All Classes
AAIntensityRankScore
AaMass
AAMS2MzFidelityScore
AASequenceImpl
AbstractIdentificationParametersCli
AdvancedProteinDatabaseDialog
Advocate
Advocate.AdvocateType
Alanine
AlignedListCellRenderer
AlignedTableCellRenderer
AlignmentBlock
AlternateRowColoursJTable
AminoAcid
AminoAcidPattern
AminoAcidPatternDialog
AminoAcidSequence
AndromedaIdfileReader
AndromedaParameters
AndromedaSettingsDialog
AnnotationSettings
AplExporter
Arginine
AScore
Asparagine
AsparticAcid
Atom
AtomChain
AtomChainDialog
AtomImpl
AtomPanel
B
BareBonesBrowserLaunch
BasicMathFunctions
BigFunctions
BigMathUtils
BinaryArrayImpl
BinningFilter
BinomialDistribution
BugReport
ByteArrayRenderer
Carbon
Charge
ChromatogramPanel
ColumnTypeConverter
CometParameters
CometSettingsDialog
CommandLineExceptionHandler
CommandLineParser
CommandLineUtils
CompareVersionNumbers
CompareVersionNumbers
ComplementarityScore
CompomicsTools
CompomicsWrapper
ConfigurationFile
Connectable
ConnectionDialog
ConnectionManager
Constants
Constructors
Contact
ContactGroup
CvTerm
Cysteine
DasAlignment
DasAnnotationServerAlingmentReader
DasAnnotationServerResultReader
DasFeature
DataRoc
DataRoc.RocInterpolation
DateChooser
DatFileFilter
DBAccessor
DBAccessorGenerator
DBElement
DBMetaData
DBResultSet
DefaultOutputLoggerImplementation
DefaultSpectrumAnnotation
DefaultStyle
Deleteable
DeleteableCode
DerbyUtil
DirecTagIdfileReader
DirecTagParameters
DirecTagSettingsDialog
Distribution
DistributionRoc
DoubleMatrix
DownloadingUtil
DownloadLatestZipFromRepo
DtaFileFilter
DualEnzyme
DummyFrame
Duration
ElementaryElement
ElementaryIon
Enzyme
Enzyme
EnzymeFactory
EnzymeSelectionDialog
ExcelWriter
ExceptionHandler
ExperimentIO
ExperimentObject
Export
ExportFactory
ExportFeature
ExportFormat
ExportFormatSelectionDialog
ExportGraphicsDialog
ExportScheme
ExportWriter
FastaFileFilter
FastaIndex
FeedBack
FeedBack.FeedBackType
FileAndFileFilter
FileDAO
FileDisplayDialog
FileFilterUtils
FileLoggerImplementation
FilenameExtensionFilter
FileSelectionDialog
FileSystemAccessor
Filter
FilterItem
FilterItemComparator
FindPdbForUniprotAccessions
Flamable
FlamableJFrame
FolderMonitor
FragmentationMethod
FragmentIonTable
FragmentIonTableCellRenderer
FrameExceptionHandler
FTP
FTPClient
FtpConnectionException
FTPDownloader
FtpLoginException
FtpProtocolException
GeneDetailsDialog
GeneFactory
GenePreferences
GeneratorException
GettersAndSetters
GlutamicAcid
Glutamine
Glycan
Glycine
GlyconFactory
GOFactory
GraphicsPanel
GraphicsPanel.DrawingStyle
GraphicsPanel.GraphicsPanelType
GraphicsPanelTableCellRenderer
GUIFileDAO
GuiUtilities
Header
Header.DatabaseType
HeadlessFileDAO
Helium
HelpDialog
HelpWindow
Histidine
Hydrogen
Identification
IdentificationAlgorithmParameter
IdentificationDB
IdentificationMatch
IdentificationMatch.MatchType
IdentificationMethod
IdentificationParameters
IdentificationParametersCLIParams
IdentificationParametersInputBean
IdfileReader
IdfileReaderFactory
IdMatchValidationPreferences
ImageType
ImmoniumIon
ImportSequencesFromDnaDialog
ImportSequencesFromFilesDialog
ImportSequencesFromUniprotDialog
ImportSettingsDialog
InstanceVariables
Instrument
IntensityHistogram
IntensityRankScore
Iodine
Ion
Ion.IonType
IonFactory
IonLabelColorTableModel
IonMatch
IonMatch.MzErrorType
Isoleucine
IsotopeDistributionGui
IsotopicDistribution
IsotopicDistributionPanel
IsotopicDistributionSpectrum
IsotopicElement
J
JarFileFilter
JavaHomeDialog
JavaHomeOrMemoryDialogParent
JavaMemoryDialog
JavaSettingsDialog
JExceptionDialog
JFrameForBytes
JLabelAndComponentPanel
JOptionEditorPane
JpegFileFilter
JTableForDB
KMeansClustering
LastSelectedFolder
Leucine
LinearRegression
ListChooser
Lithium
Logger
Lysine
MascotEnzymeReader
MassCalc
MassCalcServlet
MassErrorBubblePlot
MassErrorPlot
MassGap
MavenJarFile
MDScore
MedianRegression
MemoryConsumptionStatus
MetaDataXMLParser
Methionine
MetricsPrefix
MgfFileFilter
MgfFileIterator
MgfIndex
MgfReader
MirroredSpectraTestDialog
ModelOrganism
Modification
ModificationFactory
ModificationImplementation
ModificationMatch
ModificationProfile
ModificationsDialog
ModificationTemplate
MolecularElement
MolecularFormula
Monitorable
MonitorableFileInputStream
MonitorableInputStream
MonitorDimension
MS1Spectrum
Ms2Exporter
Ms2FileFilter
Ms2Identification
MS2MzFidelityScore
MsAmandaIdfileReader
MsAmandaParameters
MsAmandaSettingsDialog
MsConvertParameters
MsConvertParametersDialog
MsExperiment
MsFormat
MsgfParameters
MsgfSettingsDialog
MSnSpectrum
Mutation
MutationFactory
MutationMatrix
MyriMatchParameters
MyriMatchSettingsDialog
MzDataFileFilter
MzIdentMLIdfileReader
MzIdentMLIdfileSearchParametersConverter
MzMlFileFilter
MzXmlFileFilter
NeutralLoss
NeutralLossesMap
Nitrogen
Node
NonSymmetricalNormalDistribution
NormalDistribution
NormalKernelDensityEstimator
NotesDialog
NotificationDialog
NotificationDialogParent
NovorIdfileReader
NovorParameters
NovorSettingsDialog
NucleotideSequence
NucleotideSequenceImpl
ObjectsCache
ObjectsDB
OmssaParameters
OmssaSettingsDialog
OmxFileFilter
OperatingSystemEnum
OutFileFilter
Oxygen
PathKey
PathSettingsDialog
Patient
PatientInformation
PdbBlock
PdbParameter
PdfFileFilter
Peak
PeffFileFilter
PepnovoAssumptionDetails
PepNovoIdfileReader
PepnovoParameters
Peptide
PeptideAssumption
PeptideAssumptionFilter
PeptideFragmentIon
PeptideMatch
PeptideMatchesIterator
PeptideShakerSetupDialog
PeptideSpectrumAnnotator
PepXmlFileFilter
PepxmlIdfileReader
Persistable
PersistableCode
Phenylalanine
PhosphoRS
Phosphorus
PickUp
PklFile
PklFileFilter
PklSpoFileFilter
PkxFileFilter
PngFileFilter
PNovoIdfileReader
PNovoParameters
PNovoSettingsDialog
Precursor
PrecursorAccuracy
PrecursorIon
PrideObject
PrideObjectsFactory
PrideXmlValidator
PrivacySettingsDialog
ProbabilityFilter
ProcessingPreferencesDialog
ProgressDialog
ProgressDialogX
Proline
PropertiesManager
Protein
Protein
ProteinInferencePreferences
ProteinMatch
ProteinMatchesIterator
ProteinSequencePane
ProteinSequencesManager
ProteinSequencesManagerGUI
ProteinSequencesPreferencesDialog
ProteinTree
ProteinTreeComponentsFactory
ProteomicAnalysis
ProteoWizardFilter
ProteoWizardSetupDialog
Protocol
ProtXmlFileFilter
PsmIterator
PsmScores
PsmScoringPreferences
PSProcessingPreferences
PTM
PtmChooser
PtmDialog
PTMFactory
PtmScore
PTMScoringPreferences
PtmSettings
PtmSiteMapping
PtmtableContent
PtmToPrideMap
PushBackStringReader
Pyrrolysine
Quantification
Quantification.QuantificationMethod
QueryType
Reagent
Reference
ReferenceArea
ReferenceGroup
RegExEnzyme
RegressionStatistics
ReportEditor
ReporterIon
ReporterIonQuantification
ReporterMethod
ReporterMethodFactory
ReporterSetupDialog
RescalingEvent
Retrievable
RetrievableCode
ROC
Sample
Sample
SampleAnalysisSet
SampleSelection
SearchGuiSetupDialog
SearchParameters
SearchParameters.MassAccuracyType
SearchSettingsDialog
Selenium
Selenocysteine
SelfUpdatingTableModel
Sequence
SequenceContentType
SequenceDbDetailsDialog
SequenceFactory
SequenceFragmentationPanel
SequenceInputType
SequenceMatchingPreferences
SequenceMatchingPreferences.MatchingType
SequenceModificationPanel
SequenceSegment
SequestParamsFileFilter
SerializationUtils
Serine
ShotgunProtocol
SimpleLinearRegression
Sodium
SpeciesDialog
SpecificAnnotationSettings
Spectrum
SpectrumAnnotation
SpectrumAnnotator
SpectrumCounting
SpectrumCounting.SpectrumCountingMethod
SpectrumFactory
SpectrumFile
SpectrumIdentificationAssumption
SpectrumMatch
SpectrumPanel
SpectrumPanelListener
SplashScreen
StandardUnit
StartBrowser
StartEndPosition
StreamGobbler
StringListChooser
Sulfur
SvgFileFilter
SwingUtils
SwingWorker
TableMap
TableMouseWheelListener
TableProperties
TableScrollBarListener
TableSorter
TableValueWrapper
Tag
TagAssumption
TagComponent
TagFactory
TagFragmentIon
TagMatcher
TagSpectrumAnnotator
TarUtils
TaxonomyTreeDialog
TaxonomyTreePanel
TempFilesManager
TestCaseLM
TextWriter
Threonine
TideIdfileReader
TideParameters
TideSettingsDialog
TiffFileFilter
TimestampRenderer
ToolFactory
ToolTipComboBoxRenderer
Translate
Tryptophan
Tyrosine
UniProtQuery
UniprotTaxonomyProvider
UnitOfMeasurement
UnknownElementMassException
Updateable
UpdateableCode
UrParameter
Util
UtilitiesDemo
UtilitiesGUIDefaults
UtilitiesPathPreferences
UtilitiesPathPreferences.UtilitiesPathKey
UtilitiesUserPreferences
ValidationQCPreferences
ValidationQCPreferencesDialog
ValidationQCPreferencesDialogParent
Valine
VennDiagram
VennDiagramDialog
VennDiagramLegendLocationDialog
VennDiagramPanel
VennDiagramPanel.VennDiagramType
VisibleTableColumnsDialog
VisibleTableColumnsDialogParent
WaitingActionListener
WaitingDialog
WaitingDialogExceptionHandler
WaitingHandler
WaitingHandlerCLIImpl
WaitingHandlerDummy
WebDAO
WorkbookStyle
X
XmlFileFilter
XMLValidationErrorHandler
XtandemParameters
XTandemSettingsDialog
XYPlotFiltersDialog
XYPlottingDialog
XYPlottingDialog.PlottingDialogPlotType
XYZDataPoint
Z
ZipUtils