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
createLibraSummaryIsotopicContributionsContributingChannel() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory
createLibraSummaryIsotopicContributionsContributingChannelAffectedChannel() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory
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
createMsmsPipelineAnalysisDatasetDerivation() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory
createMsmsPipelineAnalysisDatasetDerivationDataFilter() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummary() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummaryAnalysisTimestamp() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySampleEnzyme() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySampleEnzymeSpecificity() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySearchSummary() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySearchSummaryAminoacidModification() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySearchSummaryEnzymaticSearchConstraint() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySearchSummarySearchDatabase() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySearchSummarySequenceSearchConstraint() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySearchSummaryTerminalModification() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySpectrumQuery() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySpectrumQuerySearchResult() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySpectrumQuerySearchResultSearchHit() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySpectrumQuerySearchResultSearchHitAlternativeProtein() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySpectrumQuerySearchResultSearchHitAnalysisResult() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySpectrumQuerySearchResultSearchHitModificationInfo() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySpectrumQuerySearchResultSearchHitModificationInfoModAminoacidMass() - Method in class org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory
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
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
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.proteomi