All Classes
AAMassCalculator
AbsoluteTolerance
AbstractAminoAcidSequenceReader
AbstractAminoAcidSequenceWriter
AbstractAvroReader
AbstractAvroWritable
AbstractAvroWriter
AbstractConsensusSpectrumBuilder
AbstractContactType
AbstractIntervalSpectrumLibrary
AbstractLibPeakAnnotationWriter
AbstractMapSpectrumLibrary
AbstractMergePeakFilter
AbstractMergePeakFilter.IntensityMode
AbstractMgfReader
AbstractMgfWriter
AbstractMgfWriter.Parameters
AbstractMsReader
AbstractMsReader.ParseContext
AbstractParamType
AbstractPeakList
AbstractPeakList.AbstractMergePeakSink
AbstractPeakListReader
AbstractPeakListValue
AbstractPeakListWriter
AbstractPeakPairProcessor
AbstractPeakProcessor
AbstractPsmCsvReader
AbstractSimFunc
AbstractSptxtWriter
AcceptAllDigestionController
ActivationMethodType
AddFlankingPeaksTransformer
AffiliationType
AffineTransformer
AllCrossRingCutType
AmbiguousResidueType
AminoAcid
AminoacidModificationHashable
AminoAcidSequence
AnalysisCollectionType
AnalysisDataType
AnalysisProtocolCollectionType
AnalysisSampleCollectionType
AnalysisSoftwareListType
AnalysisSoftwareType
AnalystTitleParser
AnnotatedPeak
AnnotationResolver
Anomericity
ArcsinhTransformer
ArrayCursor
ArrayDigestDB
ArrayDigestDB.Builder
ArrayIndexComparator
ArrayIndexSorter
AsapratioContribution
AsapratioLcHeavypeak
AsapratioLcLightpeak
AsapratioPeptideData
AsapratioResult
AsapratioSummary
AsapratioTimestamp
Atom
AtomicCompositionParser
AtomicSymbol
AuditCollectionType
AvroExternalizable
AvroIO
AvroReader
AvroWritable
AvroWriter
BackbonePeakGenerator
BibliographicReferenceType
BinnedSpectrumFilter
BinnedSpectrumFilter.IntensityMode
BinomialUtils
BioJavaFastaProteinReader
BytesUtils
Cached
CachedAbsoluteTolerance
CachedPpmTolerance
CentroidFilter
CentroidFilter.IntensityMode
CentroidFilter.PeakIntensityInfo
ChargeMzSplitter
Classification
Classifier
CleavageSiteFinder
CleavageSiteFinderImpl
CleavageSiteMatcher
CleavageSiteParseException
CleavageSiteVisitor
CleavedMonosaccharide
ClusterBuilder
CompositeModResolver
Composition
Composition.Builder
CompositionReader
CompositionT
CompositionWriter
CompoundClusterBuilder
ConcatIterativeReader
ConsensusPeakSink
ConsensusSpectrum
ConsensusSpectrum.Builder
ConsistencyCheck
ConsistencyChecker
ConsistencyCheckException
ConsistencyCheckHandler
ConsoleProgressBar
ConsoleProgressBar.View
ContactRoleType
ContrastEnhancingTransformer
Copyable
CorruptedPSMFileException
Counter
CrossRingCutType
CutDescriptor
CutDescriptorGenerator
CutDirection
CutIndexes
CVListType
CVParamHelper
CVParamType
CvType
DatabaseFiltersType
DatabaseRefreshTimestamp
DatabaseTranslationType
DataCollectionType
DbSearchPaperExample
DBSequenceType
DefaultGlycanMassCalculator
DefaultGlycoCtResolver
DefaultMonosaccharideLookup
DefaultPeakListAligner
DefaultPeakListAligner.OverlapListener
DefaultSpectrumKeyRawComparator
DefaultSpectrumLibrary
DefaultSubstituentLookup
DelayedPeakPairProcessor
DelayedPeakProcessor
DelegatingRegexTitleParser
DenseSimilarityGraph
DenseSimilarityGraph.AbstractBuilder
DenseSimilarityGraph.Builder
Digest
DigestDB
DigestDB.AmbiguousAminoAcidAction
DigestionController
DiscreteSpectrumLibrary
DoubleConstantPeakList
DoubleFloatPeakList
DoubleFunction
DoublePeakList
DpSimFunc
DtaReader
EbiMzmlReader
ElemRefT
EngineType
EnzymesType
EnzymeType
ExternalDataType
FastaHeaderParser
FastaProteinReader
FileFormatType
FilterType
FirstMzCheck
FirstRankScoreStatistics
FitDecoyScoreStatistics
FloatConstantPeakList
FloatPeakList
FMeasure
FragmentAnnotationFilter
FragmentArrayType
FragmentationTableType
FragmentationType
FragmentType
FrequencyTable
GlobalThresholdClusterBuilder
Glycan
Glycan.Builder
GlycanFragAnnotation
GlycanFragAnnotation.FragBuilder
GlycanFragment
GlycanFragment.Builder
GlycanFragmenter
GlycanFragmentPeakGenerator
GlycanMassCalculator
GlycanNode
GlycanPeakGenerator
GlycanSpectrum
GlycoCTReader
GlycoCtResolver
GlycosidicLinkage
GWPWriter
HadoopSpectraReader
HadoopSpectraWriter
HighestPeakPerBinNormalizer
Histogram
Histogram.Normalization
Histogram.Normalization.NormType
HistogramImpl
IdentifiableType
IdentityPeakProcessor
InputSpectraType
InputSpectrumIdentificationsType
InputsType
InteractSummary
InteractSummary.Inputfile
IntervalList
IntervalSpectrumLibrary
InverseArcsinhTransformer
IonCurrentNormalizer
IonType
IonTypeType
IterativeReader
IterativeReaders
JungSimGraphWrapper
KMeansPlusPlusClusterBuilder
KryoAvroSerializer
LastMzCheck
LengthDigestionController
LibPeakAnnotation
LibPeakAnnotationReader
LibPeakAnnotationWriter
LibraResult
LibraResult.Intensity
LibraryMergePeakFilter
LibrarySpectrumBuilder
LibraSummary
LibraSummary.FragmentMasses
LibraSummary.IsotopicContributions
LibraSummary.IsotopicContributions.ContributingChannel
LibraSummary.IsotopicContributions.ContributingChannel.AffectedChannel
Linkage
LinkageAcceptor
Log10Transformer
LogTransformer
Mass
MassCalculator
MassTableType
MassType
MaxQuantPsmReader
McNdpSimFunc
MeasureType
MgfParameters
MgfReader
MgfWriter
MixedRadixNtupleGenerator
MixedRadixNtupleGenerator.Handler
MixedRadixNtupleGenerator.NtupleContainer
MODaPsmReader
ModAttachment
ModelDisType
Modification
ModificationList
ModificationLists
ModificationMap
ModificationMatch
ModificationMatchResolver
ModificationParamsType
ModificationReader
ModificationResolver
ModificationsT
ModificationType
ModificationTypeAdapter
ModificationWriter
ModifiedPeptideFactory
ModifiedPeptideFactory.Builder
ModListModMatchResolver
ModT
MonitoredIterativeReader
Monosaccharide
MonosaccharideClass
MonosaccharideLookup
MonosaccharideSuperclass
MsLibReader
MsmsPipelineAnalysis
MsmsPipelineAnalysis.AnalysisSummary
MsmsPipelineAnalysis.DatasetDerivation
MsmsPipelineAnalysis.DatasetDerivation.DataFilter
MsmsPipelineAnalysis.MsmsRunSummary
MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp
MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme
MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity
MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint
MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SequenceSearchConstraint
MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo.ModAminoacidMass
MsnSpectrum
MsnSpectrumMetaDataReader
MsnSpectrumMetaDataWriter
MsnSpectrumReader
MsnSpectrumValue
MsnSpectrumWriter
MspAnnotationResolver
MspCommentParser
MspReader
MspReader.Builder
MsReaderFactory
MSTClusterBuilder
MzAffineTransformer
MzIdentMlReader
MzIdentMLType
MzJavaKryoRegistrator
MzJavaSerialization
MzJavaSparkUtils
MzmlConsistencyCheck
MzmlSpectrumCheck
MzRangeFilter
MzxmlReader
MzxmlReader.ConsistencyCheck
MzxmlReader.ConsistencyCheckException
MzxmlReader.XMLEventUtils
NamespaceFilterXMLReader
NameValueType
NdpSimFunc
NeutralLoss
NeutralLossT
NHighestPeaksNormalizer
NodeSet
NormalizedDotProduct
NPeaksFilter
NPeaksPerBinFilter
NPeaksPerSlidingWindowFilter
NthPeakNormalizer
NumberFormatFactory
NumericMass
NumericMassReader
NumericMassWriter
NumericModificationResolver
ObjectFactory
ObjectFactory
ObjectFactory
OrganizationType
ParamListType
ParamType
ParentOrganizationType
PathUtils
Peak
PeakAnnotation
PeakCollectorSink
PeakCountEqualizer
PeakCursor
PeakList
PeakList.Precision
PeakListAligner
PeakListComparator
PeakListFactory
PeakListMerger
PeakListPrecisionFormat
PeakListReader
PeakListSimGraphFactory
PeakListUtils
PeakListValue
PeakListWriter
PeakPairIntensityLog10Transformer
PeakPairIntensityLogETransformer
PeakPairIntensitySqrtTransformer
PeakPairIonCurrentNormalizer
PeakPairProcessor
PeakPairProcessorChain
PeakPairSink
PeakPairSource
PeakProcessor
PeakProcessorChain
PeakReader
PeakSink
PeakSource
PeakWriter
PearsonsCorrelationCoeff
PearsonsSimFunc
PepFragAnnotation
PepFragAnnotation.Builder
PepFragAnnotationReader
PepFragAnnotationWriter
PepLibPeakAnnotation
PepLibPeakAnnotationReader
PepLibPeakAnnotationWriter
PepNeutralLossT
Peptide
PeptideBuilder
PeptideConsensusPeakSink
PeptideConsensusSpectrum
PeptideConsensusSpectrum.AnnotationParametersSetter
PeptideConsensusSpectrum.Builder
PeptideConsensusSpectrum.BuilderOld
PeptideConsensusSpectrum.ConsensusParametersSetter
PeptideConsensusSpectrum.FilterParametersSetter
PeptideConsensusSpectrum.Status
PeptideConsensusSpectrumReader
PeptideConsensusSpectrumValue
PeptideConsensusSpectrumWriter
PeptideEvidenceRefType
PeptideEvidenceType
PeptideFragment
PeptideFragmentAnnotator
PeptideFragmentAnnotator
PeptideFragmenter
PeptideFragmenterFactory
PeptideFragmentReader
PeptideFragmentWriter
PeptideHypothesisType
PeptideMatch
PeptideMatchComparator
PeptideNeutralLossPeakGenerator
PeptideNeutralLossPeakGenerator.ModifiedAaPresencePredicate
PeptideParseException
PeptidePeakGenerator
PeptideprophetResult
PeptideprophetResult.SearchScoreSummary
PeptideProteinMatch
PeptideProteinMatch.HitType
PeptideReader
PeptideSpectrum
PeptideSpectrumCache
PeptideSpectrumDB
PeptideSpectrumDB.DigestDSL
PeptideSpectrumDB.DigestSourceDSL
PeptideSpectrumDB.EndDSL
PeptideSpectrumDB.FragmentDSL
PeptideSpectrumDB.StartDSL
PeptideSpectrumReader
PeptideSpectrumValue
PeptideSpectrumWriter
PeptideType
PeptideWriter
PepXmlReader
PepXmlReader.ModMassStorage
PepXmlReader.NamespaceRewriteDelegate
PepXmlWriter
PepXmlWriter.ConsistencyCheck
PepXmlWriterBuilder
PepXmlWriterBuilder.Builder
PepXmlWriterBuilder.EnzymeEnd
PepXmlWriterBuilder.SampleEnzymeBuilder
PepXmlWriterBuilder.SpecificityBuilder
PeriodicTable
PersonType
PirPrfFastaHeaderParser
PoissonUtils
Polarity
PositionT
PpmTolerance
PrecursorSplitter
PrimitiveArrayUtils
Procedure
ProgressBar
Protease
Protein
Protein.Builder
ProteinAmbiguityGroupType
ProteinDetectionHypothesisType
ProteinDetectionListType
ProteinDetectionProtocolType
ProteinDetectionType
ProteinDigester
ProteinDigester.Builder
ProteinDigester.CleavageSiteIteration
ProteinFactory
ProteinPilotModificationResolver
ProteinPilotPsmReader
ProtocolApplicationType
ProviderType
PsmReader
PSMReaderCallback
PspcSimFunc
RankNormalizer
RegexConstants
RegexScanNumTitleParser
ResidueType
RetentionTime
RetentionTimeComparator
RetentionTimeDiscrete
RetentionTimeDiscreteReader
RetentionTimeDiscreteWriter
RetentionTimeInterval
RetentionTimeIntervalReader
RetentionTimeIntervalWriter
RetentionTimeList
RetentionTimeListReader
RetentionTimeListWriter
RetentionTimeSplitter
RingType
ROCTable
RoleType
SaccharideGraph
SaccharideGraph.AbstractBuilder
SaccharideGraph.AbstractBuilder.BuildSate
SaccharideGraph.Traversal
SampleType
ScanNumber
ScanNumberDiscrete
ScanNumberDiscreteReader
ScanNumberDiscreteWriter
ScanNumberIncrementer
ScanNumberIndexSearchResultMap
ScanNumberInterval
ScanNumberIntervalReader
ScanNumberIntervalWriter
ScanNumberList
ScanNumberListReader
ScanNumberListWriter
ScanNumberSearchResultMap
ScatterPlotTable
ScoreStatistics
ScoreStatistics.SortAction
ScriptConfiguredTool
ScriptConfiguredToolRunner
SearchDatabaseRefType
SearchDatabaseType
SearchModificationType
SearchResultMap
SEdge
SequenceCollectionType
SharedPeakSimFunc
SimEdge
SimFunc
SimFuncProcedure
SimilarityGraph
SimilarityGraphBuilder
SimROCTable
SkipAnnotationResolver
SNode
SoftRefPepSpectrumCache
SourceFileType
SparseSimilarityGraph
SparseSimilarityGraph.Builder
SpecificityRulesType
SpecificityT
SpectraDataType
SpectraLibCommentParser
SpectraStAnnotationResolver
SpectraStCommentParser
Spectrum
SpectrumClusterEvaluator
SpectrumIdentificationItemRefType
SpectrumIdentificationItemType
SpectrumIdentificationListType
SpectrumIdentificationProtocolType
SpectrumIdentificationResultType
SpectrumIdentificationType
SpectrumIdentifier
SpectrumIDFormatType
SpectrumIdParser
SpectrumKey
SpectrumLibrary
Splitter
SptxtReader
SptxtReader.Builder
SptxtWriter
SqrtTransformer
SubSampleType
Substituent
SubstituentLinkage
SubstituentLookup
SubstitutionModificationType
Symbol
SymbolSequence
ThermoFisherOrbitrapTitleParser
ThresholdFilter
ThresholdFilter.Inequality
ThresholdPeakPairFilter
TicCheck
TimeUnit
TitleParser
TitleSearchResultMap
Tolerance
Tolerance.Location
ToleranceType
TopNList
TopPeakPairTransformer
TranslationTableType
TraversalComparator
UnimodManager
UnimodMod
UnimodMod.Builder
UnimodModificationResolver
UnimodT
UniprotFastaHeaderParser
UnitVectorNormalizer
UnitVectorPeakPairTransformer
UnknownModListener
UnresolvableModificationMatchException
UnsortedPeakListException
URIBuilder
UserParamType
UUIDReader
UUIDWriter
Weighable
WeightedPearsonsCorrelationCoeff
WeightedPearsonsSimFunc
XpressratioResult
XpressratioSummary
XpressratioTimestamp
XrefT