashMap<List<A>>) - Method in class org.expasy.mzjava.core.ms.peaklist.peaktransformer.IonCurrentNormalizer
 
processCached(TDoubleArrayList, TDoubleArrayList, TIntObjectHashMap<List<PeakAnnotation>>) - Method in class org.expasy.mzjava.core.ms.peaklist.peaktransformer.NHighestPeaksNormalizer
 
processCached(TDoubleArrayList, TDoubleArrayList, TIntObjectHashMap<List<A>>) - Method in class org.expasy.mzjava.core.ms.peaklist.peaktransformer.NthPeakNormalizer
 
processCached(TDoubleArrayList, TDoubleArrayList, TIntObjectHashMap<List<A>>) - Method in class org.expasy.mzjava.core.ms.peaklist.peaktransformer.RankNormalizer
 
processCached(TDoubleArrayList, TDoubleArrayList, TIntObjectHashMap<List<A>>) - Method in class org.expasy.mzjava.core.ms.peaklist.peaktransformer.UnitVectorNormalizer
 
processGeneratedSpectraWith(PeakProcessorChain<PepFragAnnotation>) - Method in interface org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumDB.FragmentDSL

Set the processorChain that is used to process the generated spectra

processingInstruction(String, String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.NamespaceFilterXMLReader
 
processPeak(double, double, List<A>) - Method in class org.expasy.mzjava.core.ms.consensus.ConsensusPeakSink
 
processPeak(double, double, List<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList.AbstractMergePeakSink
 
processPeak(double, double, List<IN>) - Method in class org.expasy.mzjava.core.ms.peaklist.DelayedPeakProcessor
 
processPeak(double, double, List<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.PeakCollectorSink
 
processPeak(double, double, List<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.FragmentAnnotationFilter
 
processPeak(double, double, List<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.MzRangeFilter
 
processPeak(double, double, List<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.NPeaksFilter
 
processPeak(double, double, List<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.NPeaksPerBinFilter
 
processPeak(double, double, List<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.ThresholdFilter
 
processPeak(double, double, List<A>) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakSink

Process the peak

processPeak(double, double, List<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.peaktransformer.AffineTransformer
 
processPeak(double, double, List<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.peaktransformer.ArcsinhTransformer
 
processPeak(double, double, List<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.peaktransformer.IdentityPeakProcessor
 
processPeak(double, double, List<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.peaktransformer.InverseArcsinhTransformer
 
processPeak(double, double, List<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.peaktransformer.IonCurrentNormalizer
 
processPeak(double, double, List<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.peaktransformer.Log10Transformer
 
processPeak(double, double, List<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.peaktransformer.LogTransformer
 
processPeak(double, double, List<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.peaktransformer.MzAffineTransformer
 
processPeak(double, double, List<PeakAnnotation>) - Method in class org.expasy.mzjava.core.ms.peaklist.peaktransformer.NHighestPeaksNormalizer
 
processPeak(double, double, List<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.peaktransformer.NthPeakNormalizer
 
processPeak(double, double, List<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.peaktransformer.SqrtTransformer
 
processPeak(double, double, List<PepLibPeakAnnotation>) - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusPeakSink
 
processPeak(double, double, List<PepLibPeakAnnotation>) - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideFragmentAnnotator
 
processPeakPair(double, double, double, List<X>, List<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.DpSimFunc
 
processPeakPair(double, double, double, List<X>, List<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.McNdpSimFunc
 
processPeakPair(double, double, double, List<X>, List<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.NdpSimFunc
 
processPeakPair(double, double, double, List<X>, List<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.DelayedPeakPairProcessor
 
processPeakPair(double, double, double, List<X>, List<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.filter.ThresholdPeakPairFilter
 
processPeakPair(double, double, double, List<X>, List<Y>) - Method in interface org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.PeakPairSink

Pushes the next peak pair to this sink

processPeakPair(double, double, double, List<X>, List<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.PeakCountEqualizer
 
processPeakPair(double, double, double, List<X>, List<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.PeakPairIntensityLog10Transformer
 
processPeakPair(double, double, double, List<X>, List<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.PeakPairIntensityLogETransformer
 
processPeakPair(double, double, double, List<X>, List<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.PeakPairIntensitySqrtTransformer
 
processPeakPair(double, double, double, List<X>, List<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.PeakPairIonCurrentNormalizer
 
processPeakPair(double, double, double, List<X>, List<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.TopPeakPairTransformer
 
processPeakPair(double, double, double, List<X>, List<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.PearsonsSimFunc
 
processPeakPair(double, double, double, List<X>, List<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.PspcSimFunc
 
processPeakPair(double, double, double, List<X>, List<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.SharedPeakSimFunc
 
processPeakPair(double, double, double, List<X>, List<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.WeightedPearsonsSimFunc
 
processSearchHit(PSMReaderCallback, SpectrumIdentifier, MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader
 
ProgressBar - Interface in org.expasy.mzjava.app.pb

All progress bar classes will have to implements these methods.

PROPERTY_GLYCOCT_MONOSACCHARIDES - Static variable in class org.expasy.mzjava.glycomics.io.mol.glycoct.DefaultGlycoCtResolver
 
PROPERTY_GLYCOCT_SUBSTITUENTS - Static variable in class org.expasy.mzjava.glycomics.io.mol.glycoct.DefaultGlycoCtResolver
 
PROPERTY_MONOSACCHARIDE_LOOKUP - Static variable in class org.expasy.mzjava.glycomics.mol.DefaultMonosaccharideLookup
 
PROPERTY_SUBSTITUENT_LOOKUP - Static variable in class org.expasy.mzjava.glycomics.mol.DefaultSubstituentLookup
 
Protease - Enum in org.expasy.mzjava.proteomics.mol.digest

http://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html

protein - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
 
protein - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
Protein - Class in org.expasy.mzjava.proteomics.mol
 
Protein(String, String) - Constructor for class org.expasy.mzjava.proteomics.mol.Protein

Create an instance from a sequence string

Protein(String, AminoAcid...) - Constructor for class org.expasy.mzjava.proteomics.mol.Protein

Create an instance from a list of AminoAcids

Protein.Builder - Class in org.expasy.mzjava.proteomics.mol
 
Protein.Builder(int) - Constructor for class org.expasy.mzjava.proteomics.mol.Protein.Builder
 
Protein.Builder(String) - Constructor for class org.expasy.mzjava.proteomics.mol.Protein.Builder
 
proteinAmbiguityGroup - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionListType
 
ProteinAmbiguityGroupType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

A set of logically related results from a protein detection, for example to represent conflicting assignments of peptides to proteins.

ProteinAmbiguityGroupType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinAmbiguityGroupType
 
proteinDescr - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
 
proteinDescr - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
proteinDetection - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisCollectionType
 
proteinDetectionHypothesis - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinAmbiguityGroupType
 
ProteinDetectionHypothesisType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

A single result of the ProteinDetection analysis (i.e.

ProteinDetectionHypothesisType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionHypothesisType
 
proteinDetectionList - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisDataType
 
proteinDetectionListRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionType
 
ProteinDetectionListType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

The protein list resulting from a protein detection process.

ProteinDetectionListType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionListType
 
proteinDetectionProtocol - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisProtocolCollectionType
 
proteinDetectionProtocolRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionType
 
ProteinDetectionProtocolType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

The parameters and settings of a ProteinDetection process.

ProteinDetectionProtocolType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionProtocolType
 
ProteinDetectionType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

An Analysis which assembles a set of peptides (e.g.

ProteinDetectionType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionType
 
ProteinDigester - Class in org.expasy.mzjava.proteomics.mol.digest

A ProteinDigester is defined by a name and a cleavage site matcher
 that match the sites to be digested.

ProteinDigester(ProteinDigester.Builder) - Constructor for class org.expasy.mzjava.proteomics.mol.digest.ProteinDigester
 
ProteinDigester.Builder - Class in org.expasy.mzjava.proteomics.mol.digest
 
ProteinDigester.Builder(Protease) - Constructor for class org.expasy.mzjava.proteomics.mol.digest.ProteinDigester.Builder
 
ProteinDigester.Builder(CleavageSiteMatcher) - Constructor for class org.expasy.mzjava.proteomics.mol.digest.ProteinDigester.Builder
 
ProteinDigester.CleavageSiteIteration - Enum in org.expasy.mzjava.proteomics.mol.digest
 
ProteinFactory - Class in org.expasy.mzjava.core.mol.polymer.prot

This factory creates new instance of Protein by wrapping biojava Sequence or delegating to biojava objects.

proteinMw - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
 
proteinMw - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
ProteinPilotModificationResolver - Class in org.expasy.mzjava.proteomics.io.ms.ident

The default ProteinPilot Modification Resolver

ProteinPilotModificationResolver() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.ProteinPilotModificationResolver
 
ProteinPilotPsmReader - Class in org.expasy.mzjava.proteomics.io.ms.ident

A peptide spectrum match reader for ProteinPilot Peptide Summary Overview tsv file.

ProteinPilotPsmReader() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.ProteinPilotPsmReader

Default constructor with default resolver ProteinPilotModificationResolver

ProteinPilotPsmReader(ModificationResolver) - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.ProteinPilotPsmReader
 
proteinTerminus - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
 
ProtocolApplicationType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

The use of a protocol with the requisite Parameters and ParameterValues.

ProtocolApplicationType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProtocolApplicationType
 
PROTON_MASS - Static variable in class org.expasy.mzjava.core.mol.MassCalculator
 
provider - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType
 
ProviderType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

The provider of the document in terms of the Contact and the software the produced the document instance.

ProviderType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProviderType
 
psmBuffer - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader
 
psmInfoParser - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader
 
PsmReader - Interface in org.expasy.mzjava.proteomics.io.ms.ident

A Peptide spectrum match (PSM) reader.

PSMReaderCallback - Interface in org.expasy.mzjava.proteomics.io.ms.ident

This object method is callback when a PSM is read by a PsmReader.

PspcSimFunc<X extends PeakAnnotation,Y extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.spectrasim

Poisson shared peak count similarity function.

PspcSimFunc(int, Tolerance) - Constructor for class org.expasy.mzjava.core.ms.spectrasim.PspcSimFunc
 
PspcSimFunc(int, PeakListAligner<X, Y>, PeakPairProcessor<X, Y>...) - Constructor for class org.expasy.mzjava.core.ms.spectrasim.PspcSimFunc
 
publication - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType
 
publisher - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType
 
put(PeptideSpectrum) - Method in interface org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumCache
 
put(PeptideSpectrum) - Method in class org.expasy.mzjava.proteomics.ms.dbsearch.SoftRefPepSpectrumCache
 
put(SpectrumIdentifier, PeptideMatch) - Method in class org.expasy.mzjava.proteomics.ms.ident.SearchResultMap
 
putOverrideUnimod(String, Modification) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodModificationResolver

Override the modification that the name is mapped to in Unimod.

putTranslate(String, String) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodModificationResolver

Add a translation for the name.





Q

quadsToDoubles(byte[], double[]) - Static method in class org.expasy.mzjava.core.io.ms.spectrum.BytesUtils
 
quadsToFloats(byte[], float[]) - Static method in class org.expasy.mzjava.core.io.ms.spectrum.BytesUtils
 
quadToFloat(byte...) - Static method in class org.expasy.mzjava.core.io.ms.spectrum.BytesUtils

Convert four bytes into one float

quantLabelMasses - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioTimestamp
 
qValues - Variable in class org.expasy.mzjava.stats.statscores.ScoreStatistics
 




R

rangeCheck(int) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList

Checks if the given index is in range.

rank - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType
 
RankNormalizer<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist.peaktransformer

Class to rank apply intensities.

RankNormalizer() - Constructor for class org.expasy.mzjava.core.ms.peaklist.peaktransformer.RankNormalizer
 
RankNormalizer(TiesStrategy) - Constructor for class org.expasy.mzjava.core.ms.peaklist.peaktransformer.RankNormalizer
 
ratio - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioContribution
 
ratio - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult
 
ratioConfidenceInterval95(int, int) - Static method in class org.expasy.mzjava.stats.PoissonUtils

Calculates the 95% confidence interval for the ratio of the two means.

rawData - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary
 
rawDataType - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary
 
read(Decoder) - Method in class org.expasy.mzjava.avro.io.AbstractPeakListReader
 
read(Decoder) - Method in interface org.expasy.mzjava.avro.io.AvroReader

Read the object from the decoder

read(Decoder) - Method in class org.expasy.mzjava.avro.io.CompositionReader
 
read(Decoder) - Method in class org.expasy.mzjava.avro.io.LibPeakAnnotationReader
 
read(Decoder) - Method in class org.expasy.mzjava.avro.io.MsnSpectrumMetaDataReader
 
read(Decoder) - Method in class org.expasy.mzjava.avro.io.MsnSpectrumReader
 
read(Decoder) - Method in class org.expasy.mzjava.avro.io.NumericMassReader
 
read(Decoder) - Method in class org.expasy.mzjava.avro.io.PeakListReader
 
read(Decoder) - Method in class org.expasy.mzjava.avro.io.PeakReader
 
read(Decoder) - Method in class org.expasy.mzjava.avro.io.RetentionTimeDiscreteReader
 
read(Decoder) - Method in class org.expasy.mzjava.avro.io.RetentionTimeIntervalReader
 
read(Decoder) - Method in class org.expasy.mzjava.avro.io.RetentionTimeListReader
 
read(Decoder) - Method in class org.expasy.mzjava.avro.io.ScanNumberDiscreteReader
 
read(Decoder) - Method in class org.expasy.mzjava.avro.io.ScanNumberIntervalReader
 
read(Decoder) - Method in class org.expasy.mzjava.avro.io.ScanNumberListReader
 
read(Decoder) - Method in class org.expasy.mzjava.avro.io.UUIDReader
 
read(String, String) - Method in class org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCTReader
 
read(Decoder) - Method in class org.expasy.mzjava.proteomics.avro.io.ModificationReader
 
read(Decoder) - Method in class org.expasy.mzjava.proteomics.avro.io.PepFragAnnotationReader
 
read(Decoder) - Method in class org.expasy.mzjava.proteomics.avro.io.PepLibPeakAnnotationReader
 
read(Decoder) - Method in class org.expasy.mzjava.proteomics.avro.io.PeptideConsensusSpectrumReader
 
read(Decoder) - Method in class org.expasy.mzjava.proteomics.avro.io.PeptideFragmentReader
 
read(Decoder) - Method in class org.expasy.mzjava.proteomics.avro.io.PeptideReader
 
read(Decoder) - Method in class org.expasy.mzjava.proteomics.avro.io.PeptideSpectrumReader
 
read(Kryo, Input, Class<O>) - Method in class org.expasy.mzjava.spark.KryoAvroSerializer
 
readAnalysisResult(MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit, PeptideMatch) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader
 
readArray(AbstractAvroReader<E>, C, Decoder) - Method in class org.expasy.mzjava.avro.io.AbstractAvroReader

Read an array that contains records into collection

readDouble(byte[], int) - Static method in class org.expasy.mzjava.hadoop.io.DefaultSpectrumKeyRawComparator

Parse a double from a byte array.

readFields(DataInput) - Method in class org.expasy.mzjava.hadoop.io.AvroWritable
 
readFields(DataInput) - Method in class org.expasy.mzjava.hadoop.io.SpectrumKey
 
readFile - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader
 
readInt(byte[], int) - Static method in class org.expasy.mzjava.hadoop.io.DefaultSpectrumKeyRawComparator

Parse an integer from a byte array.

readLIN(List<String>) - Method in class org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCTReader
 
readLong(byte[], int) - Static method in class org.expasy.mzjava.hadoop.io.DefaultSpectrumKeyRawComparator

Parse a long from a byte array.

readMap(Function<String, K>, Function<Decoder, V>, Decoder) - Method in class org.expasy.mzjava.avro.io.AbstractAvroReader
 
readMap(Function<String, K>, Decoder) - Method in class org.expasy.mzjava.avro.io.AbstractAvroReader
 
readMap(Function<String, K>, AbstractAvroReader<V>, Decoder) - Method in class org.expasy.mzjava.avro.io.AbstractAvroReader
 
readOptional(AbstractAvroReader<C>, Decoder) - Method in class org.expasy.mzjava.avro.io.AbstractAvroReader

Read an union of C and null and return a Optional.of() or Optional.absent()

readPeptide(String, SequenceCollectionType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.MzIdentMlReader
 
readPeptideIDProteinMap(MzIdentMLType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.MzIdentMlReader
 
readPeptideIDProteinPositionMap(MzIdentMLType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.MzIdentMlReader
 
readRES(List<String>) - Method in class org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCTReader
 
readSequence(PeptideBuilder, Decoder) - Method in class org.expasy.mzjava.proteomics.avro.io.AbstractAminoAcidSequenceReader
 
readStringArray(C, Decoder) - Method in class org.expasy.mzjava.avro.io.AbstractAvroReader

Read an the String's from an array into the provided collection.

readUnion(Class<C>, Decoder) - Method in class org.expasy.mzjava.avro.io.AbstractAvroReader

Read a union

readUnionArray(Class<C>, Collection<C>, Decoder) - Method in class org.expasy.mzjava.avro.io.AbstractAvroReader

Read an array that contains unions of classes that have recordSuperclass as a superclass

REAL - Static variable in class org.expasy.mzjava.utils.RegexConstants

float expression

recordId - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT
 
RegexConstants - Class in org.expasy.mzjava.utils

A list of static regular expressions.

RegexScanNumTitleParser - Class in org.expasy.mzjava.core.io.ms.spectrum.mgf

Implementation of a title parser that uses a regex pattern to extract the scan number from the title

RegexScanNumTitleParser(Pattern) - Constructor for class org.expasy.mzjava.core.io.ms.spectrum.mgf.RegexScanNumTitleParser
 
registerClasses(Kryo) - Method in class org.expasy.mzjava.spark.MzJavaKryoRegistrator
 
registerUnion(Class, U...) - Method in class org.expasy.mzjava.avro.io.AvroIO

Register a union

reject - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraResult.Intensity
 
releaseDate - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchDatabaseType
 
remove(A) - Method in class org.expasy.mzjava.core.ms.spectrum.AnnotatedPeak

Remove annotation from this AnnotatedPeak

remove(int) - Method in class org.expasy.mzjava.core.ms.spectrum.AnnotatedPeak

Removes the annotation at the specified position in this peak.

remove(Object) - Method in class org.expasy.mzjava.glycomics.mol.NodeSet
 
removeAll(Collection<?>) - Method in class org.expasy.mzjava.glycomics.mol.NodeSet
 
removeAnnotation(A, int) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
 
removeAnnotation(A, int) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Remove the annotation from the peak at index

removeAnnotation(A, int) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
removeConsistencyChecks(Set<MzxmlReader.ConsistencyCheck>) - Method in class org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader
 
removeConsistencyChecks(Set<PepXmlWriter.ConsistencyCheck>) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriter
 
removeEdge(SimEdge<V>) - Method in class org.expasy.mzjava.core.ms.cluster.JungSimGraphWrapper
 
removeExtension(String) - Static method in class org.expasy.mzjava.proteomics.ms.ident.SearchResultMap

Removes the file extension

removeVertex(V) - Method in class org.expasy.mzjava.core.ms.cluster.JungSimGraphWrapper
 
replace(Set<AminoAcid>, AminoAcid) - Method in class org.expasy.mzjava.proteomics.mol.Peptide
 
replacementResidue - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SubstitutionModificationType
 
reportAnnotations(PeakList<PepFragAnnotation>, int, List<PepFragAnnotation>) - Method in class org.expasy.mzjava.proteomics.ms.fragment.PeptideFragmentAnnotator
 
required - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.PepNeutralLossT
 
reset() - Method in class org.expasy.mzjava.proteomics.mol.Protein.Builder
 
reset() - Method in class org.expasy.mzjava.utils.Counter

Reset the count to 0

resetCursor() - Method in class org.expasy.mzjava.core.ms.peaklist.ArrayCursor
 
resetCursor() - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakCursor

Reset this cursor

resetCursor() - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.TopNList

Reset the cursor

resetIndeterminateBar() - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar.View
 
residue - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MassTableType
 
residues - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ModificationType
 
residues - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchModificationType
 
ResidueType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

Java class for ResidueType complex type.

ResidueType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ResidueType
 
resolve(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.ProteinPilotModificationResolver
 
resolve(String) - Method in class org.expasy.mzjava.proteomics.mol.modification.CompositeModResolver
 
resolve(String) - Method in interface org.expasy.mzjava.proteomics.mol.modification.ModificationResolver

Create or fetch a modification for input

resolve(String) - Method in class org.expasy.mzjava.proteomics.mol.modification.NumericModificationResolver
 
resolve(String) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodModificationResolver
 
resolve(ModificationMatch) - Method in interface org.expasy.mzjava.proteomics.ms.ident.ModificationMatchResolver
 
resolve(ModificationMatch) - Method in class org.expasy.mzjava.proteomics.ms.ident.ModListModMatchResolver
 
resolveAnnotations(String, Peptide) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.msp.MspAnnotationResolver
 
resolveAnnotations(String, Peptide) - Method in interface org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.AnnotationResolver
 
resolveAnnotations(String, Peptide) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.SkipAnnotationResolver
 
resolveAnnotations(String, Peptide) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.SpectraStAnnotationResolver
 
resolveComposition(String) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.msp.MspAnnotationResolver
 
resolveComposition(String) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.SpectraStAnnotationResolver
 
resolveMod(ModificationMatch) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader
 
resultRead(SpectrumIdentifier, PeptideMatch) - Method in interface org.expasy.mzjava.proteomics.io.ms.ident.PSMReaderCallback

Handle a peptide spectrum match

retainAll(Collection<?>) - Method in class org.expasy.mzjava.glycomics.mol.NodeSet
 
retainDigest(Protein, Peptide, int) - Method in class org.expasy.mzjava.proteomics.mol.digest.AcceptAllDigestionController

Process DigestedPeptide with/without missed cleavages

retainDigest(Protein, Peptide, int) - Method in interface org.expasy.mzjava.proteomics.mol.digest.DigestionController

Process DigestedPeptide with/without missed cleavages

retainDigest(Protein, Peptide, int) - Method in class org.expasy.mzjava.proteomics.mol.digest.LengthDigestionController
 
retainPeptidesOfLength(int, int) - Method in interface org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumDB.DigestDSL

Only retain peptides that have a length >= min and <= max

retainSemiDigest(Peptide) - Method in class org.expasy.mzjava.proteomics.mol.digest.AcceptAllDigestionController

Process Semi digested products.

retainSemiDigest(Peptide) - Method in interface org.expasy.mzjava.proteomics.mol.digest.DigestionController

Process Semi digested products.

retainSemiDigest(Peptide) - Method in class org.expasy.mzjava.proteomics.mol.digest.LengthDigestionController
 
RETENTION_TIME_CV - Static variable in class org.expasy.mzjava.proteomics.io.ms.ident.MzIdentMlReader
 
RetentionTime - Interface in org.expasy.mzjava.core.ms.spectrum

A retention time can either be a discrete time number or a time interval.

RetentionTimeComparator - Class in org.expasy.mzjava.core.ms.spectrum

Date: 16/04/12
 Time: 3:21 PM

RetentionTimeComparator() - Constructor for class org.expasy.mzjava.core.ms.spectrum.RetentionTimeComparator
 
RetentionTimeDiscrete - Class in org.expasy.mzjava.core.ms.spectrum

The retention time is the time it takes for a particular
 analyte to pass through the liquid chromatography system (from the column
 inlet to the detector) under set conditions.

RetentionTimeDiscrete(double, TimeUnit) - Constructor for class org.expasy.mzjava.core.ms.spectrum.RetentionTimeDiscrete

Constructor for a retention time.

RetentionTimeDiscrete(RetentionTimeDiscrete) - Constructor for class org.expasy.mzjava.core.ms.spectrum.RetentionTimeDiscrete

Copy constructor

RetentionTimeDiscreteReader - Class in org.expasy.mzjava.avro.io
 
RetentionTimeDiscreteReader() - Constructor for class org.expasy.mzjava.avro.io.RetentionTimeDiscreteReader
 
RetentionTimeDiscreteWriter - Class in org.expasy.mzjava.avro.io
 
RetentionTimeDiscreteWriter() - Constructor for class org.expasy.mzjava.avro.io.RetentionTimeDiscreteWriter
 
RetentionTimeInterval - Class in org.expasy.mzjava.core.ms.spectrum

A retention time that stores a time interval.

RetentionTimeInterval(double, double, TimeUnit) - Constructor for class org.expasy.mzjava.core.ms.spectrum.RetentionTimeInterval

Constructor for a RetentionTimeInterval from startTime to endTime.

RetentionTimeInterval(RetentionTimeInterval) - Constructor for class org.expasy.mzjava.core.ms.spectrum.RetentionTimeInterval

Copy constructor

RetentionTimeIntervalReader - Class in org.expasy.mzjava.avro.io
 
RetentionTimeIntervalReader() - Constructor for class org.expasy.mzjava.avro.io.RetentionTimeIntervalReader
 
RetentionTimeIntervalWriter - Class in org.expasy.mzjava.avro.io
 
RetentionTimeIntervalWriter() - Constructor for class org.expasy.mzjava.avro.io.RetentionTimeIntervalWriter
 
RetentionTimeList - Class in org.expasy.mzjava.core.ms.spectrum
 
RetentionTimeList() - Constructor for class org.expasy.mzjava.core.ms.spectrum.RetentionTimeList
 
RetentionTimeList(RetentionTimeList) - Constructor for class org.expasy.mzjava.core.ms.spectrum.RetentionTimeList
 
RetentionTimeList(RetentionTime...) - Constructor for class org.expasy.mzjava.core.ms.spectrum.RetentionTimeList
 
RetentionTimeListReader - Class in org.expasy.mzjava.avro.io
 
RetentionTimeListReader() - Constructor for class org.expasy.mzjava.avro.io.RetentionTimeListReader
 
RetentionTimeListWriter - Class in org.expasy.mzjava.avro.io
 
RetentionTimeListWriter() - Constructor for class org.expasy.mzjava.avro.io.RetentionTimeListWriter
 
retentionTimeSec - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
 
RetentionTimeSplitter - Class in org.expasy.mzjava.utils.function

Splits a list of MsnSpectra into sub lists.

RetentionTimeSplitter(RetentionTimeDiscrete) - Constructor for class org.expasy.mzjava.utils.function.RetentionTimeSplitter
 
rewriteNameSpace(Class) - Method in class org.expasy.mzjava.avro.io.AvroIO

Rewrite the class namespace to the serialization namespace

rightValley - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak
 
rightValley - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak
 
RingType - Enum in org.expasy.mzjava.glycomics.mol
 
ROCTable - Class in org.expasy.mzjava.stats
 
ROCTable(double, double, double) - Constructor for class org.expasy.mzjava.stats.ROCTable
 
role - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ContactRoleType
 
RoleType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

The roles (lab equipment sales, contractor, etc.) the Contact fills.

RoleType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.RoleType
 
root - Variable in class org.expasy.mzjava.glycomics.mol.SaccharideGraph
 
rtReader - Variable in class org.expasy.mzjava.proteomics.avro.io.PeptideConsensusSpectrumReader
 
rtWriter - Variable in class org.expasy.mzjava.proteomics.avro.io.PeptideConsensusSpectrumWriter
 
run(C) - Method in interface org.expasy.mzjava.script.ScriptConfiguredTool

Execute the tool with the given configuration

run(String[], ScriptConfiguredTool<C>) - Static method in class org.expasy.mzjava.script.ScriptConfiguredToolRunner

Runs the given ScriptedTool by calling ScriptConfiguredTool#run(C), after
 creating the configuration from the script in the scriptFile.

run(File, ScriptConfiguredTool<C>) - Static method in class org.expasy.mzjava.script.ScriptConfiguredToolRunner

Runs the given ScriptedTool by calling ScriptConfiguredTool#run(C), after
 creating the configuration from the script in the scriptFile.

run(File, ScriptConfiguredTool<C>, String[]) - Static method in class org.expasy.mzjava.script.ScriptConfiguredToolRunner

Runs the given ScriptedTool by calling ScriptConfiguredTool#run(C), after
 creating the configuration from the script in the scriptFile.





S

S - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
S_MASS - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
SaccharideGraph - Class in org.expasy.mzjava.glycomics.mol
 
SaccharideGraph(Monosaccharide) - Constructor for class org.expasy.mzjava.glycomics.mol.SaccharideGraph
 
SaccharideGraph.AbstractBuilder<G extends SaccharideGraph> - Class in org.expasy.mzjava.glycomics.mol

A builder to build Glycan.

SaccharideGraph.AbstractBuilder() - Constructor for class org.expasy.mzjava.glycomics.mol.SaccharideGraph.AbstractBuilder
 
SaccharideGraph.AbstractBuilder.BuildSate - Enum in org.expasy.mzjava.glycomics.mol
 
SaccharideGraph.Traversal - Enum in org.expasy.mzjava.glycomics.mol
 
sameModPeptide(PeptideMatch) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Returns true if this PeptideMatch and match have the same peptide
 sequence and modifications.

sameScanRange - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioSummary
 
sample - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisSampleCollectionType
 
sampleEnzyme - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary
 
sampleRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType
 
sampleRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SubSampleType
 
SampleType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

A description of the sample analysed by mass spectrometry using CVParams or UserParams.

SampleType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SampleType
 
save(File) - Method in class org.expasy.mzjava.stats.ScatterPlotTable
 
save(Writer, String) - Method in class org.expasy.mzjava.stats.ScatterPlotTable
 
SCAN_NUMBER_CV - Static variable in class org.expasy.mzjava.proteomics.io.ms.ident.MzIdentMlReader
 
SCAN_NUMBER_UNKNOWN - Static variable in interface org.expasy.mzjava.core.ms.spectrum.ScanNumber
 
ScanNumber - Interface in org.expasy.mzjava.core.ms.spectrum

A scan number can either be a discrete number or a number interval.

ScanNumberDiscrete - Class in org.expasy.mzjava.core.ms.spectrum
 
ScanNumberDiscrete(int) - Constructor for class org.expasy.mzjava.core.ms.spectrum.ScanNumberDiscrete
 
ScanNumberDiscreteReader - Class in org.expasy.mzjava.avro.io
 
ScanNumberDiscreteReader() - Constructor for class org.expasy.mzjava.avro.io.ScanNumberDiscreteReader
 
ScanNumberDiscreteWriter - Class in org.expasy.mzjava.avro.io
 
ScanNumberDiscreteWriter() - Constructor for class org.expasy.mzjava.avro.io.ScanNumberDiscreteWriter
 
ScanNumberIncrementer - Class in org.expasy.mzjava.external.io.ms.spectrum.mzml
 
ScanNumberIncrementer(int) - Constructor for class org.expasy.mzjava.external.io.ms.spectrum.mzml.ScanNumberIncrementer
 
ScanNumberIndexSearchResultMap - Class in org.expasy.mzjava.proteomics.ms.ident

Maps the scan number of the pep xml to the index of the spectrum and corrects for index offsets.

ScanNumberIndexSearchResultMap() - Constructor for class org.expasy.mzjava.proteomics.ms.ident.ScanNumberIndexSearchResultMap
 
ScanNumberInterval - Class in org.expasy.mzjava.core.ms.spectrum
 
ScanNumberInterval(int, int) - Constructor for class org.expasy.mzjava.core.ms.spectrum.ScanNumberInterval
 
ScanNumberIntervalReader - Class in org.expasy.mzjava.avro.io
 
ScanNumberIntervalReader() - Constructor for class org.expasy.mzjava.avro.io.ScanNumberIntervalReader
 
ScanNumberIntervalWriter - Class in org.expasy.mzjava.avro.io
 
ScanNumberIntervalWriter() - Constructor for class org.expasy.mzjava.avro.io.ScanNumberIntervalWriter
 
ScanNumberList - Class in org.expasy.mzjava.core.ms.spectrum
 
ScanNumberList() - Constructor for class org.expasy.mzjava.core.ms.spectrum.ScanNumberList

Construct an empty ScanNumberList

ScanNumberList(ScanNumberList) - Constructor for class org.expasy.mzjava.core.ms.spectrum.ScanNumberList

Copy constructor

ScanNumberList(int...) - Constructor for class org.expasy.mzjava.core.ms.spectrum.ScanNumberList

Construct a ScanNumberList that contains a ScanNumberDiscrete for each entry in scanNumbers

ScanNumberList(ScanNumber...) - Constructor for class org.expasy.mzjava.core.ms.spectrum.ScanNumberList

Construct a ScanNumberList that contains the ScanNumber's in scanNumbers

ScanNumberListReader - Class in org.expasy.mzjava.avro.io
 
ScanNumberListReader() - Constructor for class org.expasy.mzjava.avro.io.ScanNumberListReader
 
ScanNumberListWriter - Class in org.expasy.mzjava.avro.io
 
ScanNumberListWriter() - Constructor for class org.expasy.mzjava.avro.io.ScanNumberListWriter
 
ScanNumberSearchResultMap - Class in org.expasy.mzjava.proteomics.ms.ident
 
ScanNumberSearchResultMap() - Constructor for class org.expasy.mzjava.proteomics.ms.ident.ScanNumberSearchResultMap
 
ScatterPlotTable - Class in org.expasy.mzjava.stats
 
ScatterPlotTable() - Constructor for class org.expasy.mzjava.stats.ScatterPlotTable
 
ScatterPlotTable(String, String) - Constructor for class org.expasy.mzjava.stats.ScatterPlotTable
 
ScoreStatistics - Class in org.expasy.mzjava.stats.statscores
 
ScoreStatistics() - Constructor for class org.expasy.mzjava.stats.statscores.ScoreStatistics
 
ScoreStatistics(float[], float[]) - Constructor for class org.expasy.mzjava.stats.statscores.ScoreStatistics
 
ScoreStatistics(float[], float[], ScoreStatistics.SortAction) - Constructor for class org.expasy.mzjava.stats.statscores.ScoreStatistics
 
ScoreStatistics(double[], double[]) - Constructor for class org.expasy.mzjava.stats.statscores.ScoreStatistics
 
ScoreStatistics(double[], double[], ScoreStatistics.SortAction) - Constructor for class org.expasy.mzjava.stats.statscores.ScoreStatistics
 
ScoreStatistics(TFloatList, TFloatList) - Constructor for class org.expasy.mzjava.stats.statscores.ScoreStatistics
 
ScoreStatistics(TFloatList, TFloatList, ScoreStatistics.SortAction) - Constructor for class org.expasy.mzjava.stats.statscores.ScoreStatistics
 
ScoreStatistics(TDoubleList, TDoubleList) - Constructor for class org.expasy.mzjava.stats.statscores.ScoreStatistics
 
ScoreStatistics(TDoubleList, TDoubleList, ScoreStatistics.SortAction) - Constructor for class org.expasy.mzjava.stats.statscores.ScoreStatistics
 
ScoreStatistics.SortAction - Enum in org.expasy.mzjava.stats.statscores
 
ScriptConfiguredTool<C> - Interface in org.expasy.mzjava.script

A tool interface that allows the tool to be configured using a scripting
 language such as javascript, groovy or python.

ScriptConfiguredToolRunner - Class in org.expasy.mzjava.script

A utility to help run ScriptConfiguredTools.

sdSimScore - Variable in class org.expasy.mzjava.core.ms.cluster.SpectrumClusterEvaluator
 
searchCVParam(List<CVParam>, String...) - Static method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.CVParamHelper

Search a list of CVParams from given identifier(s)

searchCVParams(List<CVParam>, String...) - Static method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.CVParamHelper

Search a list of CVParams from given identifier(s)

searchDatabase - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.InputsType
 
searchDatabase - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
 
searchDatabase(File) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder.Builder

Set the search_database element of element search_summary

searchDatabaseRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DBSequenceType
 
searchDatabaseRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchDatabaseRefType
 
searchDatabaseRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationType
 
SearchDatabaseRefType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

One of the search databases used.

SearchDatabaseRefType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchDatabaseRefType
 
SearchDatabaseType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

A database for searching mass spectra.

SearchDatabaseType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchDatabaseType
 
searchEngine - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
 
searchHit - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult
 
searchHitRank(int) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder.Builder

Set the number of maximum result hits retained

searchId - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
 
searchId - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult
 
searchModification - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ModificationParamsType
 
SearchModificationType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

Specification of a search modification as parameter for a spectra search.

SearchModificationType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchModificationType
 
searchResult - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
 
SearchResultMap - Class in org.expasy.mzjava.proteomics.ms.ident
 
SearchResultMap() - Constructor for class org.expasy.mzjava.proteomics.ms.ident.SearchResultMap
 
searchRetentionTime(List<CVParam>, String) - Static method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.CVParamHelper
 
searchScore - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
searchScoreSummary - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.PeptideprophetResult
 
searchSpecification - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
 
searchSummary - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary
 
searchType - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType
 
SEdge<N extends GlycanNode,L extends Linkage> - Class in org.expasy.mzjava.glycomics.mol
 
seekNextCharacters(XMLEventReader) - Static method in class org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader.XMLEventUtils
 
seekStartElement(XMLEventReader, String) - Static method in class org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader.XMLEventUtils

Seek to the next start tag

semi() - Method in class org.expasy.mzjava.proteomics.mol.digest.ProteinDigester.Builder
 
semiSpecific - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymeType
 
sense - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity
 
seq - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DBSequenceType
 
sequence - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SequenceSearchConstraint
 
sequenceCollection - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType
 
SequenceCollectionType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

The collection of sequences (DBSequence or Peptide) identified and their relationship between each other (PeptideEvidence) to be referenced elsewhere in the results.

SequenceCollectionType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SequenceCollectionType
 
sequenceSearchConstraint - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
 
set(T) - Method in class org.expasy.mzjava.hadoop.io.AbstractAvroWritable
 
set(PL) - Method in class org.expasy.mzjava.hadoop.io.AbstractPeakListValue
 
set(Peak) - Method in class org.expasy.mzjava.hadoop.io.SpectrumKey
 
set(int, double) - Method in class org.expasy.mzjava.hadoop.io.SpectrumKey
 
setAbsolute(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraResult.Intensity

Sets the value of the absolute property.

setAccession(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.CVParamType

Sets the value of the accession property.

setAccession(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DBSequenceType

Sets the value of the accession property.

setAccessionId(String) - Method in class org.expasy.mzjava.proteomics.mol.Protein.Builder
 
setActivationMethod(ActivationMethodType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery

Sets the value of the activationMethod property.

setActivityDate(XMLGregorianCalendar) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProtocolApplicationType

Sets the value of the activityDate property.

setAdditionalSearchParams(ParamListType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType

Sets the value of the additionalSearchParams property.

setAllNttProb(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.PeptideprophetResult

Sets the value of the allNttProb property.

setAmbiguousAminoAcidAction(DigestDB.AmbiguousAminoAcidAction) - Method in class org.expasy.mzjava.proteomics.ms.dbsearch.ArrayDigestDB.Builder

Set what action the ArrayDigestDB is to take if ambiguous amino acids are encountered.

setAminoacid(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification

Sets the value of the aminoacid property.

setAnalysis(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.AnalysisSummary

Sets the value of the analysis property.

setAnalysis(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp

Sets the value of the analysis property.

setAnalysis(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult

Sets the value of the analysis property.

setAnalysis(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.PeptideprophetResult

Sets the value of the analysis property.

setAnalysisCollection(AnalysisCollectionType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType

Sets the value of the analysisCollection property.

setAnalysisData(AnalysisDataType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DataCollectionType

Sets the value of the analysisData property.

setAnalysisParams(ParamListType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionProtocolType

Sets the value of the analysisParams property.

setAnalysisProtocolCollection(AnalysisProtocolCollectionType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType

Sets the value of the analysisProtocolCollection property.

setAnalysisSampleCollection(AnalysisSampleCollectionType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType

Sets the value of the analysisSampleCollection property.

setAnalysisSoftwareList(AnalysisSoftwareListType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType

Sets the value of the analysisSoftwareList property.

setAnalysisSoftwareRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionProtocolType

Sets the value of the analysisSoftwareRef property.

setAnalysisSoftwareRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProviderType

Sets the value of the analysisSoftwareRef property.

setAnalysisSoftwareRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType

Sets the value of the analysisSoftwareRef property.

setAnnotationParameters(Tolerance, PeptideFragmenter) - Method in interface org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.AnnotationParametersSetter
 
setAnnotationParameters(Tolerance, PeptideFragmenter) - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.Builder
 
setAny(Object) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.AnalysisSummary

Sets the value of the any property.

setAny(Object) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp

Sets the value of the any property.

setAny(Object) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult

Sets the value of the any property.

setApproved(Boolean) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT

Sets the value of the approved property.

setApproved(boolean) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodMod.Builder

Set the approved flag

setArea(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak

Sets the value of the area property.

setArea(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak

Sets the value of the area property.

setAreaError(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak

Sets the value of the areaError property.

setAreaError(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak

Sets the value of the areaError property.

setAreaFlag(long) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioPeptideData

Sets the value of the areaFlag property.

setAreaFlag(BigInteger) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioSummary

Sets the value of the areaFlag property.

setArray(T...) - Method in class org.expasy.mzjava.utils.ArrayIndexComparator
 
setArrays() - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList.AbstractMergePeakSink
 
setAsapratioLcHeavypeak(AsapratioLcHeavypeak) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioContribution

Sets the value of the asapratioLcHeavypeak property.

setAsapratioLcLightpeak(AsapratioLcLightpeak) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioContribution

Sets the value of the asapratioLcLightpeak property.

setAsapratioPeptideData(AsapratioPeptideData) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioResult

Sets the value of the asapratioPeptideData property.

setAssumedCharge(BigInteger) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery

Sets the value of the assumedCharge property.

setAssumedCharge(int) - Method in class org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
 
setAuditCollection(AuditCollectionType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType

Sets the value of the auditCollection property.

setAuthor(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioSummary

Sets the value of the author property.

setAuthor(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioSummary

Sets the value of the author property.

setAuthors(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType

Sets the value of the authors property.

setAvgeMass(Double) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.CompositionT

Sets the value of the avgeMass property.

setAvgMassDelta(Double) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ModificationType

Sets the value of the avgMassDelta property.

setAvgMassDelta(Double) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SubstitutionModificationType

Sets the value of the avgMassDelta property.

setBackground(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak

Sets the value of the background property.

setBackground(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak

Sets the value of the background property.

setBarLength(int) - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar

Set the progress bar length.

setBarLength(int, boolean) - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar.View

Set the progress bar length.

setBaseName(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary

Sets the value of the baseName property.

setBaseName(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary

Sets the value of the baseName property.

setBinArrayBounds(double, double, double) - Method in class org.expasy.mzjava.utils.IntervalList

The binned array indexing the intervals goes from minVal to maxVal with bin size binWidth.

setBinary(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification

Sets the value of the binary property.

setCalcNeutralPepMass(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Sets the value of the calcNeutralPepMass property.

setCalcPI(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Sets the value of the calcPI property.

setCalculatedMassToCharge(Double) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType

Sets the value of the calculatedMassToCharge property.

setCalculatedPI(Float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType

Sets the value of the calculatedPI property.

setCentroidingPreference(int) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary

Sets the value of the centroidingPreference property.

setChannel(long) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraResult.Intensity

Sets the value of the channel property.

setChannel(long) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.FragmentMasses

Sets the value of the channel property.

setChannel(long) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.IsotopicContributions.ContributingChannel.AffectedChannel

Sets the value of the channel property.

setChannel(long) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.IsotopicContributions.ContributingChannel

Sets the value of the channel property.

setChannelCode(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary

Sets the value of the channelCode property.

setCharge(int) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.IonTypeType

Sets the value of the charge property.

setCharge(BigInteger) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioContribution

Sets the value of the charge property.

setCharge(int) - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation.Builder
 
setChargeState(int) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType

Sets the value of the chargeState property.

setCidIndex(int) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioPeptideData

Sets the value of the cidIndex property.

setClassification(String) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.SpecificityT

Sets the value of the classification property.

setCleavedRoot(Monosaccharide, FragmentType, CutIndexes) - Method in class org.expasy.mzjava.glycomics.mol.GlycanFragment.Builder

Set the cleaved root of the Glycan Fragments.

setCleavedRoot(Monosaccharide, FragmentType, Composition, CutIndexes) - Method in class org.expasy.mzjava.glycomics.mol.GlycanFragment.Builder

Set the cleaved root of the Glycan Fragments.

setCode(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AmbiguousResidueType

Sets the value of the code property.

setCode(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ResidueType

Sets the value of the code property.

setCollisionEnergy(Float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery

Sets the value of the collisionEnergy property.

setColumnNumber(int) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader.ParseContext
 
setComment(String) - Method in class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum

Set the comment

setComment(String) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.LibrarySpectrumBuilder
 
setComment(String) - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum

Set the comment

setCompensationVoltage(Float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery

Sets the value of the compensationVoltage property.

setComposition(String) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.CompositionT

Sets the value of the composition property.

setComposition(TObjectIntMap<Atom>) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodMod.Builder

Set the atom counter map that contains the composition

setConsensusParameters(double, double, AbstractMergePeakFilter.IntensityMode) - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.Builder
 
setConsensusParameters(double, double, AbstractMergePeakFilter.IntensityMode) - Method in interface org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.ConsensusParametersSetter
 
setContactRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ContactRoleType

Sets the value of the contactRef property.

setContactRole(ContactRoleType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisSoftwareType

Sets the value of the contactRole property.

setContactRole(ContactRoleType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProviderType

Sets the value of the contactRole property.

setCorrection(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.IsotopicContributions.ContributingChannel.AffectedChannel

Sets the value of the correction property.

setCreationDate(XMLGregorianCalendar) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType

Sets the value of the creationDate property.

setCTermGain(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymeType

Sets the value of the cTermGain property.

setCustomizations(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisSoftwareType

Sets the value of the customizations property.

setCut(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity

Sets the value of the cut property.

setCvList(CVListType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType

Sets the value of the cvList property.

setCvParam(CVParamType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FileFormatType

Sets the value of the cvParam property.

setCvParam(CVParamType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.IonTypeType

Sets the value of the cvParam property.

setCvParam(CVParamType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ParamType

Sets the value of the cvParam property.

setCvParam(CVParamType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.RoleType

Sets the value of the cvParam property.

setCvParam(CVParamType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIDFormatType

Sets the value of the cvParam property.

setCvRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.CVParamType

Sets the value of the cvRef property.

setDatabase(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.DatabaseRefreshTimestamp

Sets the value of the database property.

setDatabaseFilters(DatabaseFiltersType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType

Sets the value of the databaseFilters property.

setDatabaseName(ParamType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchDatabaseType

Sets the value of the databaseName property.

setDatabaseName(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase

Sets the value of the databaseName property.

setDatabaseReleaseDate(XMLGregorianCalendar) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase

Sets the value of the databaseReleaseDate property.

setDatabaseReleaseIdentifier(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase

Sets the value of the databaseReleaseIdentifier property.

setDatabaseTranslation(DatabaseTranslationType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType

Sets the value of the databaseTranslation property.

setDataCollection(DataCollectionType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType

Sets the value of the dataCollection property.

setDatasetDerivation(MsmsPipelineAnalysis.DatasetDerivation) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis

Sets the value of the datasetDerivation property.

setDate(XMLGregorianCalendar) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis

Sets the value of the date property.

setDateTimeModified(String) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT

Sets the value of the dateTimeModified property.

setDateTimePosted(String) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT

Sets the value of the dateTimePosted property.

setDBSequenceRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType

Sets the value of the dbSequenceRef property.

setDBSequenceRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionHypothesisType

Sets the value of the dbSequenceRef property.

setDecimalRatio(BigDecimal) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult

Sets the value of the decimalRatio property.

setDelta(float) - Method in class org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader
 
setDelta(float) - Method in class org.expasy.mzjava.external.io.ms.spectrum.ConsistencyChecker
 
setDelta(float) - Method in interface org.expasy.mzjava.external.io.ms.spectrum.ConsistencyCheckHandler

Set delta value

setDelta(float) - Method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.EbiMzmlReader
 
setDelta(CompositionT) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT

Sets the value of the delta property.

setDescription(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.DatasetDerivation.DataFilter

Sets the value of the description property.

setDescription(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme

Sets the value of the description property.

setDescription(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification

Sets the value of the description property.

setDescription(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification

Sets the value of the description property.

setDigestDB(DigestDB) - Method in interface org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumDB.DigestSourceDSL
 
setDigestionController(DigestionController) - Method in class org.expasy.mzjava.proteomics.ms.dbsearch.ArrayDigestDB.Builder

Set the controller for the digest.

setDirectory(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.InteractSummary

Sets the value of the directory property.

setDoi(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType

Sets the value of the doi property.

setDoneMessage(String) - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar
 
setDoneMessage(String) - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar.View
 
setEditor(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType

Sets the value of the editor property.

setElution(BigInteger) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioSummary

Sets the value of the elution property.

setEnd(Integer) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType

Sets the value of the end property.

setEndOfParsing(boolean) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader.ParseContext
 
setEndScan(long) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery

Sets the value of the endScan property.

setEnzymaticSearchConstraint(MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary

Sets the value of the enzymaticSearchConstraint property.

setEnzyme(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint

Sets the value of the enzyme property.

setEnzymeName(ParamListType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymeType

Sets the value of the enzymeName property.

setEnzymes(EnzymesType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType

Sets the value of the enzymes property.

setError(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioContribution

Sets the value of the error property.

setError(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioResult

Sets the value of the error property.

setExclude(ParamListType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FilterType

Sets the value of the exclude property.

setExCodeName(String) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT

Sets the value of the exCodeName property.

setExperimentalMassToCharge(double) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType

Sets the value of the experimentalMassToCharge property.

setExternalFormatDocumentation(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ExternalDataType

Sets the value of the externalFormatDocumentation property.

setFidelity(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme

Sets the value of the fidelity property.

setFileFormat(FileFormatType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ExternalDataType

Sets the value of the fileFormat property.

setFilename(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.InteractSummary

Sets the value of the filename property.

setFilterParameters(double, int) - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.Builder
 
setFilterParameters(double, int) - Method in interface org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.FilterParametersSetter
 
setFilterType(ParamType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FilterType

Sets the value of the filterType property.

setFirstName(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PersonType

Sets the value of the firstName property.

setFixedMod(boolean) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchModificationType

Sets the value of the fixedMod property.

setFlag(Boolean) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.NeutralLossT

Sets the value of the flag property.

setFragment(AminoAcidSequence) - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation.Builder

Set the fragment

setFragmentation(FragmentationType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType

Sets the value of the fragmentation property.

setFragmentationTable(FragmentationTableType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationListType

Sets the value of the fragmentationTable property.

setFragmentMassType(MassType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary

Sets the value of the fragmentMassType property.

setFragmentTolerance(ToleranceType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType

Sets the value of the fragmentTolerance property.

setFragMethod(String) - Method in class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum

Set the fragmentation method

setFrame(Integer) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType

Sets the value of the frame property.

setFullName(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.CvType

Sets the value of the fullName property.

setFullName(String) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT

Sets the value of the fullName property.

setFullName(String) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodMod.Builder

Set the full name.

setGenerationNo(BigInteger) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.DatasetDerivation

Sets the value of the generationNo property.

setGroupOfPoster(String) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT

Sets the value of the groupOfPoster property.

setHeavy2LightError(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioResult

Sets the value of the heavy2LightError property.

setHeavy2LightMean(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioResult

Sets the value of the heavy2LightMean property.

setHeavy2LightRatio(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult

Sets the value of the heavy2LightRatio property.

setHeavyArea(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult

Sets the value of the heavyArea property.

setHeavyFirstscan(long) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult

Sets the value of the heavyFirstscan property.

setHeavyLastscan(long) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult

Sets the value of the heavyLastscan property.

setHeavyMass(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioPeptideData

Sets the value of the heavyMass property.

setHeavyMass(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult

Sets the value of the heavyMass property.

setHidden(Boolean) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.SpecificityT

Sets the value of the hidden property.

setHighestIntensity(double) - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.CentroidFilter.PeakIntensityInfo
 
setHitRank(long) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Sets the value of the hitRank property.

setId(UUID) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
 
setId(UUID) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList
 
setId(UUID) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
setId(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.CvType

Sets the value of the id property.

setId(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.IdentifiableType

Sets the value of the id property.

setId(long) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp

Sets the value of the id property.

setId(Long) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult

Sets the value of the id property.

setInclude(ParamListType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FilterType

Sets the value of the include property.

setIncompleteMessage(String) - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar
 
setIncompleteMessage(String) - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar.View
 
setIndependent(Boolean) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymesType

Sets the value of the independent property.

setIndependent(Boolean) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme

Sets the value of the independent property.

setIndeterminate(boolean) - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar
 
setIndeterminate(boolean) - Method in interface org.expasy.mzjava.app.pb.ProgressBar

Sets the indeterminate property of the progress bar which determines
 whether the progress bar is in determinate or indeterminate mode.

setIndex(long) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery

Sets the value of the index property.

setIndex(int) - Method in class org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
 
setInputs(InputsType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DataCollectionType

Sets the value of the inputs property.

setIntensity(double) - Method in class org.expasy.mzjava.core.ms.peaklist.Peak

Set the intensity of this peak

setIntensityAt(double, int) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList

Replace the intensity at index with intensity

setIntensityAt(double, int) - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleFloatPeakList

Replace the intensity at index with intensity

setIntensityAt(double, int) - Method in class org.expasy.mzjava.core.ms.peaklist.DoublePeakList

Replace the intensity at index with intensity

setIntensityAt(double, int) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList

Replace the intensity at index with intensity

setIntensityAt(double, int) - Method in class org.expasy.mzjava.core.ms.peaklist.FloatPeakList

Replace the intensity at index with intensity

setIntensityAt(double, int) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Replace the intensity at index with intensity

setIntensityAt(double, int) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
setIntensityFormat(NumberFormat) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.AbstractSptxtWriter
 
setInterimName(String) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodMod.Builder

Set the interim name.

setIsDecoy(Boolean) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType

Sets the value of the isDecoy property.

setIsHeavy(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak

Sets the value of the isHeavy property.

setIsHeavy(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak

Sets the value of the isHeavy property.

setIsotopicContributions(LibraSummary.IsotopicContributions) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary

Sets the value of the isotopicContributions property.

setIsRejected(Boolean) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraResult

Sets the value of the isRejected property.

setIsRejected(BigInteger) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Sets the value of the isRejected property.

setIssue(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType

Sets the value of the issue property.

setLabeledResidues(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioSummary

Sets the value of the labeledResidues property.

setLabeledResidues(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioSummary

Sets the value of the labeledResidues property.

setLastName(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PersonType

Sets the value of the lastName property.

setLeftMarginLength(int) - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar
 
setLeftMarginLength(int) - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar.View

Set the left margin length (with completion infos).

setLeftValley(int) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak

Sets the value of the leftValley property.

setLeftValley(int) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak

Sets the value of the leftValley property.

setLength(Integer) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DBSequenceType

Sets the value of the length property.

setLightArea(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult

Sets the value of the lightArea property.

setLightFirstscan(long) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult

Sets the value of the lightFirstscan property.

setLightLastscan(long) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult

Sets the value of the lightLastscan property.

setLightMass(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioPeptideData

Sets the value of the lightMass property.

setLightMass(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult

Sets the value of the lightMass property.

setLoadFactor(int) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList

Set the number of elements that are added to the mz and intensity arrays when the size of this instance exceeds
 the capacity of these arrays

setLocalPath(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase

Sets the value of the localPath property.

setLocation(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ExternalDataType

Sets the value of the location property.

setLocation(Integer) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ModificationType

Sets the value of the location property.

setLocation(Integer) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SubstitutionModificationType

Sets the value of the location property.

setMajorVersion(int) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.UnimodT

Sets the value of the majorVersion property.

setMass(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ResidueType

Sets the value of the mass property.

setMass(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification

Sets the value of the mass property.

setMass(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification

Sets the value of the mass property.

setMass(double) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo.ModAminoacidMass

Sets the value of the mass property.

setMassDelta(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchModificationType

Sets the value of the massDelta property.

setMassdiff(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification

Sets the value of the massdiff property.

setMassdiff(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification

Sets the value of the massdiff property.

setMassdiff(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Sets the value of the massdiff property.

setMassdiff(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioSummary

Sets the value of the massdiff property.

setMassDiff(Optional<Double>) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Set the difference between the the theoretical and experimental mass

setMassTableRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType

Sets the value of the massTableRef property.

setMassTol(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult

Sets the value of the massTol property.

setMasstol(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioSummary

Sets the value of the masstol property.

setMassTolerance(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary

Sets the value of the massTolerance property.

setMaxAnnotationToWrite(int) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.SptxtWriter
 
setMaximum(int) - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar
 
setMaximum(int) - Method in interface org.expasy.mzjava.app.pb.ProgressBar

Sets the progress bar's minimum value to n

setMaximumDoNoResetLeftMargin(int) - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar
 
setMaxNumInternalCleavages(BigInteger) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint

Sets the value of the maxNumInternalCleavages property.

setMean(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioResult

Sets the value of the mean property.

setMeasureRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FragmentArrayType

Sets the value of the measureRef property.

setMidInitials(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PersonType

Sets the value of the midInitials property.

setMinDistance(Integer) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymeType

Sets the value of the minDistance property.

setMinimum(int) - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar
 
setMinimum(int) - Method in interface org.expasy.mzjava.app.pb.ProgressBar

Sets the progress bar's maximum value to n

setMinNumberTermini(BigInteger) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint

Sets the value of the minNumberTermini property.

setMinNumEnzTerm(BigInteger) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.DatabaseRefreshTimestamp

Sets the value of the minNumEnzTerm property.

setMinorVersion(int) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.UnimodT

Sets the value of the minorVersion property.

setMinSpacing(BigInteger) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity

Sets the value of the minSpacing property.

setMiscNotes(String) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT

Sets the value of the miscNotes property.

setMiscNotes(String) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.SpecificityT

Sets the value of the miscNotes property.

setMissedCleavages(Integer) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymeType

Sets the value of the missedCleavages property.

setMissedCleavagesTo(int) - Method in interface org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumDB.DigestDSL

Set the number of missed cleavages that is allowed by the digester.

setModCtermMass(Double) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo

Sets the value of the modCtermMass property.

setModificationInfo(MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Sets the value of the modificationInfo property.

setModificationParams(ModificationParamsType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType

Sets the value of the modificationParams property.

setModifications(ModificationsT) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.UnimodT

Sets the value of the modifications property.

setModifiedPeptide(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo

Sets the value of the modifiedPeptide property.

setModNtermMass(Double) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo

Sets the value of the modNtermMass property.

setMonoisotopicMassDelta(Double) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ModificationType

Sets the value of the monoisotopicMassDelta property.

setMonoisotopicMassDelta(Double) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SubstitutionModificationType

Sets the value of the monoisotopicMassDelta property.

setMonoMass(Double) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.CompositionT

Sets the value of the monoMass property.

setMsDetector(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary

Sets the value of the msDetector property.

setMsIonization(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary

Sets the value of the msIonization property.

setMsLevel(int) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum

Set the ms level that this peak list was measured at

setMsManufacturer(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary

Sets the value of the msManufacturer property.

setMsMassAnalyzer(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary

Sets the value of the msMassAnalyzer property.

setMsModel(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary

Sets the value of the msModel property.

setMz(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.FragmentMasses

Sets the value of the mz property.

setMzAndCharge(double, int...) - Method in class org.expasy.mzjava.core.ms.peaklist.Peak

Set the m/z and chargeList of this peak

setMzFormat(NumberFormat) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.AbstractSptxtWriter
 
setName(String) - Method in class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum
 
setName(String) - Method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.MzmlSpectrumCheck
 
setName(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AbstractParamType

Sets the value of the name property.

setName(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.IdentifiableType

Sets the value of the name property.

setName(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.InteractSummary.Inputfile

Sets the value of the name property.

setName(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme

Sets the value of the name property.

setName(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis

Sets the value of the name property.

setName(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.NameValueType

Sets the value of the name property.

setName(String) - Method in class org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
 
setName(String) - Method in class org.expasy.mzjava.stats.HistogramImpl
 
setNeutralLoss(Mass) - Method in class org.expasy.mzjava.glycomics.ms.spectrum.GlycanFragAnnotation.FragBuilder

Set the neutral loss

setNeutralLoss(Mass) - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation.Builder

Set the neutral loss

setNeutralLosses(List<NeutralLoss>) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodMod.Builder

Set the neutral loss list

setNeutralPeptideMass(double) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch
 
setNoCut(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity

Sets the value of the noCut property.

setNormalization(int) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary

Sets the value of the normalization property.

setNormalized(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraResult.Intensity

Sets the value of the normalized property.

setNTermGain(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymeType

Sets the value of the nTermGain property.

setNumber(BigInteger) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.DatasetDerivation.DataFilter

Sets the value of the number property.

setNumber(Integer) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ElemRefT

Sets the value of the number property.

setNumDatabaseSequences(Long) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchDatabaseType

Sets the value of the numDatabaseSequences property.

setNumMatchedIons(BigInteger) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Sets the value of the numMatchedIons property.

setNumMatchedIons(Optional<Integer>) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Set the number of ions that were matched

setNumMissedCleavages(BigInteger) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Sets the value of the numMissedCleavages property.

setNumMissedCleavages(Optional<Integer>) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Set the number of missed cleavages that the Peptide contains

setNumResidues(Long) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchDatabaseType

Sets the value of the numResidues property.

setNumSequencesSearched(Long) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationListType

Sets the value of the numSequencesSearched property.

setNumTolTerm(BigInteger) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein

Sets the value of the numTolTerm property.

setNumTolTerm(BigInteger) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Sets the value of the numTolTerm property.

setNumTotProteins(long) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Sets the value of the numTotProteins property.

setOffset(Float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.FragmentMasses

Sets the value of the offset property.

setOrganizationRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AffiliationType

Sets the value of the organizationRef property.

setOrganizationRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ParentOrganizationType

Sets the value of the organizationRef property.

setOrigDatabaseUrl(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase

Sets the value of the origDatabaseUrl property.

setOriginalResidue(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SubstitutionModificationType

Sets the value of the originalResidue property.

setOutData(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary

Sets the value of the outData property.

setOutDataType(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary

Sets the value of the outDataType property.

setOutputType(int) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary

Sets the value of the outputType property.

setOverlapListener(DefaultPeakListAligner.OverlapListener) - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.DefaultPeakListAligner
 
setPages(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType

Sets the value of the pages property.

setParent(ParentOrganizationType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.OrganizationType

Sets the value of the parent property.

setParentFile(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.DatasetDerivation.DataFilter

Sets the value of the parentFile property.

setParentScanNumber(ScanNumber) - Method in class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum

Set the parent scan number

setParentTolerance(ToleranceType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType

Sets the value of the parentTolerance property.

setPassThreshold(boolean) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionHypothesisType

Sets the value of the passThreshold property.

setPassThreshold(boolean) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType

Sets the value of the passThreshold property.

setPeakCount(int) - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.CentroidFilter.PeakIntensityInfo
 
setPeakFilterParams(double, int) - Method in class org.expasy.mzjava.core.ms.consensus.AbstractConsensusSpectrumBuilder
 
setPeakList(PeakList<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.PeakCollectorSink
 
setPeptide(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Sets the value of the peptide property.

setPeptide(Peptide) - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum
 
setPeptideEvidenceRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceRefType

Sets the value of the peptideEvidenceRef property.

setPeptideEvidenceRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideHypothesisType

Sets the value of the peptideEvidenceRef property.

setPeptideNextAa(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein

Sets the value of the peptideNextAa property.

setPeptideNextAa(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Sets the value of the peptideNextAa property.

setPeptidePrevAa(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein

Sets the value of the peptidePrevAa property.

setPeptidePrevAa(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Sets the value of the peptidePrevAa property.

setPeptideRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType

Sets the value of the peptideRef property.

setPeptideRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType

Sets the value of the peptideRef property.

setPeptideSequence(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideType

Sets the value of the peptideSequence property.

setPeptideSequence(String) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.LibrarySpectrumBuilder
 
setPeptideTerminus(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification

Sets the value of the peptideTerminus property.

setPosition(BigInteger) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo.ModAminoacidMass

Sets the value of the position property.

setPosition(PositionT) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.SpecificityT

Sets the value of the position property.

setPost(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType

Sets the value of the post property.

setPre(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType

Sets the value of the pre property.

setPrecursor(Peak) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
 
setPrecursor(Peak) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Set the precursor peak for this peak list

setPrecursor(Peak) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
setPrecursorCharge(int) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.LibrarySpectrumBuilder
 
setPrecursorIntensity(Float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery

Sets the value of the precursorIntensity property.

setPrecursorIntensity(double) - Method in class org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
 
setPrecursorMassType(MassType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary

Sets the value of the precursorMassType property.

setPrecursorMz(double) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.LibrarySpectrumBuilder
 
setPrecursorMz(double) - Method in class org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
 
setPrecursorNeutralLosses(List<NeutralLoss>) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodMod.Builder

Set the precursor neutral loss list

setPrecursorNeutralMass(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery

Sets the value of the precursorNeutralMass property.

setPrecursorNeutralMass(double) - Method in class org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
 
setPrecursorStats(double, double) - Method in class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum
 
setPrecursorTolerance(Tolerance) - Method in interface org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumDB.StartDSL

Set the precursor tolerance

setPrintStream(PrintStream) - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar
 
setPrintStream(PrintStream) - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar.View

Set the print stream for bar display.

setProbability(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.PeptideprophetResult

Sets the value of the probability property.

setProgressBarPrintStream(PrintStream) - Method in class org.expasy.mzjava.app.io.MonitoredIterativeReader
 
setProtein(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein

Sets the value of the protein property.

setProtein(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Sets the value of the protein property.

setProteinDescr(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein

Sets the value of the proteinDescr property.

setProteinDescr(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Sets the value of the proteinDescr property.

setProteinDetection(ProteinDetectionType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisCollectionType

Sets the value of the proteinDetection property.

setProteinDetectionList(ProteinDetectionListType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisDataType

Sets the value of the proteinDetectionList property.

setProteinDetectionListRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionType

Sets the value of the proteinDetectionListRef property.

setProteinDetectionProtocol(ProteinDetectionProtocolType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisProtocolCollectionType

Sets the value of the proteinDetectionProtocol property.

setProteinDetectionProtocolRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionType

Sets the value of the proteinDetectionProtocolRef property.

setProteinMw(Double) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein

Sets the value of the proteinMw property.

setProteinMw(Double) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Sets the value of the proteinMw property.

setProteinSource(File) - Method in interface org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumDB.DigestSourceDSL

Set the fasta format protein file.

setProteinSource(IterativeReader<Protein>) - Method in interface org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumDB.DigestSourceDSL

Set the IterativeReader reader as the protein source.

setProteinTerminus(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification

Sets the value of the proteinTerminus property.

setProvider(ProviderType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType

Sets the value of the provider property.

setPsiMsName(String) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodMod.Builder

Set the psi ms name

setPublication(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType

Sets the value of the publication property.

setPublisher(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType

Sets the value of the publisher property.

setQuantLabelMasses(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioTimestamp

Sets the value of the quantLabelMasses property.

setRank(int) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType

Sets the value of the rank property.

setRank(Optional<Integer>) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Set the rank of this PeptideMatch

setRanks() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader
 
setRatio(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioContribution

Sets the value of the ratio property.

setRatio(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult

Sets the value of the ratio property.

setRawData(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary

Sets the value of the rawData property.

setRawDataType(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary

Sets the value of the rawDataType property.

setRecordId(Long) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT

Sets the value of the recordId property.

setRecordId(int) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodMod.Builder

Set the record id

setRefreshBarPeriod(int) - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar

Set the period of bar animation refresh while the bar is in indeterminate
 mode.

setRefreshBarPeriod(int) - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar.View

Set the period of bar animation refresh while the bar is in indeterminate
 mode.

setReject(Boolean) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraResult.Intensity

Sets the value of the reject property.

setRejected(Optional<Boolean>) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Set whether this PeptideMatch was rejected or not

setReleaseDate(XMLGregorianCalendar) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchDatabaseType

Sets the value of the releaseDate property.

setReplacementResidue(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SubstitutionModificationType

Sets the value of the replacementResidue property.

setRequired(Boolean) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.PepNeutralLossT

Sets the value of the required property.

setRetentionTime(Optional<RetentionTimeDiscrete>) - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum
 
setRetentionTimes(S, RetentionTimeList) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfReader

Add the retention times contained in the retentionTimeList to the spectrum.

setRetentionTimes(MsnSpectrum, RetentionTimeList) - Method in class org.expasy.mzjava.core.io.ms.spectrum.MgfReader
 
setRetentionTimeSec(Float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery

Sets the value of the retentionTimeSec property.

setRightValley(int) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak

Sets the value of the rightValley property.

setRightValley(int) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak

Sets the value of the rightValley property.

setRole(RoleType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ContactRoleType

Sets the value of the role property.

setRoot(Monosaccharide, Optional<Anomericity>, String) - Method in class org.expasy.mzjava.glycomics.mol.Glycan.Builder

Set the root of the Glycan.

setRoot(Monosaccharide, Optional<Anomericity>, String, Composition) - Method in class org.expasy.mzjava.glycomics.mol.Glycan.Builder

Set the root of the Glycan.

setRoot(Monosaccharide, FragmentType) - Method in class org.expasy.mzjava.glycomics.mol.GlycanFragment.Builder

Set the root of the Glycan Fragments.

setRoot(Monosaccharide, FragmentType, Composition) - Method in class org.expasy.mzjava.glycomics.mol.GlycanFragment.Builder

Set the root of the Glycan Fragments.

setSameScanRange(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioSummary

Sets the value of the sameScanRange property.

setSampleEnzyme(MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary

Sets the value of the sampleEnzyme property.

setSampleRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType

Sets the value of the sampleRef property.

setSampleRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SubSampleType

Sets the value of the sampleRef property.

setScanNumbers(S, ScanNumberList) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfReader

Add the scan numbers contained in the scanNumbers to the spectrum.

setScanNumbers(MsnSpectrum, ScanNumberList) - Method in class org.expasy.mzjava.core.io.ms.spectrum.MgfReader
 
setScoreStats(double, double) - Method in class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum
 
setSearchDatabase(MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary

Sets the value of the searchDatabase property.

setSearchDatabaseRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DBSequenceType

Sets the value of the searchDatabaseRef property.

setSearchDatabaseRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchDatabaseRefType

Sets the value of the searchDatabaseRef property.

setSearchEngine(EngineType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary

Sets the value of the searchEngine property.

setSearchId(long) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary

Sets the value of the searchId property.

setSearchId(Long) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult

Sets the value of the searchId property.

setSearchScoreSummary(PeptideprophetResult.SearchScoreSummary) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.PeptideprophetResult

Sets the value of the searchScoreSummary property.

setSearchSpecification(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery

Sets the value of the searchSpecification property.

setSearchType(ParamType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType

Sets the value of the searchType property.

setSegmentLength(int) - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar

Set the length of segment constantly animated in indeterminate mode.

setSegmentLength(int) - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar.View

Set the length of segment constantly animated in indeterminate mode.

setSemiSpecific(Boolean) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymeType

Sets the value of the semiSpecific property.

setSense(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity

Sets the value of the sense property.

setSeq(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DBSequenceType

Sets the value of the seq property.

setSequence(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SequenceSearchConstraint

Sets the value of the sequence property.

setSequence(String) - Method in class org.expasy.mzjava.proteomics.mol.Protein.Builder
 
setSequenceCollection(SequenceCollectionType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType

Sets the value of the sequenceCollection property.

setSink(PS) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakProcessor
 
setSink(PS) - Method in class org.expasy.mzjava.core.ms.peaklist.PeakListMerger
 
setSink(PS) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakSource

Set the next element in the peak processor chain.

setSink(PeakPairSink<X, Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.AbstractPeakPairProcessor
 
setSink(PeakPairSink<X, Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.DefaultPeakListAligner
 
setSink(PeakPairSink<X, Y>) - Method in interface org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.PeakPairSource
 
setSite(String) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.SpecificityT

Sets the value of the site property.

setSiteRegexp(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymeType

Sets the value of the siteRegexp property.

setSites(List<String>) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodMod.Builder

Set the sites list

setSizeInDbEntries(BigInteger) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase

Sets the value of the sizeInDbEntries property.

setSizeOfResidues(BigInteger) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase

Sets the value of the sizeOfResidues property.

setSoftwareName(ParamType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisSoftwareType

Sets the value of the softwareName property.

setSource(String) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.XrefT

Sets the value of the source property.

setSpecGroup(int) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.SpecificityT

Sets the value of the specGroup property.

setSpectraDataRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.InputSpectraType

Sets the value of the spectraDataRef property.

setSpectraDataRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationResultType

Sets the value of the spectraDataRef property.

setSpectrum(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery

Sets the value of the spectrum property.

setSpectrumFile(String) - Method in class org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
 
setSpectrumID(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationResultType

Sets the value of the spectrumID property.

setSpectrumIdentificationItemRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemRefType

Sets the value of the spectrumIdentificationItemRef property.

setSpectrumIdentificationListRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.InputSpectrumIdentificationsType

Sets the value of the spectrumIdentificationListRef property.

setSpectrumIdentificationListRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationType

Sets the value of the spectrumIdentificationListRef property.

setSpectrumIdentificationProtocolRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationType

Sets the value of the spectrumIdentificationProtocolRef property.

setSpectrumIDFormat(SpectrumIDFormatType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectraDataType

Sets the value of the spectrumIDFormat property.

setSpectrumIdParser(SpectrumIdParser) - Method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.EbiMzmlReader

Set parser that extract scan number from spectrum id attribute.

setSpectrumIndex(int) - Method in class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum

Set the spectrum index

setSpectrumSource(URI) - Method in class org.expasy.mzjava.core.ms.spectrum.MsnSpectrum

Set the URI that describes the source of this MsnSpectrum

setSpectrumSource(URI) - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum
 
setStart(Integer) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType

Sets the value of the start property.

setStartScan(long) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery

Sets the value of the startScan property.

setStaticQuant(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioSummary

Sets the value of the staticQuant property.

setStaticQuantLabel(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioTimestamp

Sets the value of the staticQuantLabel property.

setStatus(byte) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak

Sets the value of the status property.

setStatus(byte) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak

Sets the value of the status property.

setStatus(byte) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioPeptideData

Sets the value of the status property.

setStatus(PeptideConsensusSpectrum.Status) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.LibrarySpectrumBuilder
 
setStatus(PeptideConsensusSpectrum.Status) - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum

Set the status

setSummaryXml(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis

Sets the value of the summaryXml property.

setSymbol(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification

Sets the value of the symbol property.

setSymbol(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification

Sets the value of the symbol property.

setSymbol(String) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ElemRefT

Sets the value of the symbol property.

setTargetMass(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraResult.Intensity

Sets the value of the targetMass property.

setTaskName(String) - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar
 
setTaskName(String) - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar.View
 
setTaskName(String) - Method in interface org.expasy.mzjava.app.pb.ProgressBar

Set the task name (displayed in left margin)

setTerminal(MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.ModificationMap
 
setTerminus(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification

Sets the value of the terminus property.

setText(String) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.XrefT

Sets the value of the text property.

setThreshold(ParamListType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionProtocolType

Sets the value of the threshold property.

setThreshold(ParamListType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType

Sets the value of the threshold property.

setTime(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak

Sets the value of the time property.

setTime(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak

Sets the value of the time property.

setTime(XMLGregorianCalendar) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.AnalysisSummary

Sets the value of the time property.

setTime(XMLGregorianCalendar) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp

Sets the value of the time property.

setTimeWidth(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak

Sets the value of the timeWidth property.

setTimeWidth(float) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak

Sets the value of the timeWidth property.

setTitle(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType

Sets the value of the title property.

setTitle(String) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT

Sets the value of the title property.

setTotalIntensity(double) - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.CentroidFilter.PeakIntensityInfo
 
setTotalNumIons(Optional<Integer>) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Set the total number of ion that were generated for the Peptide

setTotNumIons(BigInteger) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit

Sets the value of the totNumIons property.

setTranslationTableRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType

Sets the value of the translationTableRef property.

setType(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.UserParamType

Sets the value of the type property.

setType(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase

Sets the value of the type property.

setType(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.NameValueType

Sets the value of the type property.

setUnimodPath(String) - Static method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodManager

Set static variable unimodPath to your local unimod.xml file version

setUnitAccession(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AbstractParamType

Sets the value of the unitAccession property.

setUnitCvRef(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AbstractParamType

Sets the value of the unitCvRef property.

setUnitName(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AbstractParamType

Sets the value of the unitName property.

setUnknownModListener(UnknownModListener) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.ProteinPilotPsmReader

Set the UnknownModListener

setUri(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisSoftwareType

Sets the value of the uri property.

setUri(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.CvType

Sets the value of the uri property.

setURL(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase

Sets the value of the url property.

setUrl(String) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.XrefT

Sets the value of the url property.

setUse(short) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioContribution

Sets the value of the use property.

setUsernameOfPoster(String) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT

Sets the value of the usernameOfPoster property.

setUserParam(UserParamType) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ParamType

Sets the value of the userParam property.

setValue(int) - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar
 
setValue(int) - Method in interface org.expasy.mzjava.app.pb.ProgressBar

Sets the progress bar's current value to n

setValue(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AbstractParamType

Sets the value of the value property.

setValue(Object) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.NameValueType

Sets the value of the value property.

setValueAttribute(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.NameValueType

Sets the value of the valueAttribute property.

setValues(MsnSpectrum) - Method in class org.expasy.mzjava.avro.io.MsnSpectrumMetaDataReader
 
setValues(double, double, int...) - Method in class org.expasy.mzjava.core.ms.peaklist.Peak

Set this peaks values

setValues(PeptideMatch, ResultSet) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.AbstractPsmCsvReader

Set PeptideMatch score values

setValues(PeptideMatch, ResultSet) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.MaxQuantPsmReader
 
setValues(PeptideMatch, ResultSet) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.ProteinPilotPsmReader
 
setVariable(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification

Sets the value of the variable property.

setVariable(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification

Sets the value of the variable property.

setVersion(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisSoftwareType

Sets the value of the version property.

setVersion(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.CvType

Sets the value of the version property.

setVersion(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType

Sets the value of the version property.

setVersion(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchDatabaseType

Sets the value of the version property.

setVersion(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioSummary

Sets the value of the version property.

setVersion(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.AnalysisSummary

Sets the value of the version property.

setVersion(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioSummary

Sets the value of the version property.

setView(ConsoleProgressBar.View) - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar
 
setVolume(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType

Sets the value of the volume property.

setWindowsParent(String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.DatasetDerivation.DataFilter

Sets the value of the windowsParent property.

setXpressLight(long) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioSummary

Sets the value of the xpressLight property.

setXpressLight(BigInteger) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioTimestamp

Sets the value of the xpressLight property.

setYear(Integer) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType

Sets the value of the year property.

shallowCopy() - Method in interface org.expasy.mzjava.stats.Histogram

Copy the bin structure only

shallowCopy() - Method in class org.expasy.mzjava.stats.HistogramImpl
 
SharedPeakSimFunc<X extends PeakAnnotation,Y extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.spectrasim

The shared peak count is the calculated using the formula

SharedPeakSimFunc(int, Tolerance) - Constructor for class org.expasy.mzjava.core.ms.spectrasim.SharedPeakSimFunc

Construct a SharedPeakSimFunc that uses the default peak list aligner.

SharedPeakSimFunc(int, PeakListAligner<X, Y>, PeakPairProcessor<X, Y>...) - Constructor for class org.expasy.mzjava.core.ms.spectrasim.SharedPeakSimFunc

Construct a SharedPeakSimFunc that uses the supplied PeakListAligner and PeakPairProcessor chain to process
 and align the peak lists.

shiftAnnotations(int) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList

Shift all annotations that have an index that is >= insertionIndex by 1

sideChainFixedModMap - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader
 
sideChainSet - Static variable in enum org.expasy.mzjava.proteomics.mol.modification.ModAttachment
 
SimEdge<V> - Class in org.expasy.mzjava.core.ms.cluster

Class to hols an undirected edge that is weighted by a score between two vertexes.

SimEdge(V, V, double) - Constructor for class org.expasy.mzjava.core.ms.cluster.SimEdge

Constructor

SimFunc<X extends PeakAnnotation,Y extends PeakAnnotation> - Interface in org.expasy.mzjava.core.ms.spectrasim

Interface for any class that can calculate the similarity between two PeakLists

SimFuncProcedure<LA extends PeakAnnotation,LPL extends PeakList<LA>,QA extends PeakAnnotation,QPL extends PeakList<QA>> - Class in org.expasy.mzjava.core.ms.library
 
SimFuncProcedure(QPL, SimFunc<LA, QA>, int) - Constructor for class org.expasy.mzjava.core.ms.library.SimFuncProcedure
 
SimilarityGraph<V> - Interface in org.expasy.mzjava.core.ms.cluster

Interface for a graph that represents the similarity between vertexes.

SimilarityGraphBuilder<V,G extends SimilarityGraph<V>> - Interface in org.expasy.mzjava.core.ms.cluster

Common interface for similarity graph builders.

SimROCTable - Class in org.expasy.mzjava.stats
 
SimROCTable(double, double, double) - Constructor for class org.expasy.mzjava.stats.SimROCTable
 
simScoreMean - Variable in class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum
 
simScoreStdev - Variable in class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum
 
sink - Variable in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakProcessor

The next element in the peak processor chain

sink - Variable in class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.AbstractPeakPairProcessor
 
site - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.SpecificityT
 
siteRegexp - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymeType
 
size() - Method in class org.expasy.mzjava.core.mol.Composition

Returns the number of atoms in this composition

size() - Method in interface org.expasy.mzjava.core.mol.SymbolSequence

Returns the number of symbols in this symbol sequence.

size - Variable in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
 
size() - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList

Returns the number of peaks in this peak list.

size - Variable in class org.expasy.mzjava.core.ms.peaklist.ArrayCursor
 
size() - Method in class org.expasy.mzjava.core.ms.peaklist.ArrayCursor
 
size() - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakCursor

Returns the number of peaks int this cursor

size() - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Returns the number of peaks in this peak list.

size() - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
size() - Method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.EbiMzmlReader
 
size() - Method in class org.expasy.mzjava.glycomics.mol.NodeSet
 
size() - Method in class org.expasy.mzjava.glycomics.mol.SaccharideGraph

Return the size of the glycan as the number of monosaccharide.

size() - Method in class org.expasy.mzjava.proteomics.mol.AminoAcidSequence

Returns the number of residues in this amino acid sequence.

size() - Method in interface org.expasy.mzjava.proteomics.mol.modification.ModificationList
 
size() - Static method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodManager
 
size() - Method in class org.expasy.mzjava.proteomics.mol.PeptideBuilder

Return the number of amino acids

size() - Method in class org.expasy.mzjava.proteomics.mol.Protein
 
size() - Method in class org.expasy.mzjava.proteomics.ms.dbsearch.ArrayDigestDB

Return the number of digests that this DigestDB contains

size() - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch
 
size() - Method in interface org.expasy.mzjava.stats.Histogram

Get the number of bins (n)

size() - Method in class org.expasy.mzjava.stats.HistogramImpl
 
size() - Method in class org.expasy.mzjava.stats.ROCTable
 
sizeInDbEntries - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
 
sizeOfResidues - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
 
SkipAnnotationResolver - Class in org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt

Annotation resolver that ignores annotations

SkipAnnotationResolver() - Constructor for class org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.SkipAnnotationResolver
 
skipIntermediaryLine(String) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfReader

Handle intermediary lines between BEGIN IONS and END IONS.

SNode<T> - Class in org.expasy.mzjava.glycomics.mol
 
SNode(int, T) - Constructor for class org.expasy.mzjava.glycomics.mol.SNode
 
SoftRefPepSpectrumCache - Class in org.expasy.mzjava.proteomics.ms.dbsearch

PeptideSpectrum cache that is memory-sensitive.

SoftRefPepSpectrumCache() - Constructor for class org.expasy.mzjava.proteomics.ms.dbsearch.SoftRefPepSpectrumCache
 
softwareName - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisSoftwareType
 
sort(ArrayIndexComparator<T>) - Method in class org.expasy.mzjava.utils.ArrayIndexSorter

Sort the indices of array's object

sortAnnotations(Comparator<A>) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
 
sortAnnotations(Comparator<A>) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Sort the annotations for each annotated peak using the comparator

sortAnnotations(Comparator<A>) - Method in class org.expasy.mzjava.core.ms.spectrum.AnnotatedPeak

Use the comparator to sort this peaks annotations

sortAnnotations(Comparator<A>) - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
source - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.XrefT
 
sourceFile - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.InputsType
 
SourceFileType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

A file from which this mzIdentML instance was created.

SourceFileType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SourceFileType
 
SparseSimilarityGraph<V> - Class in org.expasy.mzjava.core.ms.cluster
 
SparseSimilarityGraph.Builder<V> - Class in org.expasy.mzjava.core.ms.cluster
 
SparseSimilarityGraph.Builder(int) - Constructor for class org.expasy.mzjava.core.ms.cluster.SparseSimilarityGraph.Builder
 
specGroup - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.SpecificityT
 
specificity - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme
 
specificity(String, String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder.SampleEnzymeBuilder
 
specificity(String, String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder.SpecificityBuilder
 
specificity - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT
 
specificityRules - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchModificationType
 
SpecificityRulesType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

The specificity rules of the searched modification including for example the probability of a modification's presence or peptide or protein termini.

SpecificityRulesType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpecificityRulesType
 
SpecificityT - Class in org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb

Java class for specificity_t complex type.

SpecificityT() - Constructor for class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.SpecificityT
 
spectra - Variable in class org.expasy.mzjava.core.ms.consensus.AbstractConsensusSpectrumBuilder
 
spectra(Collection<? extends PeakList<PeakAnnotation>>) - Method in class org.expasy.mzjava.core.ms.consensus.AbstractConsensusSpectrumBuilder
 
spectraData - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.InputsType
 
spectraDataRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.InputSpectraType
 
spectraDataRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationResultType
 
SpectraDataType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

A data set containing spectra data (consisting of one or more spectra).

SpectraDataType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectraDataType
 
SpectraLibCommentParser - Interface in org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt
 
SpectraStAnnotationResolver - Class in org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt
 
SpectraStAnnotationResolver() - Constructor for class org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.SpectraStAnnotationResolver
 
SpectraStCommentParser - Class in org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt
 
SpectraStCommentParser() - Constructor for class org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.SpectraStCommentParser
 
Spectrum<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.spectrum
 
Spectrum(Spectrum<A>, PeakProcessor<A, A>) - Constructor for class org.expasy.mzjava.core.ms.spectrum.Spectrum

Copy constructor

Spectrum(Spectrum<A>, PeakProcessorChain<A>) - Constructor for class org.expasy.mzjava.core.ms.spectrum.Spectrum

Copy constructor

Spectrum(int, PeakList.Precision) - Constructor for class org.expasy.mzjava.core.ms.spectrum.Spectrum

Construct a Spectrum that has an initial capacity of initialCapacity and a precision
 of precision

Spectrum(int, double, PeakList.Precision) - Constructor for class org.expasy.mzjava.core.ms.spectrum.Spectrum

Construct a Spectrum that has a constant intensity.

spectrum - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
 
SpectrumClusterEvaluator<A extends PeakAnnotation,S extends PeakList<A>> - Class in org.expasy.mzjava.core.ms.cluster

Class to evaluate whether a set of spectra cluster together.

SpectrumClusterEvaluator(Tolerance, SimFunc<A, A>, ClusterBuilder<S>) - Constructor for class org.expasy.mzjava.core.ms.cluster.SpectrumClusterEvaluator
 
spectrumID - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationResultType
 
spectrumIdentification - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisCollectionType
 
spectrumIdentificationItem - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationResultType
 
spectrumIdentificationItemRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideHypothesisType
 
spectrumIdentificationItemRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemRefType
 
SpectrumIdentificationItemRefType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

Reference(s) to the SpectrumIdentificationItem element(s) that support the given PeptideEvidence element.

SpectrumIdentificationItemRefType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemRefType
 
SpectrumIdentificationItemType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

An identification of a single (poly)peptide, resulting from querying an input spectra, along with the set of confidence values for that identification.

SpectrumIdentificationItemType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType
 
spectrumIdentificationList - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisDataType
 
spectrumIdentificationListRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.InputSpectrumIdentificationsType
 
spectrumIdentificationListRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationType
 
SpectrumIdentificationListType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

Represents the set of all search results from SpectrumIdentification.

SpectrumIdentificationListType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationListType
 
spectrumIdentificationProtocol - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisProtocolCollectionType
 
spectrumIdentificationProtocolRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationType
 
SpectrumIdentificationProtocolType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

The parameters and settings of a SpectrumIdentification analysis.

SpectrumIdentificationProtocolType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType
 
spectrumIdentificationResult - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationListType
 
SpectrumIdentificationResultType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

All identifications made from searching one spectrum.

SpectrumIdentificationResultType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationResultType
 
SpectrumIdentificationType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

An Analysis which tries to identify peptides in input spectra, referencing the database searched, the input spectra, the output results and the protocol that is run.

SpectrumIdentificationType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationType
 
spectrumIdentifier - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader
 
SpectrumIdentifier - Class in org.expasy.mzjava.proteomics.ms.ident
 
SpectrumIdentifier(String) - Constructor for class org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
 
spectrumIDFormat - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectraDataType
 
SpectrumIDFormatType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

The format of the spectrum identifier within the source file

SpectrumIDFormatType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIDFormatType
 
SpectrumIdParser - Interface in org.expasy.mzjava.external.io.ms.spectrum.mzml

This interface has to be implemented by parsers that extract scan number(s)
 from a mzml spectrum id attribute.

spectrumInfoParser - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader
 
SpectrumKey - Class in org.expasy.mzjava.hadoop.io
 
SpectrumKey() - Constructor for class org.expasy.mzjava.hadoop.io.SpectrumKey
 
SpectrumKey(double, int) - Constructor for class org.expasy.mzjava.hadoop.io.SpectrumKey
 
SpectrumLibrary<S extends PeakList> - Interface in org.expasy.mzjava.core.ms.library
 
spectrumQuery - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary
 
spectrumSource - Variable in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.Builder
 
split(List<PL>) - Method in class org.expasy.mzjava.utils.function.ChargeMzSplitter
 
split(List<PL>) - Method in class org.expasy.mzjava.utils.function.RetentionTimeSplitter
 
split(List<PL>) - Method in interface org.expasy.mzjava.utils.function.Splitter
 
Splitter<V> - Interface in org.expasy.mzjava.utils.function
 
SptxtReader - Class in org.expasy.mzjava.proteomics.io.ms.spectrum
 
SptxtReader(File, PeakList.Precision) - Constructor for class org.expasy.mzjava.proteomics.io.ms.spectrum.SptxtReader
 
SptxtReader.Builder - Class in org.expasy.mzjava.proteomics.io.ms.spectrum
 
SptxtReader.Builder(Reader, URI, PeakList.Precision) - Constructor for class org.expasy.mzjava.proteomics.io.ms.spectrum.SptxtReader.Builder
 
SptxtWriter - Class in org.expasy.mzjava.proteomics.io.ms.spectrum

Write PeptideSpectrums in sptxt format.

SptxtWriter(Writer, PeakList.Precision) - Constructor for class org.expasy.mzjava.proteomics.io.ms.spectrum.SptxtWriter
 
SptxtWriter(File, boolean, PeakList.Precision) - Constructor for class org.expasy.mzjava.proteomics.io.ms.spectrum.SptxtWriter
 
SqrtTransformer<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist.peaktransformer

Performs a square root transform on peak intensities.

SqrtTransformer() - Constructor for class org.expasy.mzjava.core.ms.peaklist.peaktransformer.SqrtTransformer
 
start() - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar

Initialize progress bar (mandatory to restart bar in Indeterminate mode)

start(int) - Method in class org.expasy.mzjava.core.ms.consensus.ConsensusPeakSink
 
start(int) - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakProcessor
 
start(int) - Method in class org.expasy.mzjava.core.ms.peaklist.DelayedPeakProcessor
 
start(int) - Method in class org.expasy.mzjava.core.ms.peaklist.PeakCollectorSink
 
start(int) - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.NPeaksFilter
 
start(int) - Method in class org.expasy.mzjava.core.ms.peaklist.peakfilter.NPeaksPerBinFilter
 
start(int) - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakSink

Called before a new PeakList is processed.

start(int) - Method in class org.expasy.mzjava.core.ms.peaklist.peaktransformer.IonCurrentNormalizer
 
start - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType
 
start(int) - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusPeakSink
 
startDocument() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.NamespaceFilterXMLReader
 
startElement(String, String, String, Attributes) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.NamespaceFilterXMLReader
 
startPrefixMapping(String, String) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.NamespaceFilterXMLReader
 
startScan - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
 
staticHash(AtomicSymbol, int) - Static method in class org.expasy.mzjava.core.mol.Atom
 
staticQuant - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioSummary
 
staticQuantLabel - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioTimestamp
 
status - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak
 
status - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak
 
status - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioPeptideData
 
stop() - Method in class org.expasy.mzjava.app.pb.ConsoleProgressBar

Interrupt the task (mandatory to complete Inderminate mode)

submit(PSMReaderCallback) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader
 
subSample - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SampleType
 
SubSampleType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

References to the individual component samples within a mixed parent sample.

SubSampleType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SubSampleType
 
subSequence(int, int) - Method in class org.expasy.mzjava.proteomics.mol.Peptide

Returns a new peptide that is a sub sequence of this peptide.

subSequence(IonType, int) - Method in class org.expasy.mzjava.proteomics.mol.Peptide

Create a sub sequence for the give ion type and residue number

 Given peptide CERVILAS subSequence(y, 1) will return S, subSequence(b, 1) will return C
 subSequence(b, 3) will return CER.

Substituent - Class in org.expasy.mzjava.glycomics.mol
 
Substituent(String, Composition) - Constructor for class org.expasy.mzjava.glycomics.mol.Substituent
 
Substituent(Substituent) - Constructor for class org.expasy.mzjava.glycomics.mol.Substituent
 
substituentEdgeMultimap - Variable in class org.expasy.mzjava.glycomics.mol.SaccharideGraph
 
SubstituentLinkage - Class in org.expasy.mzjava.glycomics.mol
 
SubstituentLinkage(Integer, Composition) - Constructor for class org.expasy.mzjava.glycomics.mol.SubstituentLinkage
 
SubstituentLinkage(Optional<Integer>, Optional<Composition>) - Constructor for class org.expasy.mzjava.glycomics.mol.SubstituentLinkage
 
SubstituentLookup - Interface in org.expasy.mzjava.glycomics.mol
 
substitutionModification - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideType
 
SubstitutionModificationType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

A modification where one residue is substituted by another (amino acid change).

SubstitutionModificationType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SubstitutionModificationType
 
subtractCompositions(Composition, Composition) - Static method in class org.expasy.mzjava.core.mol.Composition
 
summaryXml - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis
 
Symbol - Interface in org.expasy.mzjava.core.mol
 
symbol - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
 
symbol - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
 
symbol - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ElemRefT
 
SymbolSequence<S extends Symbol> - Interface in org.expasy.mzjava.core.mol
 




T

targetDecoyRatio - Variable in class org.expasy.mzjava.stats.statscores.FitDecoyScoreStatistics
 
targetMass - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraResult.Intensity
 
targetScores - Variable in class org.expasy.mzjava.stats.statscores.ScoreStatistics
 
termFixedModMap - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader
 
terminalModification - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
 
terminus - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
 
termSet - Static variable in enum org.expasy.mzjava.proteomics.mol.modification.ModAttachment
 
testSignificance(double, double) - Static method in class org.expasy.mzjava.stats.PoissonUtils

Retruns d for a test of significance between two Poisson counts in samples of equal counts.

testSignificance(double, double, double, double) - Static method in class org.expasy.mzjava.stats.PoissonUtils

Retruns d for a test of significance between two Poisson counts where the sample sizes are unequal.

text - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.XrefT
 
ThermoFisherOrbitrapTitleParser - Class in org.expasy.mzjava.core.io.ms.spectrum.mgf

Title parse for data obtained from Savitski et.

ThermoFisherOrbitrapTitleParser() - Constructor for class org.expasy.mzjava.core.io.ms.spectrum.mgf.ThermoFisherOrbitrapTitleParser
 
threshold - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionProtocolType
 
threshold - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType
 
ThresholdFilter<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist.peakfilter

Peak processor that removes any peaks that have an intensity that is < threshold

ThresholdFilter(double) - Constructor for class org.expasy.mzjava.core.ms.peaklist.peakfilter.ThresholdFilter
 
ThresholdFilter(double, ThresholdFilter.Inequality) - Constructor for class org.expasy.mzjava.core.ms.peaklist.peakfilter.ThresholdFilter
 
ThresholdFilter.Inequality - Enum in org.expasy.mzjava.core.ms.peaklist.peakfilter
 
ThresholdPeakPairFilter<X extends PeakAnnotation,Y extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.filter

Peak pair processor that removes any peak pairs where both of the intensities are < threshold

ThresholdPeakPairFilter(double) - Constructor for class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.filter.ThresholdPeakPairFilter

Create a ThresholdPeakPairFilter

thresholds - Variable in class org.expasy.mzjava.stats.ROCTable
 
TicCheck - Class in org.expasy.mzjava.external.io.ms.spectrum.mzml
 
TicCheck() - Constructor for class org.expasy.mzjava.external.io.ms.spectrum.mzml.TicCheck
 
time - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak
 
time - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak
 
time - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.AnalysisSummary
 
time - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp
 
TimeUnit - Enum in org.expasy.mzjava.core.ms.spectrum

Retention time unit

timeWidth - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak
 
timeWidth - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak
 
title - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType
 
title - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT
 
TITLE_CV - Static variable in class org.expasy.mzjava.proteomics.io.ms.ident.MzIdentMlReader
 
TitleParser - Interface in org.expasy.mzjava.core.io.ms.spectrum.mgf

This interface has to be implemented by parsers that can extract information from
 the MGF TITLE line.

TitleSearchResultMap - Class in org.expasy.mzjava.proteomics.ms.ident
 
TitleSearchResultMap() - Constructor for class org.expasy.mzjava.proteomics.ms.ident.TitleSearchResultMap
 
tmpAnnotationMap - Variable in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList.AbstractMergePeakSink
 
tmpSize - Variable in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList.AbstractMergePeakSink
 
tmpTotalIonCurrent - Variable in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList.AbstractMergePeakSink
 
toArray() - Method in class org.expasy.mzjava.glycomics.mol.NodeSet
 
toArray(T[]) - Method in class org.expasy.mzjava.glycomics.mol.NodeSet
 
toArrayList(IterativeReader<T>) - Static method in class org.expasy.mzjava.core.io.IterativeReaders
 
toBarePeptide() - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Convert this PeptideMatch to a peptide containing only the bare peptide sequence.

toDefaultSpectrumQuerySpectrumAttribute(MsnSpectrum) - Static method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriter

Create the following spectrum format 'basename.scanNumberStart.scanNumberEnd.charge' or
 'basename.scanNumberIndex.scanNumberIndex.charge' if no scan numbers

toDoubles(double[], Double[]) - Static method in class org.expasy.mzjava.utils.PrimitiveArrayUtils

Convert double array to Double array.

toDoubles(double[], Double[], int) - Static method in class org.expasy.mzjava.utils.PrimitiveArrayUtils

Convert double array to Double array.

toInteger(Polarity, int) - Static method in enum org.expasy.mzjava.core.ms.peaklist.Polarity
 
Tolerance - Class in org.expasy.mzjava.core.ms

Interface for specifying a tolerance

Tolerance() - Constructor for class org.expasy.mzjava.core.ms.Tolerance
 
tolerance - Variable in class org.expasy.mzjava.utils.function.ChargeMzSplitter
 
Tolerance.Location - Enum in org.expasy.mzjava.core.ms
 
ToleranceType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

The tolerance of the search given as a plus and minus value with units.

ToleranceType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ToleranceType
 
toPeptide() - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Convert this PeptideMatch to a peptide

toPeptide(ModificationMatchResolver) - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Convert this PeptideMatch to a peptide using the supplied modificationMatchResolver
 to convert ModificationMatch instances to Modifications.

TopNList<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist.peakfilter

List that retains the size peaks that have the largest intensities.

TopNList(int) - Constructor for class org.expasy.mzjava.core.ms.peaklist.peakfilter.TopNList

Constructs a TopNList that retains the top size peaks.

topNList - Variable in class org.expasy.mzjava.core.ms.peaklist.peaktransformer.NHighestPeaksNormalizer
 
TopPeakPairTransformer<X extends PeakAnnotation,Y extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer

Normalizes each vector so that the most intense peak has an intensity of maxIntensity

TopPeakPairTransformer(double) - Constructor for class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.TopPeakPairTransformer
 
toSpectrumQuery(MsnSpectrum) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriter

Convert MsnSpectrum to PepXml element SpectrumQuery

toSptxtString() - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation

Convert this annotation to a SptxtString

toString() - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader.ParseContext
 
toString() - Method in class org.expasy.mzjava.core.mol.Atom
 
toString() - Method in class org.expasy.mzjava.core.mol.Composition.Builder

Return the atomic composition string defined in AtomicCompositionParser

toString() - Method in class org.expasy.mzjava.core.mol.Composition
 
toString() - Method in class org.expasy.mzjava.core.mol.NumericMass
 
toString() - Method in class org.expasy.mzjava.core.ms.cluster.SimEdge
 
toString() - Method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
 
toString() - Method in class org.expasy.mzjava.core.ms.peaklist.ArrayCursor
 
toString() - Method in class org.expasy.mzjava.core.ms.peaklist.Peak
 
toString() - Method in class org.expasy.mzjava.core.ms.spectrum.AnnotatedPeak
 
toString() - Method in class org.expasy.mzjava.core.ms.spectrum.LibPeakAnnotation
 
toString() - Method in class org.expasy.mzjava.core.ms.spectrum.RetentionTimeDiscrete
 
toString() - Method in class org.expasy.mzjava.core.ms.spectrum.RetentionTimeInterval
 
toString() - Method in class org.expasy.mzjava.core.ms.spectrum.ScanNumberDiscrete
 
toString() - Method in class org.expasy.mzjava.core.ms.spectrum.ScanNumberInterval
 
toString() - Method in class org.expasy.mzjava.glycomics.mol.CutIndexes
 
toString() - Method in class org.expasy.mzjava.glycomics.mol.GlycosidicLinkage
 
toString() - Method in class org.expasy.mzjava.glycomics.mol.Monosaccharide
 
toString() - Method in class org.expasy.mzjava.glycomics.mol.NodeSet
 
toString() - Method in class org.expasy.mzjava.glycomics.mol.SEdge
 
toString() - Method in class org.expasy.mzjava.glycomics.mol.SNode
 
toString() - Method in class org.expasy.mzjava.glycomics.mol.Substituent
 
toString() - Method in class org.expasy.mzjava.glycomics.mol.SubstituentLinkage
 
toString() - Method in class org.expasy.mzjava.hadoop.io.SpectrumKey
 
toString() - Method in class org.expasy.mzjava.proteomics.mol.AminoAcidSequence
 
toString() - Method in class org.expasy.mzjava.proteomics.mol.digest.CleavageSiteMatcher
 
toString() - Method in class org.expasy.mzjava.proteomics.mol.modification.Modification
 
toString() - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodManager
 
toString() - Method in class org.expasy.mzjava.proteomics.mol.Protein
 
toString() - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum
 
toString() - Method in class org.expasy.mzjava.proteomics.ms.dbsearch.Digest
 
toString() - Method in class org.expasy.mzjava.proteomics.ms.ident.ModificationMatch
 
toString(NumberFormat) - Method in class org.expasy.mzjava.proteomics.ms.ident.ModificationMatch
 
toString() - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch
 
toString() - Method in class org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
 
toString() - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation
 
toString() - Method in class org.expasy.mzjava.proteomics.ms.spectrum.PepLibPeakAnnotation
 
toString() - Method in class org.expasy.mzjava.stats.FrequencyTable
 
toString(boolean) - Method in class org.expasy.mzjava.stats.FrequencyTable

Returns a string representation of this FrequencyTable

toString(String, FrequencyTable...) - Static method in class org.expasy.mzjava.stats.FrequencyTable

Summarize the tables in one string

toString() - Method in class org.expasy.mzjava.stats.Histogram.Normalization
 
toString() - Method in class org.expasy.mzjava.stats.HistogramImpl
 
toString() - Method in class org.expasy.mzjava.stats.ROCTable
 
toString() - Method in class org.expasy.mzjava.utils.Counter
 
toString(List<int[]>) - Static method in class org.expasy.mzjava.utils.MixedRadixNtupleGenerator

A simple string converter for n-tuples.

toStringNotNormalize(String, FrequencyTable...) - Static method in class org.expasy.mzjava.stats.FrequencyTable

Summarize the tables in one string without normalizing the frequencies

toSymbolString() - Method in interface org.expasy.mzjava.core.mol.SymbolSequence

String containing the Symbols

toSymbolString() - Method in class org.expasy.mzjava.proteomics.mol.AminoAcidSequence

Returns a string containing the amino acids and ignores the modifications.

toSymbolString() - Method in class org.expasy.mzjava.proteomics.mol.Protein
 
toSymbolString() - Method in class org.expasy.mzjava.proteomics.ms.ident.PeptideMatch
 
toTable(FrequencyTable...) - Static method in class org.expasy.mzjava.stats.FrequencyTable

Create an array of TDoubleArrayList that contains the frequencies from the tables

totalIonCurrent - Variable in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList
 
totNumIons - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
translationTable - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DatabaseTranslationType
 
translationTableRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType
 
TranslationTableType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

The table used to translate codons into nucleic acids e.g.

TranslationTableType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.TranslationTableType
 
TraversalComparator - Interface in org.expasy.mzjava.glycomics.mol

A comparator function for imposing order on the children of a node in a SaccharideGraph.

trim(double[], int) - Static method in class org.expasy.mzjava.utils.PrimitiveArrayUtils

Trim the arr to the size of this DoublePeakList

trim(float[], int) - Static method in class org.expasy.mzjava.utils.PrimitiveArrayUtils

Trim the arr to the size of this DoublePeakList

trimToSize() - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList

Trims the capacity of this DoublePeakList instance to be the
 list's current size.

trimToSize() - Method in class org.expasy.mzjava.core.ms.peaklist.DoubleFloatPeakList

Trims the capacity of this DoublePeakList instance to be the
 list's current size.

trimToSize() - Method in class org.expasy.mzjava.core.ms.peaklist.DoublePeakList

Trims the capacity of this DoublePeakList instance to be the
 list's current size.

trimToSize() - Method in class org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList

Trims the capacity of this DoublePeakList instance to be the
 list's current size.

trimToSize() - Method in class org.expasy.mzjava.core.ms.peaklist.FloatPeakList

Trims the capacity of this DoublePeakList instance to be the
 list's current size.

trimToSize() - Method in interface org.expasy.mzjava.core.ms.peaklist.PeakList

Trims the capacity of this DoublePeakList instance to be the
 list's current size.

trimToSize() - Method in class org.expasy.mzjava.core.ms.spectrum.Spectrum
 
trueNegatives - Variable in class org.expasy.mzjava.stats.ROCTable
 
truePositives - Variable in class org.expasy.mzjava.stats.ROCTable
 
turnStrict(Set<C>) - Method in class org.expasy.mzjava.external.io.ms.spectrum.ConsistencyChecker

Set the given checks as strict

turnStrict(Set<C>) - Method in interface org.expasy.mzjava.external.io.ms.spectrum.ConsistencyCheckHandler

Make these checks strict (throw a ConsistencyCheckException if a check fails)

turnStrict(Set<MzmlConsistencyCheck>) - Method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.EbiMzmlReader
 
turnTolerant() - Method in class org.expasy.mzjava.external.io.ms.spectrum.ConsistencyChecker

All strict checks become tolerant

turnTolerant(Set<C>) - Method in class org.expasy.mzjava.external.io.ms.spectrum.ConsistencyChecker

Set the given checks as tolerant

turnTolerant(Set<C>) - Method in interface org.expasy.mzjava.external.io.ms.spectrum.ConsistencyCheckHandler

Make these checks tolerant (log a message if a check fails)

turnTolerant(Set<MzmlConsistencyCheck>) - Method in class org.expasy.mzjava.external.io.ms.spectrum.mzml.EbiMzmlReader
 
type - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.UserParamType
 
type - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
 
type - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.NameValueType
 




U

uncompress(byte[], int, int) - Static method in class org.expasy.mzjava.core.io.ms.spectrum.BytesUtils
 
UNDEFINED_URI - Static variable in class org.expasy.mzjava.utils.URIBuilder
 
UnimodManager - Class in org.expasy.mzjava.proteomics.mol.modification.unimod

This manager handles modifications registering and look ups from many points
 of view: the names, the masses and the modified sites (AA + terms).

UnimodMod - Class in org.expasy.mzjava.proteomics.mol.modification.unimod

A extension of the Modification class to store UniMod specific fields.

UnimodMod(int, boolean, String, String, String, TObjectIntMap<Atom>, List<String>, List<NeutralLoss>, List<NeutralLoss>) - Constructor for class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodMod
 
UnimodMod.Builder - Class in org.expasy.mzjava.proteomics.mol.modification.unimod
 
UnimodMod.Builder() - Constructor for class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodMod.Builder
 
UnimodModificationResolver - Class in org.expasy.mzjava.proteomics.mol.modification.unimod

A Modification  that converts Strings to modifications.

UnimodModificationResolver() - Constructor for class org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodModificationResolver
 
UnimodT - Class in org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb

Java class for unimod_t complex type.

UnimodT() - Constructor for class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.UnimodT
 
UniprotFastaHeaderParser - Class in org.expasy.mzjava.proteomics.io.mol.fasta
 
UniprotFastaHeaderParser() - Constructor for class org.expasy.mzjava.proteomics.io.mol.fasta.UniprotFastaHeaderParser
 
unitAccession - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AbstractParamType
 
unitCvRef - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AbstractParamType
 
unitName - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AbstractParamType
 
UnitVectorNormalizer<A extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.peaklist.peaktransformer

Rescales the intensities so that the length of the intensity vector is equal to 1.

UnitVectorNormalizer() - Constructor for class org.expasy.mzjava.core.ms.peaklist.peaktransformer.UnitVectorNormalizer
 
UnitVectorPeakPairTransformer<X extends PeakAnnotation,Y extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer

Rescales the intensities so that the length of the each intensity vector is equal to 1.

UnitVectorPeakPairTransformer() - Constructor for class org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.UnitVectorPeakPairTransformer
 
UNKNOWN - Static variable in class org.expasy.mzjava.glycomics.mol.GlycosidicLinkage
 
UNKNOWN - Static variable in class org.expasy.mzjava.glycomics.mol.SubstituentLinkage
 
UNKNOWN_AA - Static variable in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader
 
UnknownModListener - Interface in org.expasy.mzjava.proteomics.io.ms.ident

A listener that call back ProteinPilotPsmReader when a read modification
 has not been recognized

unmarshal(ModT) - Method in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModificationTypeAdapter
 
UnresolvableModificationMatchException - Exception in org.expasy.mzjava.proteomics.ms.ident
 
UnresolvableModificationMatchException(ModificationMatch) - Constructor for exception org.expasy.mzjava.proteomics.ms.ident.UnresolvableModificationMatchException
 
UnsortedPeakListException - Exception in org.expasy.mzjava.core.ms.peaklist
 
UnsortedPeakListException(int) - Constructor for exception org.expasy.mzjava.core.ms.peaklist.UnsortedPeakListException
 
UnsortedPeakListException(String, int) - Constructor for exception org.expasy.mzjava.core.ms.peaklist.UnsortedPeakListException
 
UnsortedPeakListException(String, UnsortedPeakListException) - Constructor for exception org.expasy.mzjava.core.ms.peaklist.UnsortedPeakListException
 
uri - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisSoftwareType
 
uri - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.CvType
 
uri(URI) - Method in class org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.BuilderOld
 
URIBuilder - Class in org.expasy.mzjava.utils
 
URIBuilder(String, String) - Constructor for class org.expasy.mzjava.utils.URIBuilder
 
url - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
 
url - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.XrefT
 
use - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioContribution
 
useAnnotationResolver(AnnotationResolver) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.MspReader.Builder
 
useAnnotationResolver(AnnotationResolver) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.SptxtReader.Builder
 
useDigestionController(DigestionController) - Method in interface org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumDB.DigestDSL

Set the digestion controller that is used by the digester

useModificationResolver(ModificationResolver) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.MspReader.Builder
 
useModificationResolver(ModificationResolver) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.SptxtReader.Builder
 
useMspAnnotationResolver() - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.MspReader.Builder
 
usePeakProcessorChain(PeakProcessorChain<PepLibPeakAnnotation>) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.MspReader.Builder
 
usePeakProcessorChain(PeakProcessorChain<PepLibPeakAnnotation>) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.SptxtReader.Builder
 
usernameOfPoster - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT
 
userParam - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ParamType
 
UserParamType - Class in org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110

A single user-defined parameter.

UserParamType() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.UserParamType
 
useSkipAnnotationResolver() - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.MspReader.Builder
 
useSkipAnnotationResolver() - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.SptxtReader.Builder
 
useSpectraLibCommentParser(SpectraLibCommentParser) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.MspReader.Builder
 
useSpectraLibCommentParser(SpectraLibCommentParser) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.SptxtReader.Builder
 
useSpectraStAnnotationResolver() - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.SptxtReader.Builder
 
UUIDReader - Class in org.expasy.mzjava.avro.io
 
UUIDReader() - Constructor for class org.expasy.mzjava.avro.io.UUIDReader
 
uuidReader - Variable in class org.expasy.mzjava.proteomics.avro.io.PeptideConsensusSpectrumReader
 
UUIDWriter - Class in org.expasy.mzjava.avro.io
 
UUIDWriter() - Constructor for class org.expasy.mzjava.avro.io.UUIDWriter
 
uuidWriter - Variable in class org.expasy.mzjava.proteomics.avro.io.PeptideConsensusSpectrumWriter
 




V

value - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AbstractParamType
 
value() - Method in enum org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ActivationMethodType
 
value() - Method in enum org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.EngineType
 
value() - Method in enum org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MassType
 
value() - Method in enum org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ModelDisType
 
value - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.NameValueType
 
value() - Method in enum org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.PositionT
 
valueAttribute - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.NameValueType
 
valueOf(String) - Static method in enum org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader.ConsistencyCheck

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.core.mol.AtomicSymbol

Returns the enum constant of this type with the specified name.

valueOf(String, PeakList.Precision) - Static method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList

Create a peak list from a string

valueOf(String, PeakList) - Static method in class org.expasy.mzjava.core.ms.peaklist.AbstractPeakList

Create a peak list from a string

valueOf(String) - Static method in enum org.expasy.mzjava.core.ms.peaklist.peakfilter.AbstractMergePeakFilter.IntensityMode

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.core.ms.peaklist.peakfilter.BinnedSpectrumFilter.IntensityMode

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.core.ms.peaklist.peakfilter.CentroidFilter.IntensityMode

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.core.ms.peaklist.peakfilter.ThresholdFilter.Inequality

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.core.ms.peaklist.PeakList.Precision

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.core.ms.peaklist.Polarity

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.core.ms.spectrum.FragmentType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.core.ms.spectrum.IonType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.core.ms.spectrum.TimeUnit

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.core.ms.Tolerance.Location

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.external.io.ms.spectrum.mzml.MzmlConsistencyCheck

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.glycomics.mol.Anomericity

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.glycomics.mol.CutDirection

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.glycomics.mol.MonosaccharideClass

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.glycomics.mol.MonosaccharideSuperclass

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.glycomics.mol.RingType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.glycomics.mol.SaccharideGraph.AbstractBuilder.BuildSate

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.glycomics.mol.SaccharideGraph.Traversal

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ActivationMethodType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.EngineType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MassType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ModelDisType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader.ModMassStorage

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriter.ConsistencyCheck

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.proteomics.mol.AminoAcid

Returns the enum constant of this type with the specified name.

valueOf(char) - Static method in enum org.expasy.mzjava.proteomics.mol.AminoAcid
 
valueOf(String) - Static method in enum org.expasy.mzjava.proteomics.mol.digest.Protease

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.proteomics.mol.digest.ProteinDigester.CleavageSiteIteration

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.proteomics.mol.modification.ModAttachment

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.PositionT

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.Status

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.proteomics.ms.dbsearch.DigestDB.AmbiguousAminoAcidAction

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.proteomics.ms.ident.PeptideProteinMatch.HitType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.stats.Classification

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.stats.Histogram.Normalization.NormType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.expasy.mzjava.stats.statscores.ScoreStatistics.SortAction

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in class org.expasy.mzjava.utils.NumberFormatFactory
 
valueOf(int) - Static method in class org.expasy.mzjava.utils.NumberFormatFactory

Make a new instance of DecimalFormat with one maximum integer digit.

valueOf(int, int) - Static method in class org.expasy.mzjava.utils.NumberFormatFactory

Make a new instance of DecimalFormat given the maximum integer and fraction digits.

valueOfBinNumWidthMin(int, double, double) - Static method in class org.expasy.mzjava.stats.HistogramImpl
 
valueOfBinWidthMinMax(double, double, double) - Static method in class org.expasy.mzjava.stats.HistogramImpl
 
values() - Static method in enum org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader.ConsistencyCheck

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.core.mol.AtomicSymbol

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.core.ms.peaklist.peakfilter.AbstractMergePeakFilter.IntensityMode

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.core.ms.peaklist.peakfilter.BinnedSpectrumFilter.IntensityMode

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.core.ms.peaklist.peakfilter.CentroidFilter.IntensityMode

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.core.ms.peaklist.peakfilter.ThresholdFilter.Inequality

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.core.ms.peaklist.PeakList.Precision

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.core.ms.peaklist.Polarity

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.core.ms.spectrum.FragmentType

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.core.ms.spectrum.IonType

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.core.ms.spectrum.TimeUnit

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.core.ms.Tolerance.Location

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.external.io.ms.spectrum.mzml.MzmlConsistencyCheck

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.glycomics.mol.Anomericity

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.glycomics.mol.CutDirection

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Method in class org.expasy.mzjava.glycomics.mol.DefaultMonosaccharideLookup

Return a list of the monosaccharides specified in Monosaccharide Lookup file.

values() - Method in class org.expasy.mzjava.glycomics.mol.DefaultSubstituentLookup

Return a list of the substituents specified in Substituent Lookup file.

values() - Static method in enum org.expasy.mzjava.glycomics.mol.MonosaccharideClass

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Method in interface org.expasy.mzjava.glycomics.mol.MonosaccharideLookup

Return a list of the monosaccharides specified in Monosaccharide Lookup file.

values() - Static method in enum org.expasy.mzjava.glycomics.mol.MonosaccharideSuperclass

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.glycomics.mol.RingType

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.glycomics.mol.SaccharideGraph.AbstractBuilder.BuildSate

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.glycomics.mol.SaccharideGraph.Traversal

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Method in interface org.expasy.mzjava.glycomics.mol.SubstituentLookup

Return a list of the substituents specified in Substituent Lookup file.

values - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FragmentArrayType
 
values() - Static method in enum org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ActivationMethodType

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.EngineType

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MassType

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ModelDisType

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader.ModMassStorage

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriter.ConsistencyCheck

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.proteomics.mol.AminoAcid

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.proteomics.mol.digest.Protease

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.proteomics.mol.digest.ProteinDigester.CleavageSiteIteration

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.proteomics.mol.modification.ModAttachment

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.PositionT

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.Status

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.proteomics.ms.dbsearch.DigestDB.AmbiguousAminoAcidAction

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.proteomics.ms.ident.PeptideProteinMatch.HitType

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.stats.Classification

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.stats.Histogram.Normalization.NormType

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum org.expasy.mzjava.stats.statscores.ScoreStatistics.SortAction

Returns an array containing the constants of this enum type, in
the order they are declared.

variable - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
 
variable - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
 
vectorize(PeakList<X>, PeakList<Y>) - Method in class org.expasy.mzjava.core.ms.spectrasim.AbstractSimFunc

Aligns the two PeakLists and then processes the aligned peak tupplets using the
 PeakPairProcessor chain.

version - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisSoftwareType
 
version - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.CvType
 
version - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType
 
version - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchDatabaseType
 
version - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioSummary
 
version - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.AnalysisSummary
 
version - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioSummary
 
version(String) - Method in class org.expasy.mzjava.utils.URIBuilder
 
visit(SymbolSequence<AminoAcid>, int) - Method in interface org.expasy.mzjava.proteomics.mol.digest.CleavageSiteVisitor
 
volume - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType
 




W

Weighable - Interface in org.expasy.mzjava.core.mol

The Weighable interface should be implemented by any object that has
 a molecular mass measured.

WeightedPearsonsCorrelationCoeff - Class in org.expasy.mzjava.stats

Static methods to calculate the weighted Pearson's correlation coefficient

WeightedPearsonsSimFunc<X extends PeakAnnotation,Y extends PeakAnnotation> - Class in org.expasy.mzjava.core.ms.spectrasim

Calculates PeakList similarity using the weighted Pearson's correlation coefficient.

WeightedPearsonsSimFunc(Tolerance) - Constructor for class org.expasy.mzjava.core.ms.spectrasim.WeightedPearsonsSimFunc
 
WeightedPearsonsSimFunc(PeakListAligner<X, Y>, PeakPairProcessor<X, Y>...) - Constructor for class org.expasy.mzjava.core.ms.spectrasim.WeightedPearsonsSimFunc
 
wilson(int, int) - Static method in class org.expasy.mzjava.stats.BinomialUtils

Computes the Wilson Interval
 (see http://en.wikipedia.org/wiki/Binomial_proportion_confidence_interval#Wilson_score_interval)
 Given the total number of events and the number of "correct" events, returns in a double-array
 in the first component the center of the Wilson interval and in the second component the
 width of the interval.

windowsParent - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.DatasetDerivation.DataFilter
 
withinTolerance(double, double) - Method in class org.expasy.mzjava.core.ms.AbsoluteTolerance
 
withinTolerance(double, double) - Method in class org.expasy.mzjava.core.ms.PpmTolerance
 
withinTolerance(double, double) - Method in class org.expasy.mzjava.core.ms.Tolerance

Returns true if the actual is within tolerance of the expected

write(O, Encoder) - Method in interface org.expasy.mzjava.avro.io.AvroWriter

Write the value to the encoder

write(Composition, Encoder) - Method in class org.expasy.mzjava.avro.io.CompositionWriter
 
write(LibPeakAnnotation, Encoder) - Method in class org.expasy.mzjava.avro.io.LibPeakAnnotationWriter
 
write(MsnSpectrum, Encoder) - Method in class org.expasy.mzjava.avro.io.MsnSpectrumWriter
 
write(NumericMass, Encoder) - Method in class org.expasy.mzjava.avro.io.NumericMassWriter
 
write(PeakList, Encoder) - Method in class org.expasy.mzjava.avro.io.PeakListWriter
 
write(Peak, Encoder) - Method in class org.expasy.mzjava.avro.io.PeakWriter
 
write(RetentionTimeDiscrete, Encoder) - Method in class org.expasy.mzjava.avro.io.RetentionTimeDiscreteWriter
 
write(RetentionTimeInterval, Encoder) - Method in class org.expasy.mzjava.avro.io.RetentionTimeIntervalWriter
 
write(RetentionTimeList, Encoder) - Method in class org.expasy.mzjava.avro.io.RetentionTimeListWriter
 
write(ScanNumberDiscrete, Encoder) - Method in class org.expasy.mzjava.avro.io.ScanNumberDiscreteWriter
 
write(ScanNumberInterval, Encoder) - Method in class org.expasy.mzjava.avro.io.ScanNumberIntervalWriter
 
write(ScanNumberList, Encoder) - Method in class org.expasy.mzjava.avro.io.ScanNumberListWriter
 
write(UUID, Encoder) - Method in class org.expasy.mzjava.avro.io.UUIDWriter
 
write(MsnSpectrum) - Method in class org.expasy.mzjava.core.io.ms.spectrum.MgfWriter
 
write(String, PeakList, String, String, int) - Method in class org.expasy.mzjava.glycomics.io.ms.gwp.GWPWriter

Write the spectrum

write(DataOutput) - Method in class org.expasy.mzjava.hadoop.io.AvroWritable
 
write(S) - Method in class org.expasy.mzjava.hadoop.io.HadoopSpectraWriter
 
write(DataOutput) - Method in class org.expasy.mzjava.hadoop.io.SpectrumKey
 
write(Modification, Encoder) - Method in class org.expasy.mzjava.proteomics.avro.io.ModificationWriter
 
write(PepFragAnnotation, Encoder) - Method in class org.expasy.mzjava.proteomics.avro.io.PepFragAnnotationWriter
 
write(PepLibPeakAnnotation, Encoder) - Method in class org.expasy.mzjava.proteomics.avro.io.PepLibPeakAnnotationWriter
 
write(PeptideConsensusSpectrum, Encoder) - Method in class org.expasy.mzjava.proteomics.avro.io.PeptideConsensusSpectrumWriter
 
write(PeptideFragment, Encoder) - Method in class org.expasy.mzjava.proteomics.avro.io.PeptideFragmentWriter
 
write(PeptideSpectrum, Encoder) - Method in class org.expasy.mzjava.proteomics.avro.io.PeptideSpectrumWriter
 
write(Peptide, Encoder) - Method in class org.expasy.mzjava.proteomics.avro.io.PeptideWriter
 
write(OutputStream, URI) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriter

Write the PepXml after peptide identifications been collected (see add(spectrum, peptideMatches))

write(File) - Method in class org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriter

Write the PepXml after peptide identifications been collected (see add(spectrum, peptideMatches))

write(PeakList<? extends PeakAnnotation>, Peptide, Collection<String>) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.AbstractSptxtWriter
 
write(PeptideSpectrum) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.SptxtWriter
 
write(PeptideConsensusSpectrum) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.SptxtWriter
 
write(Kryo, Output, O) - Method in class org.expasy.mzjava.spark.KryoAvroSerializer
 
writeAllEventsUntilStartElement(XMLEventReader, String, Writer) - Static method in class org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader.XMLEventUtils
 
writeArray(AbstractAvroWriter<C>, Collection<C>, Encoder) - Method in class org.expasy.mzjava.avro.io.AbstractAvroWriter

Write an array of the objects in list

writeCharge(PeakList, M, Writer) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfWriter
 
writeComment(String) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfWriter
 
writeComment(PeakList, Peptide, Writer, Collection<String>) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.AbstractSptxtWriter
 
writeLibAnnotation(LibPeakAnnotation, Encoder) - Method in class org.expasy.mzjava.avro.io.AbstractLibPeakAnnotationWriter
 
writeLibId(PeakList, Peptide, Writer) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.AbstractSptxtWriter
 
writeLibId(PeakList, Peptide, Writer) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.SptxtWriter
 
writeMap(AbstractAvroWriter<V>, Map<K, V>, Function<K, String>, Encoder) - Method in class org.expasy.mzjava.avro.io.AbstractAvroWriter
 
writeMap(TObjectDoubleMap<K>, Function<K, String>, Encoder) - Method in class org.expasy.mzjava.avro.io.AbstractAvroWriter
 
writeMap(Map<K, ? extends Number>, Function<K, String>, Encoder) - Method in class org.expasy.mzjava.avro.io.AbstractAvroWriter
 
writeMetaData(MsnSpectrum, Encoder) - Method in class org.expasy.mzjava.avro.io.MsnSpectrumMetaDataWriter
 
writeMs1Header(P, Writer) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfWriter
 
writeMs1Header(MgfParameters, Writer) - Method in class org.expasy.mzjava.core.io.ms.spectrum.MgfWriter
 
writeMs2(PeakList<? extends A>, M) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfWriter
 
writeMs2Header(PeakList, M, Writer) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfWriter
 
writeName(PeakList, Peptide, Writer) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.AbstractSptxtWriter
 
writeOptional(AbstractAvroWriter<C>, Optional<C>, Encoder) - Method in class org.expasy.mzjava.avro.io.AbstractAvroWriter

Write an Optional, this writes a union with null

writePeakAnnotations(List<? extends A>, Writer) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfWriter

Subclasses that want to add annotation information to a peak can override this method.

writePeakList(PeakList, Encoder) - Method in class org.expasy.mzjava.avro.io.AbstractPeakListWriter
 
writePeaks(PeakList<? extends A>, Writer) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfWriter
 
writePeaks(PeakList<? extends PeakAnnotation>, Writer) - Method in class org.expasy.mzjava.proteomics.io.ms.spectrum.AbstractSptxtWriter
 
writePepmass(PeakList, Writer) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfWriter
 
writeRtInSeconds(M, Writer) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfWriter
 
writeScans(M, Writer) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfWriter
 
writeSequence(AminoAcidSequence, Encoder) - Method in class org.expasy.mzjava.proteomics.avro.io.AbstractAminoAcidSequenceWriter
 
writeStringArray(Collection<String>, Encoder) - Method in class org.expasy.mzjava.avro.io.AbstractAvroWriter

Writes a collection containing strings as an array

writeTitle(M, Writer) - Method in class org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfWriter
 
writeUnion(Class<C>, C, Encoder) - Method in class org.expasy.mzjava.avro.io.AbstractAvroWriter

Write a union

writeUnionArray(Class<C>, Collection<C>, Encoder) - Method in class org.expasy.mzjava.avro.io.AbstractAvroWriter

Write an array containing a union





X

xpressLight - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioSummary
 
xpressLight - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioTimestamp
 
XpressratioResult - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

XpressratioResult() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult
 
XpressratioSummary - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

XpressratioSummary() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioSummary
 
XpressratioTimestamp - Class in org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117

Java class for anonymous complex type.

XpressratioTimestamp() - Constructor for class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioTimestamp
 
xref - Variable in class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT
 
XrefT - Class in org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb

Java class for xref_t complex type.

XrefT() - Constructor for class org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.XrefT
 




Y

year - Variable in class org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType
 




Z

ZERO - Static variable in class org.expasy.mzjava.core.mol.Mass
 
Zn - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 
Zn_MASS - Static variable in class org.expasy.mzjava.core.mol.PeriodicTable
 

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z