All Classes
AAIdentityFeature
AAIdentityFeatureAbsolute
AAIdentityFeatureRelative
AaMass
AaOccurrence
AAPropertyFeature
AAPropertyFeatureAbsolute
AAPropertyFeatureRelative
AAPropertyRelationshipFeature
AAPropertyRelationshipFeature.Relationship
AASequenceFeature
AASequenceFeature.Function
AASequenceImpl
AaSubstitutionMatrix
AaSubstitutionMatrixTableModel
AbstractIdentificationParametersCli
AccessionMetaData
Advocate
Advocate.AdvocateType
Alanine
AlgorithmParametersDialog
AlignedListCellRenderer
AlignedTableCellRenderer
AlignmentBlock
AlternateRowColoursJTable
AmbiguousSequenceIterator
AminoAcid
AminoAcid.Property
AminoAcidPattern
AminoAcidPatternDialog
AminoAcidSequence
AminoAcidSubstitution
AndromedaIdfileReader
AndromedaParameters
AndromedaParameters.AndromedaDecoyMode
AndromedaParametersDialog
AnnotationParameters
AnnotationParameters.IntensityThresholdType
AnnotationParametersDialog
AplFileWriter
Arginine
ArrayUtil
Asparagine
AsparticAcid
AssumptionFilter
AssumptionFilterItem
Atom
AtomChain
AtomChainDialog
AtomImpl
AtomPanel
B
BackgroundSpeciesDialog
BareBonesBrowserLaunch
BasicMathFunctions
BigFunctions
BigMathUtils
BinaryArrayImpl
BinningFilter
BinomialDistribution
BiomartMapping
BlobObject
BoxedObject
BugReport
ByteArrayRenderer
CacheElement
Calcium
Carbon
Charge
ChromatogramPanel
CliLogger
CmsFileIterator
CmsFileReader
CmsFileUtils
CmsFileWriter
CmsFolder
ColorAdapter
ColumnTypeConverter
CometParameters
CometParameters.CometOutputFormat
CometParametersDialog
CommandLineExceptionHandler
CommandLineParser
CommandLineUtils
CommandParameter
CompareVersionNumbers
CompareVersionNumbers
ComplementaryIonAminoAcidFeature
ComplementaryIonFeature
CompomicsTools
CompomicsWrapper
Connectable
ConnectionDialog
Constants
Constructors
Contact
ContactGroup
Copper
CossIdfileReader
CvTerm
Cysteine
DasAlignment
DasAnnotationServerAlingmentReader
DasAnnotationServerResultReader
DasFeature
DataRoc
DataRoc.RocInterpolation
DateChooser
DatFileFilter
DBAccessor
DBAccessorGenerator
DBElement
DBMetaData
DbMutex
DBResultSet
DecoyConverter
DefaultOutputLoggerImplementation
DefaultSpectrumAnnotation
DefaultStyle
Deleteable
DeleteableCode
Deletion
DigestionParameters
DigestionParameters.CleavageParameter
DigestionParameters.Specificity
DirecTagIdfileReader
DirecTagParameters
DirecTagParametersDialog
Distribution
DistributionRoc
DoubleMatrix
DownloadLatestZipFromRepo
DtaFileFilter
DualEnzyme
Dummy
DummyFrame
DummyParameters
Duration
ElementaryElement
ElementaryIon
EmptyCollections
EnsemblGenomesSpecies
EnsemblGenomesSpecies.EnsemblGenomeDivision
EnsemblSpecies
EnsemblVersion
Enzyme
Enzyme
EnzymeFactory
EnzymeParametersDialog
EnzymesCLI
EnzymesCLIInputBean
EnzymesCLIParams
EnzymesDialog
ExcelWriter
ExceptionHandler
ExperimentObject
Export
ExportFactory
ExportFeature
ExportFormat
ExportFormatSelectionDialog
ExportGraphicsDialog
ExportScheme
ExportWriter
ExtendedPeptide
FastaFileFilter
FastaIterator
FastaMapper
FastaParameters
FastaParametersCLIParams
FastaParametersDialog
FastaParametersInputBean
FastaSummary
FeaturesGenerator
FeaturesMap
FeaturesMapManager
FeedBack
FeedBack.FeedBackType
FileAdapter
FileAndFileFilter
FileChooserUtil
FileDAO
FileDisplayDialog
FileFilterUtils
FileLoggerImplementation
FilenameExtensionFilter
FileSelectionDialog
FileSystemAccessor
FileType
Filter
FilterDialog
FilterItem
FilterItemComparator
FilterParameters
FindPdbForUniprotAccessions
Flamable
FlamableJFrame
Fluorine
FMIndex
FolderMonitor
ForwardIonAminoAcidFeature
ForwardIonFeature
FractionParameters
FractionParametersDialog
FragmentAnnotator
FragmentAnnotatorNL
FragmentationMethod
FragmentIonTable
FragmentIonTableCellRenderer
FragmentItensityPredictor
FrameExceptionHandler
FTP
FTPClient
FtpConnectionException
FTPDownloader
FtpLoginException
FtpProtocolException
GeneDetailsDialog
GeneMapping
GeneMaps
GeneParameters
GeneParametersDialog
GeneratorException
GenericFastaConverter
GettersAndSetters
GlutamicAcid
Glutamine
Glycan
Glycine
GoDomains
GoMapping
GraphicsPanel
GraphicsPanel.DrawingStyle
GraphicsPanel.GraphicsPanelType
GraphicsPanelTableCellRenderer
GUIFileDAO
GuiUtilities
GzUtils
Header
HeaderIterator
HeadlessFileDAO
Helium
HelpDialog
HelpWindow
Histidine
HistogramUtils
Hydrogen
HyperScore
Identification
IdentificationAlgorithmParameter
IdentificationFeaturesCache
IdentificationFeaturesCache.ObjectType
IdentificationFeaturesGenerator
IdentificationKeys
IdentificationMatch
IdentificationMatch.MatchType
IdentificationMethod
IdentificationParameters
IdentificationParametersCLI
IdentificationParametersCLIParams
IdentificationParametersEditionDialog
IdentificationParametersFactory
IdentificationParametersInputBean
IdentificationParametersMarshaller
IdentificationParametersNameDialog
IdentificationParametersOverviewDialog
IdfileReader
IdfileReaderFactory
IdMatchValidationParameters
ImageType
ImmoniumIon
ImmoniumIonAnnotator
IndexedMgfReader
Insertion
InstanceVariables
Instrument
IntDecoder
IntensityHistogram
InterfaceAdapter
Iodine
Ion
Ion.IonType
IonFactory
IonFeature
IonFeature.Property
IonLabelColorTableModel
IonMatch
IonMatch.MzErrorType
IonMatchKeysCache
IoUtil
Iron
Isoleucine
IsotopeDistributionGui
IsotopicDistribution
IsotopicDistributionPanel
IsotopicDistributionSpectrum
IsotopicElement
IteratorFactory
J
JarFileFilter
JavaHomeDialog
JavaHomeOrMemoryDialogParent
JavaMemoryDialog
JavaParametersDialog
JExceptionDialog
JFrameForBytes
JLabelAndComponentPanel
JOptionEditorPane
JpegFileFilter
JsonMarshaller
JTableForDB
KMeansClustering
KMeansClusteringSettings
LastSelectedFolder
Leucine
LinearRegression
ListChooser
Lithium
Logger
Lysine
Magnesium
MappingWorker
MarshallableParameter
MarshallableParameter.Type
MascotEnzymeReader
MascotIdfileReader
MassCalc
MassCalcServlet
MassErrorBubblePlot
MassErrorPlot
MassGap
MassIndexMap
MatchesImportParametersDialog
MatchesIterator
MatchFilter
MatchFilter.FilterType
MatchValidationLevel
MatrixContent
MavenJarFile
MDScore
MedianRegression
MemoryConsumptionStatus
MetaDataXMLParser
MetaMorpheusParameters
MetaMorpheusParameters.MetaMorpheusDecoyType
MetaMorpheusParameters.MetaMorpheusDissociationType
MetaMorpheusParameters.MetaMorpheusFragmentationTerminusType
MetaMorpheusParameters.MetaMorpheusInitiatorMethionineBehaviorType
MetaMorpheusParameters.MetaMorpheusMassDiffAcceptorType
MetaMorpheusParameters.MetaMorpheusSearchType
MetaMorpheusParameters.MetaMorpheusToleranceType
MetaMorpheusParametersDialog
Methionine
Metrics
MetricsPrefix
MgfFileFilter
MgfFileIterator
MgfFileUtils
MgfFileWriter
MgfIndex
MirroredSpectraTestDialog
Modification
Modification
ModificationCategory
ModificationChooser
ModificationDialog
ModificationFactory
ModificationFactory
ModificationFeature
ModificationFeature.Property
ModificationImplementation
ModificationLocalizationMapper
ModificationLocalizationParameters
ModificationLocalizationParametersDialog
ModificationLocalizationScore
ModificationMassMapper
ModificationMatch
ModificationNameMapper
ModificationParameters
ModificationProfile
ModificationProvider
ModificationsCLI
ModificationsCLIInputBean
ModificationsCLIParams
ModificationScoring
ModificationsDialog
ModificationSiteMapping
ModificationTable
ModificationtableContent
ModificationTemplate
ModificationType
ModificationUtils
MolecularElement
MolecularFormula
Monitorable
MonitorableFileInputStream
MonitorableInputStream
MonitorDimension
Ms2Exporter
Ms2FileFilter
Ms2FileWriter
Ms2pipFeature
MsAmandaIdfileReader
MsAmandaParameters
MsAmandaParametersDialog
MsConvertParameters
MsConvertParametersDialog
MsFileExporter
MsFileExporter.Format
MsFileHandler
MsFileIterator
MsFilePerformance
MsgfParameters
MsgfParametersDialog
MSNumpress
MultipleAAPropertyFeature
MutexMap
MyriMatchParameters
MyriMatchParametersDialog
MzDataFileFilter
MzIdentMLIdfileReader
MzIdentMLIdfileReader.RawValueConversionType
MzIdentMLIdfileSearchParametersConverter
MzIdentMLVersion
MzMlFileFilter
MzmlFileIterator
MzmlFileIterator.Precision
MzmlFileUtils
MzXmlFileFilter
NeutralLoss
NeutralLossCombination
NeutralLossesMap
NewEnzymeDialog
Nitrogen
NoDigestionCombinationIterator
NoDigestionIterator
NonSymmetricalNormalDistribution
NormalDistribution
NormalizationFactors
NormalKernelDensityEstimator
NotesDialog
NotificationDialog
NotificationDialogParent
NovorIdfileReader
NovorParameters
NovorParametersDialog
NucleotideSequence
NucleotideSequenceImpl
ObjectMutex
ObjectsCache
ObjectsDB
OmssaParameters
OmssaParametersDialog
OmxFileFilter
OnyaseIdfileReader
OperatingSystemEnum
OutFileFilter
OutputParameters
Oxygen
PathKey
PathParametersDialog
PathSettingsCLI
PathSettingsCLIInputBean
PathSettingsCLIParams
Patient
PatientInformation
PdbBlock
PdbParameter
PdfFileFilter
Peak
PeffFileFilter
PepnovoAssumptionDetails
PepNovoIdfileReader
PepnovoParameters
PepNovoParametersDialog
Peptide
PeptideAminoAcidFeature
PeptideAndProteinBuilder
PeptideAssumption
PeptideAssumptionFilter
PeptideDraft
PeptideFeature
PeptideFeature.Property
PeptideFilter
PeptideFilterItem
PeptideFragmentationModel
PeptideFragmentIon
PeptideInference
PeptideMapperCLI
PeptideMatch
PeptideMatchesIterator
PeptideProteinMapping
PeptideShakerSetupDialog
PeptideSpectrumAnnotator
PeptideUtils
PeptideVariantMatches
PeptideVariantsParameters
PeptideVariantsParameters.VariantType
PeptideVariantsParametersDialog
PepXmlFileFilter
PepxmlIdfileReader
Persistable
PersistableCode
Phenylalanine
PhosphoRS
Phosphorus
PickUp
PklFile
PklFileFilter
PklSpoFileFilter
PkxFileFilter
PngFileFilter
PNovoIdfileReader
PNovoParameters
PNovoParametersDialog
Potassium
Precursor
PrecursorAccuracy
PrecursorAnnotator
PrecursorIon
PrecursorMap
PrideFilter
PrideFilterType
PrideMarshaller
PrideObject
PrideObjectsFactory
PrideQuery
PrideWebService
PrideXmlValidator
PrivacyParametersDialog
ProbabilityFilter
ProcessingParameters
ProcessingParameters.ProcessingType
ProcessingParametersDialog
ProgressDialog
ProgressDialogX
ProjectParameters
ProjectType
Proline
PropertiesManager
Protein
Protein
ProteinDatabase
ProteinDetailsProvider
ProteinFilter
ProteinFilterItem
ProteinGeneDetailsProvider
ProteinInferenceParameters
ProteinInferenceParametersDialog
ProteinIterator
ProteinIteratorUtils
ProteinMatch
ProteinMatchesIterator
ProteinSequencePane
ProteinUtils
ProteoWizardFilter
ProteoWizardMsFormat
ProteoWizardSetupDialog
Protocol
ProtXmlFileFilter
PsAnnotationFeature
PsFragmentFeature
PsIdentificationAlgorithmMatchesFeature
PsInputFilterFeature
PsmFilter
PsmFilterItem
PSModificationScores
PsmScore
PsmScoresEstimator
PsmScoringParameters
PsmScoringParametersDialog
PSParameter
PsPeptideFeature
PsProjectFeature
PsProteinFeature
PsPsmFeature
PsPtmScoringFeature
PsSearchFeature
PsSpectrumCountingFeature
PsValidationFeature
PTMFactoryMarshaller
PtmToPrideMap
PushBackStringReader
Pyrrolysine
Quantification
Quantification.QuantificationMethod
Rank
Reagent
RecalibrationUtils
Reference
ReferenceArea
ReferenceGroup
RegExEnzyme
RegressionStatistics
RelatedIon
ReportEditor
ReporterExportFeature
ReporterIon
ReporterIonAnnotator
ReporterIonQuantification
ReporterMethod
ReporterMethodFactory
ReporterPeptideFeature
ReporterProteinFeatures
ReporterPsmFeatures
ReporterSetupDialog
RescalingEvent
Retrievable
RetrievableCode
ROC
Sample
SampleSelection
ScalingFactorsEstimators
SearchGuiSetupDialog
SearchParameters
SearchParameters.MassAccuracyType
SearchParametersDialog
Selenium
Selenocysteine
SelfUpdatingTableModel
Sequence
SequenceDbDetailsDialog
SequenceFragmentationPanel
SequenceIterator
SequenceMatchingParameters
SequenceMatchingParameters.MatchingType
SequenceMatchingParametersDialog
SequenceModificationPanel
SequenceProvider
SequestFragmentationModel
SequestParamsFileFilter
SerializationUtils
Serine
SimpleFileReader
SimpleFileWriter
SimpleGzReader
SimpleLinearRegression
SimpleMzIdentMLExporter
SimpleNoiseDistribution
SimplePeptideAnnotator
SimplePeptideAnnotator.IonSeries
SimpleSemaphore
SimpleTextReader
SimpleXmlWriter
SingleAAPropertyFeature
SingleProteinSequenceProvider
SNPElement
SnrScore
Sodium
SparklineColorsDialog
SpeciesDialog
SpeciesFactory
SpecificAnnotationParameters
SpecificSingleEnzymeCombinationIterator
SpecificSingleEnzymeIterator
Spectrum
SpectrumAnnotation
SpectrumAnnotator
SpectrumAnnotator.TiesResolution
SpectrumCountingMethod
SpectrumCountingParameters
SpectrumFile
SpectrumIdentificationAssumption
SpectrumIndex
SpectrumMatch
SpectrumMatchesIterator
SpectrumPanel
SpectrumPanelListener
SpectrumProvider
SpectrumUtil
SplashScreen
StandardMasses
StandardUnit
StartBrowser
StartEndPosition
StreamGobbler
StreamUtil
StringListChooser
Substitution
Sulfur
SvgFileFilter
Swap
SwingUtils
SwingWorker
TableMap
TableMouseWheelListener
TableProperties
TableScrollBarListener
TableSorter
TableValueWrapper
Tag
TagAssumption
TagComponent
TagElement
TagFactory
TagFragmentIon
TagSpectrumAnnotator
TagUtils
TarUtils
TempByteArray
TempFilesManager
TestCaseLM
TextWriter
ThermoRawFileParserOutputFormat
ThermoRawFileParserParameters
ThermoRawFileParserParametersDialog
Threonine
TideIdfileReader
TideParameters
TideParametersDialog
TiffFileFilter
TimestampRenderer
ToolFactory
ToolTipComboBoxRenderer
Translate
Tryptophan
Tyrosine
UniformFragmentation
UniprotTaxonomy
UnitOfMeasurement
Units
UnknownElementMassException
UnspecificCombinationIterator
UnspecificIterator
Updateable
UpdateableCode
UrParameter
Util
UtilitiesDemo
UtilitiesGUIDefaults
UtilitiesPathParameters
UtilitiesPathParameters.UtilitiesPathKey
UtilitiesUserParameters
ValidationParametersDialog
ValidationQcParameters
ValidationQCParametersDialog
Valine
Variant
VennDiagram
VennDiagramDialog
VennDiagramLegendLocationDialog
VennDiagramPanel
VennDiagramPanel.VennDiagramType
VisibleTableColumnsDialog
VisibleTableColumnsDialogParent
WaitingActionListener
WaitingDialog
WaitingDialogExceptionHandler
WaitingHandler
WaitingHandlerCLIImpl
WaitingHandlerDummy
WaveletTree
WebDAO
WorkbookStyle
WriterBySection
X
XmlFileFilter
XMLValidationErrorHandler
XTandemIdfileReader
XtandemParameters
XTandemParametersDialog
XYPlotFiltersDialog
XYPlottingDialog
XYPlottingDialog.PlottingDialogPlotType
XYZDataPoint
Z
Zinc
ZipUtils
ZstdUtils