Hierarchy For All Packages

Package Hierarchies:

• org.expasy.mzjava.app.io,
• org.expasy.mzjava.app.pb,
• org.expasy.mzjava.avro.io,
• org.expasy.mzjava.core.io,
• org.expasy.mzjava.core.io.ms.spectrum,
• org.expasy.mzjava.core.io.ms.spectrum.mgf,
• org.expasy.mzjava.core.mol,
• org.expasy.mzjava.core.mol.polymer.prot,
• org.expasy.mzjava.core.ms,
• org.expasy.mzjava.core.ms.cluster,
• org.expasy.mzjava.core.ms.consensus,
• org.expasy.mzjava.core.ms.library,
• org.expasy.mzjava.core.ms.peaklist,
• org.expasy.mzjava.core.ms.peaklist.peakfilter,
• org.expasy.mzjava.core.ms.peaklist.peaktransformer,
• org.expasy.mzjava.core.ms.spectrasim,
• org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor,
• org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.filter,
• org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer,
• org.expasy.mzjava.core.ms.spectrum,
• org.expasy.mzjava.external.io.ms.spectrum,
• org.expasy.mzjava.external.io.ms.spectrum.mzml,
• org.expasy.mzjava.glycomics.io.mol.glycoct,
• org.expasy.mzjava.glycomics.io.ms.gwp,
• org.expasy.mzjava.glycomics.mol,
• org.expasy.mzjava.glycomics.ms.fragment,
• org.expasy.mzjava.glycomics.ms.spectrum,
• org.expasy.mzjava.hadoop.io,
• org.expasy.mzjava.proteomics.avro.io,
• org.expasy.mzjava.proteomics.cookbook,
• org.expasy.mzjava.proteomics.hadoop.io,
• org.expasy.mzjava.proteomics.io.mol,
• org.expasy.mzjava.proteomics.io.mol.fasta,
• org.expasy.mzjava.proteomics.io.ms.ident,
• org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110,
• org.expasy.mzjava.proteomics.io.ms.ident.pepxml,
• org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117,
• org.expasy.mzjava.proteomics.io.ms.spectrum,
• org.expasy.mzjava.proteomics.io.ms.spectrum.msp,
• org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt,
• org.expasy.mzjava.proteomics.mol,
• org.expasy.mzjava.proteomics.mol.digest,
• org.expasy.mzjava.proteomics.mol.modification,
• org.expasy.mzjava.proteomics.mol.modification.unimod,
• org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb,
• org.expasy.mzjava.proteomics.ms.consensus,
• org.expasy.mzjava.proteomics.ms.dbsearch,
• org.expasy.mzjava.proteomics.ms.fragment,
• org.expasy.mzjava.proteomics.ms.ident,
• org.expasy.mzjava.proteomics.ms.spectrum,
• org.expasy.mzjava.script,
• org.expasy.mzjava.spark,
• org.expasy.mzjava.stats,
• org.expasy.mzjava.stats.statscores,
• org.expasy.mzjava.utils,
• org.expasy.mzjava.utils.function

Class Hierarchy

• java.lang.Object
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • java.util.AbstractList<E> (implements java.util.List<E>)
      • java.util.ArrayList<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
        • org.expasy.mzjava.core.ms.spectrum.RetentionTimeList (implements org.expasy.mzjava.utils.Copyable<T>)
        • org.expasy.mzjava.core.ms.spectrum.ScanNumberList (implements org.expasy.mzjava.utils.Copyable<T>)
    • java.util.AbstractSet<E> (implements java.util.Set<E>)
      • org.expasy.mzjava.glycomics.mol.NodeSet<E> (implements java.util.Set<E>)
  • org.expasy.mzjava.core.ms.consensus.AbstractConsensusSpectrumBuilder<A,B,C>
    • org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum.Builder
    • org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.BuilderOld
  • edu.uci.ics.jung.graph.AbstractGraph<V,E> (implements edu.uci.ics.jung.graph.Graph<V,E>, java.io.Serializable)
    • edu.uci.ics.jung.graph.AbstractTypedGraph<V,E>
      • org.expasy.mzjava.core.ms.cluster.JungSimGraphWrapper<V> (implements edu.uci.ics.jung.graph.UndirectedGraph<V,E>)
  • org.expasy.mzjava.core.ms.library.AbstractMapSpectrumLibrary<S> (implements org.expasy.mzjava.core.ms.library.SpectrumLibrary<S>)
    • org.expasy.mzjava.core.ms.library.AbstractIntervalSpectrumLibrary<S>
      • org.expasy.mzjava.core.ms.library.DefaultSpectrumLibrary<S>
      • org.expasy.mzjava.core.ms.library.IntervalSpectrumLibrary<S>
    • org.expasy.mzjava.core.ms.library.DiscreteSpectrumLibrary<S>
  • org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfWriter<A,M,P>
    • org.expasy.mzjava.core.io.ms.spectrum.MgfWriter
  • org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader<A,S> (implements org.expasy.mzjava.core.io.IterativeReader<T>)
    • org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfReader<A,S>
      • org.expasy.mzjava.core.io.ms.spectrum.MgfReader
    • org.expasy.mzjava.proteomics.io.ms.spectrum.DtaReader
    • org.expasy.mzjava.proteomics.io.ms.spectrum.MsLibReader
      • org.expasy.mzjava.proteomics.io.ms.spectrum.MspReader
      • org.expasy.mzjava.proteomics.io.ms.spectrum.SptxtReader
    • org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader
  • org.expasy.mzjava.core.io.ms.spectrum.AbstractMsReader.ParseContext
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AbstractParamType
    • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.CVParamType
    • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.UserParamType
  • org.expasy.mzjava.core.ms.peaklist.AbstractPeakList<A> (implements org.expasy.mzjava.core.ms.peaklist.PeakList<A>)
    • org.expasy.mzjava.core.ms.peaklist.DoubleConstantPeakList<A>
    • org.expasy.mzjava.core.ms.peaklist.DoubleFloatPeakList<A>
    • org.expasy.mzjava.core.ms.peaklist.DoublePeakList<A>
    • org.expasy.mzjava.core.ms.peaklist.FloatConstantPeakList<A>
    • org.expasy.mzjava.core.ms.peaklist.FloatPeakList<A>
  • org.expasy.mzjava.core.ms.peaklist.AbstractPeakList.AbstractMergePeakSink<A,L> (implements org.expasy.mzjava.core.ms.peaklist.PeakSink<A>)
  • org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.AbstractPeakPairProcessor<X,Y> (implements org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.PeakPairProcessor<X,Y>)
    • org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.DelayedPeakPairProcessor<X,Y>
      • org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.TopPeakPairTransformer<X,Y>
      • org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.UnitVectorPeakPairTransformer<X,Y>
    • org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.PeakCountEqualizer<X,Y>
    • org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.PeakPairIntensityLog10Transformer<X,Y>
    • org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.PeakPairIntensityLogETransformer<X,Y>
    • org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.PeakPairIntensitySqrtTransformer<X,Y>
    • org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.transformer.PeakPairIonCurrentNormalizer<X,Y>
    • org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.filter.ThresholdPeakPairFilter<X,Y>
  • org.expasy.mzjava.core.ms.peaklist.AbstractPeakProcessor<IN,OUT> (implements org.expasy.mzjava.core.ms.peaklist.PeakProcessor<IN,OUT>)
    • org.expasy.mzjava.core.ms.peaklist.peaktransformer.AffineTransformer<A>
    • org.expasy.mzjava.core.ms.peaklist.peaktransformer.ArcsinhTransformer<A>
    • org.expasy.mzjava.core.ms.peaklist.DelayedPeakProcessor<IN,OUT>
      • org.expasy.mzjava.core.ms.peaklist.peakfilter.AbstractMergePeakFilter<IN,OUT>
        • org.expasy.mzjava.core.ms.peaklist.peakfilter.LibraryMergePeakFilter<A>
      • org.expasy.mzjava.core.ms.peaklist.peaktransformer.AddFlankingPeaksTransformer<A>
      • org.expasy.mzjava.core.ms.peaklist.peakfilter.BinnedSpectrumFilter<A>
      • org.expasy.mzjava.core.ms.peaklist.peakfilter.CentroidFilter<A>
      • org.expasy.mzjava.core.ms.peaklist.peaktransformer.ContrastEnhancingTransformer<A>
      • org.expasy.mzjava.core.ms.peaklist.peaktransformer.HighestPeakPerBinNormalizer<A>
      • org.expasy.mzjava.core.ms.peaklist.peaktransformer.IonCurrentNormalizer<A>
      • org.expasy.mzjava.core.ms.peaklist.peaktransformer.NHighestPeaksNormalizer
      • org.expasy.mzjava.core.ms.peaklist.peakfilter.NPeaksPerSlidingWindowFilter<A>
      • org.expasy.mzjava.core.ms.peaklist.peaktransformer.NthPeakNormalizer<A>
      • org.expasy.mzjava.core.ms.peaklist.peaktransformer.RankNormalizer<A>
      • org.expasy.mzjava.core.ms.peaklist.peaktransformer.UnitVectorNormalizer<A>
    • org.expasy.mzjava.core.ms.peaklist.peakfilter.FragmentAnnotationFilter<A>
    • org.expasy.mzjava.core.ms.peaklist.peaktransformer.IdentityPeakProcessor<A>
    • org.expasy.mzjava.core.ms.peaklist.peaktransformer.InverseArcsinhTransformer<A>
    • org.expasy.mzjava.core.ms.peaklist.peaktransformer.Log10Transformer<A>
    • org.expasy.mzjava.core.ms.peaklist.peaktransformer.LogTransformer<A>
    • org.expasy.mzjava.core.ms.peaklist.peaktransformer.MzAffineTransformer<A>
    • org.expasy.mzjava.core.ms.peaklist.peakfilter.MzRangeFilter<A>
    • org.expasy.mzjava.core.ms.peaklist.peakfilter.NPeaksFilter<A>
    • org.expasy.mzjava.core.ms.peaklist.peakfilter.NPeaksPerBinFilter<A>
    • org.expasy.mzjava.proteomics.ms.consensus.PeptideFragmentAnnotator
    • org.expasy.mzjava.core.ms.peaklist.peaktransformer.SqrtTransformer<A>
    • org.expasy.mzjava.core.ms.peaklist.peakfilter.ThresholdFilter<A>
  • org.expasy.mzjava.proteomics.io.ms.ident.AbstractPsmCsvReader (implements org.expasy.mzjava.proteomics.io.ms.ident.PsmReader)
    • org.expasy.mzjava.proteomics.io.ms.ident.MaxQuantPsmReader
    • org.expasy.mzjava.proteomics.io.ms.ident.ProteinPilotPsmReader
  • org.expasy.mzjava.core.ms.spectrasim.AbstractSimFunc<X,Y> (implements org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.PeakPairSink<X,Y>, org.expasy.mzjava.core.ms.spectrasim.SimFunc<X,Y>)
    • org.expasy.mzjava.core.ms.spectrasim.DpSimFunc<X,Y>
    • org.expasy.mzjava.core.ms.spectrasim.McNdpSimFunc<X,Y>
    • org.expasy.mzjava.core.ms.spectrasim.NdpSimFunc<X,Y>
    • org.expasy.mzjava.core.ms.spectrasim.PearsonsSimFunc<X,Y>
    • org.expasy.mzjava.core.ms.spectrasim.PspcSimFunc<X,Y>
    • org.expasy.mzjava.core.ms.spectrasim.SharedPeakSimFunc<X,Y>
    • org.expasy.mzjava.core.ms.spectrasim.WeightedPearsonsSimFunc<X,Y>
  • org.expasy.mzjava.proteomics.io.ms.spectrum.AbstractSptxtWriter
    • org.expasy.mzjava.proteomics.io.ms.spectrum.SptxtWriter
  • org.expasy.mzjava.proteomics.mol.digest.AcceptAllDigestionController (implements org.expasy.mzjava.proteomics.mol.digest.DigestionController)
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AffiliationType
  • org.expasy.mzjava.glycomics.mol.AllCrossRingCutType (implements org.expasy.mzjava.glycomics.mol.CrossRingCutType)
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AmbiguousResidueType
  • org.expasy.mzjava.proteomics.mol.AminoAcidSequence (implements org.expasy.mzjava.core.mol.SymbolSequence<S>)
    • org.expasy.mzjava.proteomics.mol.Peptide (implements org.expasy.mzjava.core.mol.Weighable)
    • org.expasy.mzjava.proteomics.mol.PeptideFragment
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisCollectionType
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisDataType
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisProtocolCollectionType
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisSampleCollectionType
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisSoftwareListType
  • org.expasy.mzjava.core.io.ms.spectrum.mgf.AnalystTitleParser (implements org.expasy.mzjava.core.io.ms.spectrum.mgf.TitleParser)
  • org.expasy.mzjava.core.ms.peaklist.ArrayCursor<A> (implements org.expasy.mzjava.core.ms.peaklist.PeakCursor<A>)
  • org.expasy.mzjava.proteomics.ms.dbsearch.ArrayDigestDB (implements org.expasy.mzjava.proteomics.ms.dbsearch.DigestDB)
  • org.expasy.mzjava.proteomics.ms.dbsearch.ArrayDigestDB.Builder
  • org.expasy.mzjava.utils.ArrayIndexComparator<T> (implements java.util.Comparator<T>)
  • org.expasy.mzjava.utils.ArrayIndexSorter
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioContribution
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcHeavypeak
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioLcLightpeak
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioPeptideData
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioResult
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioSummary
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.AsapratioTimestamp
  • org.expasy.mzjava.core.mol.Atom (implements java.lang.Comparable<T>)
  • org.expasy.mzjava.core.mol.AtomicCompositionParser
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AuditCollectionType
  • org.expasy.mzjava.avro.io.AvroIO<U>
    • org.expasy.mzjava.avro.io.AbstractAvroReader<O> (implements org.expasy.mzjava.avro.io.AvroReader<O>)
      • org.expasy.mzjava.proteomics.avro.io.AbstractAminoAcidSequenceReader<O>
        • org.expasy.mzjava.proteomics.avro.io.PeptideFragmentReader
        • org.expasy.mzjava.proteomics.avro.io.PeptideReader
      • org.expasy.mzjava.avro.io.AbstractPeakListReader<A,PL>
        • org.expasy.mzjava.avro.io.MsnSpectrumReader
        • org.expasy.mzjava.avro.io.PeakListReader
        • org.expasy.mzjava.proteomics.avro.io.PeptideConsensusSpectrumReader
        • org.expasy.mzjava.proteomics.avro.io.PeptideSpectrumReader
      • org.expasy.mzjava.avro.io.CompositionReader
      • org.expasy.mzjava.avro.io.LibPeakAnnotationReader
      • org.expasy.mzjava.proteomics.avro.io.ModificationReader
      • org.expasy.mzjava.avro.io.NumericMassReader
      • org.expasy.mzjava.avro.io.PeakReader
      • org.expasy.mzjava.proteomics.avro.io.PepFragAnnotationReader
      • org.expasy.mzjava.proteomics.avro.io.PepLibPeakAnnotationReader
      • org.expasy.mzjava.avro.io.RetentionTimeDiscreteReader
      • org.expasy.mzjava.avro.io.RetentionTimeIntervalReader
      • org.expasy.mzjava.avro.io.RetentionTimeListReader
      • org.expasy.mzjava.avro.io.ScanNumberDiscreteReader
      • org.expasy.mzjava.avro.io.ScanNumberIntervalReader
      • org.expasy.mzjava.avro.io.ScanNumberListReader
      • org.expasy.mzjava.avro.io.UUIDReader
    • org.expasy.mzjava.avro.io.AbstractAvroWriter<O> (implements org.expasy.mzjava.avro.io.AvroWriter<O>)
      • org.expasy.mzjava.proteomics.avro.io.AbstractAminoAcidSequenceWriter<O>
        • org.expasy.mzjava.proteomics.avro.io.PeptideFragmentWriter
        • org.expasy.mzjava.proteomics.avro.io.PeptideWriter
      • org.expasy.mzjava.avro.io.AbstractLibPeakAnnotationWriter<A>
        • org.expasy.mzjava.avro.io.LibPeakAnnotationWriter
        • org.expasy.mzjava.proteomics.avro.io.PepLibPeakAnnotationWriter
      • org.expasy.mzjava.avro.io.AbstractPeakListWriter<PL>
        • org.expasy.mzjava.avro.io.MsnSpectrumWriter
        • org.expasy.mzjava.avro.io.PeakListWriter
        • org.expasy.mzjava.proteomics.avro.io.PeptideConsensusSpectrumWriter
        • org.expasy.mzjava.proteomics.avro.io.PeptideSpectrumWriter
      • org.expasy.mzjava.avro.io.CompositionWriter
      • org.expasy.mzjava.proteomics.avro.io.ModificationWriter
      • org.expasy.mzjava.avro.io.NumericMassWriter
      • org.expasy.mzjava.avro.io.PeakWriter
      • org.expasy.mzjava.proteomics.avro.io.PepFragAnnotationWriter
      • org.expasy.mzjava.avro.io.RetentionTimeDiscreteWriter
      • org.expasy.mzjava.avro.io.RetentionTimeIntervalWriter
      • org.expasy.mzjava.avro.io.RetentionTimeListWriter
      • org.expasy.mzjava.avro.io.ScanNumberDiscreteWriter
      • org.expasy.mzjava.avro.io.ScanNumberIntervalWriter
      • org.expasy.mzjava.avro.io.ScanNumberListWriter
      • org.expasy.mzjava.avro.io.UUIDWriter
  • org.expasy.mzjava.hadoop.io.AvroWritable (implements org.apache.hadoop.io.Writable)
    • org.expasy.mzjava.hadoop.io.AbstractAvroWritable<T>
    • org.expasy.mzjava.hadoop.io.AbstractPeakListValue<PL>
      • org.expasy.mzjava.hadoop.io.MsnSpectrumValue
      • org.expasy.mzjava.hadoop.io.PeakListValue
      • org.expasy.mzjava.proteomics.hadoop.io.PeptideConsensusSpectrumValue
      • org.expasy.mzjava.proteomics.hadoop.io.PeptideSpectrumValue
  • org.expasy.mzjava.proteomics.ms.fragment.BackbonePeakGenerator (implements org.expasy.mzjava.proteomics.ms.fragment.PeptidePeakGenerator<A>)
  • org.expasy.mzjava.stats.BinomialUtils
  • org.expasy.mzjava.core.mol.polymer.prot.BioJavaFastaProteinReader (implements org.expasy.mzjava.core.io.IterativeReader<T>)
  • org.expasy.mzjava.core.io.ms.spectrum.BytesUtils
  • org.expasy.mzjava.spark.Cached<T> (implements java.io.Serializable)
    • org.expasy.mzjava.spark.CachedAbsoluteTolerance
    • org.expasy.mzjava.spark.CachedPpmTolerance
  • org.expasy.mzjava.core.ms.peaklist.peakfilter.CentroidFilter.PeakIntensityInfo
  • org.expasy.mzjava.utils.function.ChargeMzSplitter<V> (implements org.expasy.mzjava.utils.function.Splitter<V>)
    • org.expasy.mzjava.utils.function.PrecursorSplitter
  • org.expasy.mzjava.proteomics.mol.digest.CleavageSiteFinderImpl (implements org.expasy.mzjava.proteomics.mol.digest.CleavageSiteFinder)
  • org.expasy.mzjava.proteomics.mol.digest.CleavageSiteMatcher
  • org.expasy.mzjava.glycomics.mol.CleavedMonosaccharide
  • org.expasy.mzjava.proteomics.mol.modification.CompositeModResolver (implements org.expasy.mzjava.proteomics.mol.modification.ModificationResolver)
  • org.expasy.mzjava.core.mol.Composition.Builder
  • org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.CompositionT
    • org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.NeutralLossT
    • org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.PepNeutralLossT
  • org.expasy.mzjava.core.ms.cluster.CompoundClusterBuilder<V> (implements org.expasy.mzjava.core.ms.cluster.ClusterBuilder<V>)
  • org.expasy.mzjava.core.io.ConcatIterativeReader<T> (implements org.expasy.mzjava.core.io.IterativeReader<T>)
  • org.expasy.mzjava.core.ms.consensus.ConsensusPeakSink<A> (implements org.expasy.mzjava.core.ms.peaklist.PeakSink<A>)
  • org.expasy.mzjava.external.io.ms.spectrum.ConsistencyChecker<C> (implements org.expasy.mzjava.external.io.ms.spectrum.ConsistencyCheckHandler<C>)
  • org.expasy.mzjava.app.pb.ConsoleProgressBar (implements org.expasy.mzjava.app.pb.ProgressBar)
  • org.expasy.mzjava.app.pb.ConsoleProgressBar.View
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ContactRoleType
  • org.expasy.mzjava.utils.Counter
  • org.expasy.mzjava.glycomics.mol.CutDescriptor
  • org.expasy.mzjava.glycomics.mol.CutDescriptorGenerator
  • org.expasy.mzjava.glycomics.mol.CutIndexes
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.CVListType
  • org.expasy.mzjava.external.io.ms.spectrum.mzml.CVParamHelper
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.CvType
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DatabaseFiltersType
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.DatabaseRefreshTimestamp
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DatabaseTranslationType
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DataCollectionType
  • org.expasy.mzjava.proteomics.cookbook.DbSearchPaperExample
  • org.expasy.mzjava.glycomics.mol.DefaultGlycanMassCalculator (implements org.expasy.mzjava.glycomics.mol.GlycanMassCalculator)
  • org.expasy.mzjava.glycomics.io.mol.glycoct.DefaultGlycoCtResolver (implements org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCtResolver)
  • org.expasy.mzjava.glycomics.mol.DefaultMonosaccharideLookup (implements org.expasy.mzjava.glycomics.mol.MonosaccharideLookup)
  • org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.DefaultPeakListAligner<X,Y> (implements org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.PeakListAligner<X,Y>)
  • org.expasy.mzjava.hadoop.io.DefaultSpectrumKeyRawComparator (implements org.apache.hadoop.io.RawComparator<T>)
  • org.expasy.mzjava.glycomics.mol.DefaultSubstituentLookup (implements org.expasy.mzjava.glycomics.mol.SubstituentLookup)
  • org.expasy.mzjava.core.io.ms.spectrum.mgf.DelegatingRegexTitleParser (implements org.expasy.mzjava.core.io.ms.spectrum.mgf.TitleParser)
  • org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph<V> (implements org.expasy.mzjava.core.ms.cluster.SimilarityGraph<V>)
  • org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph.AbstractBuilder<V,G> (implements org.expasy.mzjava.core.ms.cluster.SimilarityGraphBuilder<V,G>)
    • org.expasy.mzjava.core.ms.cluster.DenseSimilarityGraph.Builder<V>
  • org.expasy.mzjava.proteomics.ms.dbsearch.Digest (implements org.expasy.mzjava.core.mol.Weighable)
  • org.expasy.mzjava.external.io.ms.spectrum.mzml.EbiMzmlReader<S> (implements org.expasy.mzjava.external.io.ms.spectrum.ConsistencyCheckHandler<C>, org.expasy.mzjava.core.io.IterativeReader<T>)
  • org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ElemRefT
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymesType
  • org.expasy.mzjava.proteomics.io.mol.FastaProteinReader (implements org.expasy.mzjava.core.io.IterativeReader<T>)
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FileFormatType
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FilterType
  • org.expasy.mzjava.core.ms.cluster.FMeasure
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FragmentArrayType
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FragmentationTableType
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.FragmentationType
  • org.expasy.mzjava.stats.FrequencyTable
  • org.expasy.mzjava.core.ms.cluster.GlobalThresholdClusterBuilder<V> (implements org.expasy.mzjava.core.ms.cluster.ClusterBuilder<V>)
  • org.expasy.mzjava.glycomics.ms.spectrum.GlycanFragAnnotation (implements org.expasy.mzjava.core.ms.peaklist.PeakAnnotation)
  • org.expasy.mzjava.glycomics.ms.spectrum.GlycanFragAnnotation.FragBuilder
  • org.expasy.mzjava.glycomics.ms.fragment.GlycanFragmenter
  • org.expasy.mzjava.glycomics.ms.fragment.GlycanFragmentPeakGenerator (implements org.expasy.mzjava.glycomics.ms.fragment.GlycanPeakGenerator<A>)
  • org.expasy.mzjava.glycomics.mol.GlycanNode (implements org.expasy.mzjava.core.mol.Weighable)
    • org.expasy.mzjava.glycomics.mol.Monosaccharide
    • org.expasy.mzjava.glycomics.mol.Substituent
  • org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCTReader
  • org.expasy.mzjava.glycomics.mol.GlycosidicLinkage (implements org.expasy.mzjava.glycomics.mol.Linkage)
  • org.expasy.mzjava.glycomics.io.ms.gwp.GWPWriter
  • org.expasy.mzjava.hadoop.io.HadoopSpectraReader<A,S> (implements org.expasy.mzjava.core.io.IterativeReader<T>)
  • org.expasy.mzjava.hadoop.io.HadoopSpectraWriter<S>
  • org.expasy.mzjava.stats.Histogram.Normalization
  • org.expasy.mzjava.stats.HistogramImpl (implements org.expasy.mzjava.stats.Histogram)
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.IdentifiableType
    • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AbstractContactType
      • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.OrganizationType
      • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PersonType
    • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.AnalysisSoftwareType
    • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.BibliographicReferenceType
    • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.DBSequenceType
    • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.EnzymeType
    • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ExternalDataType
      • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchDatabaseType
      • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SourceFileType
      • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectraDataType
    • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MassTableType
    • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MeasureType
    • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.MzIdentMLType
    • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceType
    • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideType
    • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinAmbiguityGroupType
    • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionHypothesisType
    • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionListType
    • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionProtocolType
    • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProtocolApplicationType
      • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProteinDetectionType
      • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationType
    • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ProviderType
    • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SampleType
    • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemType
    • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationListType
    • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationProtocolType
    • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationResultType
    • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.TranslationTableType
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.InputSpectraType
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.InputSpectrumIdentificationsType
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.InputsType
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.InteractSummary
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.InteractSummary.Inputfile
  • org.expasy.mzjava.utils.IntervalList
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.IonTypeType
  • org.expasy.mzjava.core.io.IterativeReaders
  • org.expasy.mzjava.core.ms.cluster.KMeansPlusPlusClusterBuilder<V> (implements org.expasy.mzjava.core.ms.cluster.ClusterBuilder<V>)
  • org.expasy.mzjava.proteomics.mol.digest.LengthDigestionController (implements org.expasy.mzjava.proteomics.mol.digest.DigestionController)
  • org.expasy.mzjava.core.ms.spectrum.LibPeakAnnotation (implements org.expasy.mzjava.core.ms.peaklist.PeakAnnotation)
    • org.expasy.mzjava.proteomics.ms.spectrum.PepLibPeakAnnotation
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraResult
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraResult.Intensity
  • org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.LibrarySpectrumBuilder
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.FragmentMasses
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.IsotopicContributions
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.IsotopicContributions.ContributingChannel
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.LibraSummary.IsotopicContributions.ContributingChannel.AffectedChannel
  • org.expasy.mzjava.core.mol.Mass (implements org.expasy.mzjava.core.mol.Weighable)
    • org.expasy.mzjava.core.mol.Composition
      • org.expasy.mzjava.proteomics.mol.modification.NeutralLoss
    • org.expasy.mzjava.core.mol.NumericMass
  • org.expasy.mzjava.core.mol.MassCalculator
    • org.expasy.mzjava.proteomics.mol.AAMassCalculator
  • org.expasy.mzjava.core.io.ms.spectrum.MgfParameters (implements org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfWriter.Parameters)
  • org.expasy.mzjava.utils.MixedRadixNtupleGenerator
  • org.expasy.mzjava.utils.MixedRadixNtupleGenerator.NtupleContainer (implements org.expasy.mzjava.utils.MixedRadixNtupleGenerator.Handler)
  • org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader (implements org.expasy.mzjava.proteomics.io.ms.ident.PsmReader)
  • org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader.PeptideInfoParser
  • org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader.PSMInfoParser
  • org.expasy.mzjava.proteomics.io.ms.ident.MODaPsmReader.SpectrumInfoParser
  • org.expasy.mzjava.proteomics.mol.modification.Modification (implements org.expasy.mzjava.core.mol.Weighable)
    • org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodMod
  • org.expasy.mzjava.proteomics.mol.modification.ModificationLists
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.ModificationMap
  • org.expasy.mzjava.proteomics.ms.ident.ModificationMatch
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ModificationParamsType
  • org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModificationsT
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ModificationType
  • org.expasy.mzjava.proteomics.mol.ModifiedPeptideFactory
  • org.expasy.mzjava.proteomics.mol.ModifiedPeptideFactory.Builder
  • org.expasy.mzjava.proteomics.ms.ident.ModListModMatchResolver (implements org.expasy.mzjava.proteomics.ms.ident.ModificationMatchResolver)
  • org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModT
  • org.expasy.mzjava.app.io.MonitoredIterativeReader<T> (implements org.expasy.mzjava.core.io.IterativeReader<T>)
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.AnalysisSummary
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.DatasetDerivation
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.DatasetDerivation.DataFilter
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
    • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.AminoacidModificationHashable
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SequenceSearchConstraint
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo.ModAminoacidMass
  • org.expasy.mzjava.avro.io.MsnSpectrumMetaDataReader
  • org.expasy.mzjava.avro.io.MsnSpectrumMetaDataWriter
  • org.expasy.mzjava.proteomics.io.ms.spectrum.msp.MspAnnotationResolver (implements org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.AnnotationResolver)
  • org.expasy.mzjava.proteomics.io.ms.spectrum.MspReader.Builder
  • org.expasy.mzjava.proteomics.io.ms.spectrum.MsReaderFactory
  • org.expasy.mzjava.core.ms.cluster.MSTClusterBuilder<V> (implements org.expasy.mzjava.core.ms.cluster.ClusterBuilder<V>)
  • org.expasy.mzjava.proteomics.io.ms.ident.MzIdentMlReader (implements org.expasy.mzjava.proteomics.io.ms.ident.PsmReader)
  • org.expasy.mzjava.spark.MzJavaKryoRegistrator (implements org.apache.spark.serializer.KryoRegistrator)
  • org.expasy.mzjava.hadoop.io.MzJavaSerialization (implements org.apache.hadoop.io.serializer.Serialization<T>)
  • org.expasy.mzjava.spark.MzJavaSparkUtils
  • org.expasy.mzjava.external.io.ms.spectrum.mzml.MzmlSpectrumCheck (implements org.expasy.mzjava.external.io.ms.spectrum.ConsistencyCheck)
    • org.expasy.mzjava.external.io.ms.spectrum.mzml.FirstMzCheck
    • org.expasy.mzjava.external.io.ms.spectrum.mzml.LastMzCheck
    • org.expasy.mzjava.external.io.ms.spectrum.mzml.TicCheck
  • org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader.XMLEventUtils
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.NameValueType
  • org.expasy.mzjava.stats.NormalizedDotProduct
  • org.expasy.mzjava.utils.NumberFormatFactory
  • org.expasy.mzjava.proteomics.mol.modification.NumericModificationResolver (implements org.expasy.mzjava.proteomics.mol.modification.ModificationResolver)
  • org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ObjectFactory
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ObjectFactory
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ObjectFactory
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ParamListType
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ParamType
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ParentOrganizationType
  • org.expasy.mzjava.utils.PathUtils
  • org.expasy.mzjava.core.ms.peaklist.Peak (implements java.lang.Comparable<T>, org.expasy.mzjava.utils.Copyable<T>)
    • org.expasy.mzjava.core.ms.spectrum.AnnotatedPeak<A>
  • org.expasy.mzjava.core.ms.peaklist.PeakCollectorSink<A> (implements org.expasy.mzjava.core.ms.peaklist.PeakSink<A>)
  • org.expasy.mzjava.core.ms.peaklist.PeakListComparator (implements java.util.Comparator<T>, java.io.Serializable)
  • org.expasy.mzjava.core.ms.peaklist.PeakListFactory
  • org.expasy.mzjava.core.ms.peaklist.PeakListMerger<A> (implements org.expasy.mzjava.core.ms.peaklist.PeakSource<A>)
  • org.expasy.mzjava.core.io.ms.spectrum.PeakListPrecisionFormat
  • org.expasy.mzjava.core.ms.cluster.PeakListSimGraphFactory
  • org.expasy.mzjava.core.ms.peaklist.PeakListUtils
  • org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.PeakPairProcessorChain<X,Y>
  • org.expasy.mzjava.core.ms.peaklist.PeakProcessorChain<A>
  • org.expasy.mzjava.stats.PearsonsCorrelationCoeff
  • org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation (implements org.expasy.mzjava.core.ms.peaklist.PeakAnnotation)
  • org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation.Builder
  • org.expasy.mzjava.proteomics.mol.PeptideBuilder
  • org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusPeakSink (implements org.expasy.mzjava.core.ms.peaklist.PeakSink<A>)
  • org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.Builder (implements org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.AnnotationParametersSetter, org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.ConsensusParametersSetter, org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.FilterParametersSetter)
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideEvidenceRefType
  • org.expasy.mzjava.proteomics.ms.fragment.PeptideFragmentAnnotator
  • org.expasy.mzjava.proteomics.ms.fragment.PeptideFragmenter
  • org.expasy.mzjava.proteomics.ms.fragment.PeptideFragmenterFactory
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.PeptideHypothesisType
  • org.expasy.mzjava.proteomics.ms.ident.PeptideMatch (implements java.lang.Comparable<T>, org.expasy.mzjava.core.mol.SymbolSequence<S>)
  • org.expasy.mzjava.proteomics.ms.ident.PeptideMatchComparator (implements java.util.Comparator<T>, java.io.Serializable)
  • org.expasy.mzjava.proteomics.ms.fragment.PeptideNeutralLossPeakGenerator (implements org.expasy.mzjava.proteomics.ms.fragment.PeptidePeakGenerator<A>)
  • org.expasy.mzjava.proteomics.ms.fragment.PeptideNeutralLossPeakGenerator.ModifiedAaPresencePredicate (implements com.google.common.base.Predicate<T>)
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.PeptideprophetResult
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.PeptideprophetResult.SearchScoreSummary
  • org.expasy.mzjava.proteomics.ms.ident.PeptideProteinMatch
  • org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumDB
  • org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader (implements org.expasy.mzjava.proteomics.io.ms.ident.PsmReader)
  • org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriter
  • org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder
  • org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder.Builder
  • org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder.SampleEnzymeBuilder (implements org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder.EnzymeEnd)
  • org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder.SpecificityBuilder (implements org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder.EnzymeEnd)
  • org.expasy.mzjava.core.mol.PeriodicTable
  • org.expasy.mzjava.proteomics.io.mol.fasta.PirPrfFastaHeaderParser (implements org.expasy.mzjava.proteomics.io.mol.fasta.FastaHeaderParser)
  • org.expasy.mzjava.stats.PoissonUtils
  • org.expasy.mzjava.utils.PrimitiveArrayUtils
  • org.expasy.mzjava.proteomics.mol.Protein (implements org.expasy.mzjava.core.mol.SymbolSequence<S>)
  • org.expasy.mzjava.proteomics.mol.Protein.Builder
  • org.expasy.mzjava.proteomics.mol.digest.ProteinDigester
  • org.expasy.mzjava.proteomics.mol.digest.ProteinDigester.Builder
  • org.expasy.mzjava.core.mol.polymer.prot.ProteinFactory
  • org.expasy.mzjava.utils.RegexConstants
  • org.expasy.mzjava.core.io.ms.spectrum.mgf.RegexScanNumTitleParser (implements org.expasy.mzjava.core.io.ms.spectrum.mgf.TitleParser)
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ResidueType
  • org.expasy.mzjava.core.ms.spectrum.RetentionTimeComparator (implements java.util.Comparator<T>, java.io.Serializable)
  • org.expasy.mzjava.core.ms.spectrum.RetentionTimeDiscrete (implements org.expasy.mzjava.core.ms.spectrum.RetentionTime)
  • org.expasy.mzjava.core.ms.spectrum.RetentionTimeInterval (implements org.expasy.mzjava.core.ms.spectrum.RetentionTime)
  • org.expasy.mzjava.utils.function.RetentionTimeSplitter (implements org.expasy.mzjava.utils.function.Splitter<V>)
  • org.expasy.mzjava.stats.ROCTable
    • org.expasy.mzjava.stats.SimROCTable
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.RoleType
  • org.expasy.mzjava.glycomics.mol.SaccharideGraph
    • org.expasy.mzjava.glycomics.mol.Glycan
    • org.expasy.mzjava.glycomics.mol.GlycanFragment
  • org.expasy.mzjava.glycomics.mol.SaccharideGraph.AbstractBuilder<G>
    • org.expasy.mzjava.glycomics.mol.Glycan.Builder
    • org.expasy.mzjava.glycomics.mol.GlycanFragment.Builder
  • org.expasy.mzjava.core.ms.spectrum.ScanNumberDiscrete (implements org.expasy.mzjava.core.ms.spectrum.ScanNumber)
  • org.expasy.mzjava.external.io.ms.spectrum.mzml.ScanNumberIncrementer (implements org.expasy.mzjava.external.io.ms.spectrum.mzml.SpectrumIdParser)
  • org.expasy.mzjava.core.ms.spectrum.ScanNumberInterval (implements org.expasy.mzjava.core.ms.spectrum.ScanNumber)
  • org.expasy.mzjava.stats.ScatterPlotTable
  • org.expasy.mzjava.stats.statscores.ScoreStatistics
    • org.expasy.mzjava.stats.statscores.FirstRankScoreStatistics
    • org.expasy.mzjava.stats.statscores.FitDecoyScoreStatistics
  • org.expasy.mzjava.script.ScriptConfiguredToolRunner
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchDatabaseRefType
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SearchModificationType
  • org.expasy.mzjava.proteomics.ms.ident.SearchResultMap
    • org.expasy.mzjava.proteomics.ms.ident.ScanNumberIndexSearchResultMap
    • org.expasy.mzjava.proteomics.ms.ident.ScanNumberSearchResultMap
    • org.expasy.mzjava.proteomics.ms.ident.TitleSearchResultMap
  • org.expasy.mzjava.glycomics.mol.SEdge<N,L>
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SequenceCollectionType
  • com.esotericsoftware.kryo.Serializer<T>
    • org.expasy.mzjava.spark.KryoAvroSerializer<O>
  • org.expasy.mzjava.core.ms.cluster.SimEdge<V>
  • org.expasy.mzjava.core.ms.library.SimFuncProcedure<LA,LPL,QA,QPL> (implements org.expasy.mzjava.utils.function.Procedure<T>)
  • org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.SkipAnnotationResolver (implements org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.AnnotationResolver)
  • org.expasy.mzjava.glycomics.mol.SNode<T> (implements java.lang.Comparable<T>)
  • org.expasy.mzjava.proteomics.ms.dbsearch.SoftRefPepSpectrumCache (implements org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumCache)
  • org.expasy.mzjava.core.ms.cluster.SparseSimilarityGraph<V> (implements org.expasy.mzjava.core.ms.cluster.SimilarityGraph<V>)
  • org.expasy.mzjava.core.ms.cluster.SparseSimilarityGraph.Builder<V> (implements org.expasy.mzjava.core.ms.cluster.SimilarityGraphBuilder<V,G>)
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpecificityRulesType
  • org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.SpecificityT
  • org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.SpectraStAnnotationResolver (implements org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.AnnotationResolver)
  • org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.SpectraStCommentParser (implements org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.SpectraLibCommentParser)
    • org.expasy.mzjava.proteomics.io.ms.spectrum.msp.MspCommentParser
  • org.expasy.mzjava.core.ms.spectrum.Spectrum<A> (implements org.expasy.mzjava.core.ms.peaklist.PeakList<A>)
    • org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum<A>
      • org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum
    • org.expasy.mzjava.glycomics.ms.spectrum.GlycanSpectrum
    • org.expasy.mzjava.core.ms.spectrum.MsnSpectrum
    • org.expasy.mzjava.proteomics.ms.spectrum.PeptideSpectrum
  • org.expasy.mzjava.core.ms.cluster.SpectrumClusterEvaluator<A,S>
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIdentificationItemRefType
  • org.expasy.mzjava.proteomics.ms.ident.SpectrumIdentifier
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SpectrumIDFormatType
  • org.expasy.mzjava.hadoop.io.SpectrumKey (implements org.apache.hadoop.io.WritableComparable<T>)
  • org.expasy.mzjava.proteomics.io.ms.spectrum.SptxtReader.Builder
  • javax.xml.stream.util.StreamReaderDelegate (implements javax.xml.stream.XMLStreamReader)
    • org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader.NamespaceRewriteDelegate
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SubSampleType
  • org.expasy.mzjava.glycomics.mol.SubstituentLinkage (implements org.expasy.mzjava.glycomics.mol.Linkage)
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.SubstitutionModificationType
  • org.expasy.mzjava.core.io.ms.spectrum.mgf.ThermoFisherOrbitrapTitleParser (implements org.expasy.mzjava.core.io.ms.spectrum.mgf.TitleParser)
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • java.lang.RuntimeException
        • org.expasy.mzjava.external.io.ms.spectrum.ConsistencyCheckException
        • org.expasy.mzjava.proteomics.io.ms.ident.CorruptedPSMFileException
        • java.lang.IllegalArgumentException
          • org.expasy.mzjava.proteomics.mol.digest.CleavageSiteParseException
          • org.expasy.mzjava.proteomics.mol.PeptideParseException
        • org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader.ConsistencyCheckException
        • org.expasy.mzjava.proteomics.ms.ident.UnresolvableModificationMatchException
        • org.expasy.mzjava.core.ms.peaklist.UnsortedPeakListException
  • org.expasy.mzjava.core.ms.Tolerance
    • org.expasy.mzjava.core.ms.AbsoluteTolerance
    • org.expasy.mzjava.core.ms.PpmTolerance
  • org.expasy.mzjava.proteomics.io.ms.ident.mzidentml.v110.ToleranceType
  • org.expasy.mzjava.core.ms.peaklist.peakfilter.TopNList<A>
  • org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodManager
  • org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodMod.Builder
  • org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodModificationResolver (implements org.expasy.mzjava.proteomics.mol.modification.ModificationResolver)
    • org.expasy.mzjava.proteomics.io.ms.ident.ProteinPilotModificationResolver
  • org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.UnimodT
  • org.expasy.mzjava.proteomics.io.mol.fasta.UniprotFastaHeaderParser (implements org.expasy.mzjava.proteomics.io.mol.fasta.FastaHeaderParser)
  • org.expasy.mzjava.utils.URIBuilder
  • org.expasy.mzjava.stats.WeightedPearsonsCorrelationCoeff
  • javax.xml.bind.annotation.adapters.XmlAdapter<ValueType,BoundType>
    • org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.ModificationTypeAdapter
  • org.xml.sax.helpers.XMLFilterImpl (implements org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler, org.xml.sax.XMLFilter)
    • org.expasy.mzjava.proteomics.io.ms.ident.NamespaceFilterXMLReader
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioResult
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioSummary
  • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.XpressratioTimestamp
  • org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.XrefT

Interface Hierarchy

• org.expasy.mzjava.core.io.ms.spectrum.AbstractMgfWriter.Parameters
• org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.AnnotationResolver
• org.expasy.mzjava.avro.io.AvroExternalizable
  • org.expasy.mzjava.avro.io.AvroReader<O>
  • org.expasy.mzjava.avro.io.AvroWriter<O>
• org.expasy.mzjava.stats.Classifier<E>
• org.expasy.mzjava.proteomics.mol.digest.CleavageSiteFinder
• org.expasy.mzjava.proteomics.mol.digest.CleavageSiteVisitor
• org.expasy.mzjava.core.ms.cluster.ClusterBuilder<V>
• org.expasy.mzjava.external.io.ms.spectrum.ConsistencyCheck
• org.expasy.mzjava.external.io.ms.spectrum.ConsistencyCheckHandler<C>
• org.expasy.mzjava.utils.Copyable<T>
  • org.expasy.mzjava.stats.Histogram
  • org.expasy.mzjava.core.ms.peaklist.PeakAnnotation
• org.expasy.mzjava.glycomics.mol.CrossRingCutType
• org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.DefaultPeakListAligner.OverlapListener
• org.expasy.mzjava.proteomics.ms.dbsearch.DigestDB
• org.expasy.mzjava.proteomics.mol.digest.DigestionController
• org.expasy.mzjava.utils.function.DoubleFunction<V>
• org.expasy.mzjava.proteomics.io.mol.fasta.FastaHeaderParser
• org.expasy.mzjava.glycomics.mol.GlycanMassCalculator
• org.expasy.mzjava.glycomics.ms.fragment.GlycanPeakGenerator<A>
• org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCtResolver
• java.lang.Iterable<T>
  • java.util.Collection<E>
    • java.util.List<E>
      • org.expasy.mzjava.proteomics.mol.modification.ModificationList (also extends org.expasy.mzjava.core.mol.Weighable)
    • org.expasy.mzjava.proteomics.mol.modification.ModificationList (also extends java.util.List<E>, org.expasy.mzjava.core.mol.Weighable)
  • java.util.List<E>
    • org.expasy.mzjava.proteomics.mol.modification.ModificationList (also extends org.expasy.mzjava.core.mol.Weighable)
  • org.expasy.mzjava.proteomics.mol.modification.ModificationList (also extends java.util.List<E>, org.expasy.mzjava.core.mol.Weighable)
• org.expasy.mzjava.core.io.IterativeReader<T>
• org.expasy.mzjava.glycomics.mol.LinkageAcceptor
• org.expasy.mzjava.utils.MixedRadixNtupleGenerator.Handler
• org.expasy.mzjava.proteomics.ms.ident.ModificationMatchResolver
• org.expasy.mzjava.proteomics.mol.modification.ModificationResolver
• org.expasy.mzjava.glycomics.mol.MonosaccharideLookup
• org.expasy.mzjava.core.ms.peaklist.PeakCursor<A>
• org.expasy.mzjava.core.ms.peaklist.PeakList<A>
• org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.PeakPairSink<X,Y>
  • org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.PeakPairProcessor<X,Y> (also extends org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.PeakPairSource<X,Y>)
• org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.PeakPairSource<X,Y>
  • org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.PeakListAligner<X,Y>
  • org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.PeakPairProcessor<X,Y> (also extends org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.PeakPairSink<X,Y>)
• org.expasy.mzjava.core.ms.peaklist.PeakSink<A>
  • org.expasy.mzjava.core.ms.peaklist.PeakProcessor<IN,OUT> (also extends org.expasy.mzjava.core.ms.peaklist.PeakSource<A>)
• org.expasy.mzjava.core.ms.peaklist.PeakSource<A>
  • org.expasy.mzjava.core.ms.peaklist.PeakProcessor<IN,OUT> (also extends org.expasy.mzjava.core.ms.peaklist.PeakSink<A>)
• org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.AnnotationParametersSetter
• org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.ConsensusParametersSetter
• org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.FilterParametersSetter
• org.expasy.mzjava.proteomics.ms.fragment.PeptidePeakGenerator<A>
• org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumCache
• org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumDB.DigestDSL
• org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumDB.DigestSourceDSL
• org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumDB.EndDSL
• org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumDB.FragmentDSL
• org.expasy.mzjava.proteomics.ms.dbsearch.PeptideSpectrumDB.StartDSL
• org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriterBuilder.EnzymeEnd
• org.expasy.mzjava.utils.function.Procedure<T>
• org.expasy.mzjava.app.pb.ProgressBar
• org.expasy.mzjava.proteomics.io.ms.ident.PsmReader
• org.expasy.mzjava.proteomics.io.ms.ident.PSMReaderCallback
• org.expasy.mzjava.core.ms.spectrum.RetentionTime
• org.expasy.mzjava.core.ms.spectrum.ScanNumber
• org.expasy.mzjava.script.ScriptConfiguredTool<C>
• org.expasy.mzjava.core.ms.spectrasim.SimFunc<X,Y>
• org.expasy.mzjava.core.ms.cluster.SimilarityGraph<V>
• org.expasy.mzjava.core.ms.cluster.SimilarityGraphBuilder<V,G>
• org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt.SpectraLibCommentParser
• org.expasy.mzjava.external.io.ms.spectrum.mzml.SpectrumIdParser
• org.expasy.mzjava.core.ms.library.SpectrumLibrary<S>
• org.expasy.mzjava.utils.function.Splitter<V>
• org.expasy.mzjava.glycomics.mol.SubstituentLookup
• org.expasy.mzjava.core.mol.Symbol
• org.expasy.mzjava.core.mol.SymbolSequence<S>
• org.expasy.mzjava.core.io.ms.spectrum.mgf.TitleParser
• org.expasy.mzjava.glycomics.mol.TraversalComparator
• org.expasy.mzjava.proteomics.io.ms.ident.UnknownModListener
• org.expasy.mzjava.core.mol.Weighable
  • org.expasy.mzjava.glycomics.mol.Linkage
  • org.expasy.mzjava.proteomics.mol.modification.ModificationList (also extends java.util.List<E>)

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • org.expasy.mzjava.core.ms.peaklist.Polarity
    • org.expasy.mzjava.core.ms.peaklist.PeakList.Precision
    • org.expasy.mzjava.core.ms.peaklist.peakfilter.CentroidFilter.IntensityMode
    • org.expasy.mzjava.core.ms.peaklist.peakfilter.ThresholdFilter.Inequality
    • org.expasy.mzjava.core.ms.peaklist.peakfilter.AbstractMergePeakFilter.IntensityMode
    • org.expasy.mzjava.core.ms.peaklist.peakfilter.BinnedSpectrumFilter.IntensityMode
    • org.expasy.mzjava.core.ms.Tolerance.Location
    • org.expasy.mzjava.core.ms.spectrum.IonType
    • org.expasy.mzjava.core.ms.spectrum.FragmentType
    • org.expasy.mzjava.core.ms.spectrum.TimeUnit
    • org.expasy.mzjava.core.mol.AtomicSymbol (implements org.expasy.mzjava.core.mol.Symbol)
    • org.expasy.mzjava.core.io.ms.spectrum.MzxmlReader.ConsistencyCheck
    • org.expasy.mzjava.stats.Histogram.Normalization.NormType
    • org.expasy.mzjava.stats.Classification
    • org.expasy.mzjava.stats.statscores.ScoreStatistics.SortAction
    • org.expasy.mzjava.proteomics.ms.ident.PeptideProteinMatch.HitType
    • org.expasy.mzjava.proteomics.ms.dbsearch.DigestDB.AmbiguousAminoAcidAction
    • org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.Status
    • org.expasy.mzjava.proteomics.mol.AminoAcid (implements org.expasy.mzjava.core.mol.Symbol)
    • org.expasy.mzjava.proteomics.mol.digest.Protease (implements org.expasy.mzjava.proteomics.mol.digest.CleavageSiteFinder)
    • org.expasy.mzjava.proteomics.mol.digest.ProteinDigester.CleavageSiteIteration
    • org.expasy.mzjava.proteomics.mol.modification.ModAttachment
    • org.expasy.mzjava.proteomics.mol.modification.unimod.jaxb.PositionT
    • org.expasy.mzjava.proteomics.io.ms.ident.PepXmlWriter.ConsistencyCheck
    • org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader.ModMassStorage
    • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.EngineType
    • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.MassType
    • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ActivationMethodType
    • org.expasy.mzjava.proteomics.io.ms.ident.pepxml.v117.ModelDisType
    • org.expasy.mzjava.glycomics.mol.Anomericity
    • org.expasy.mzjava.glycomics.mol.RingType
    • org.expasy.mzjava.glycomics.mol.SaccharideGraph.Traversal
    • org.expasy.mzjava.glycomics.mol.SaccharideGraph.AbstractBuilder.BuildSate
    • org.expasy.mzjava.glycomics.mol.MonosaccharideClass
    • org.expasy.mzjava.glycomics.mol.CutDirection
    • org.expasy.mzjava.glycomics.mol.MonosaccharideSuperclass
    • org.expasy.mzjava.external.io.ms.spectrum.mzml.MzmlConsistencyCheck (implements org.expasy.mzjava.external.io.ms.spectrum.ConsistencyCheck)