All Classes

AASequenceImpl Advocate AdvocateFactory Alanine AlignedListCellRenderer AlignedTableCellRenderer AlignmentBlock AlternateRowColoursJTable AminoAcid AminoAcidPattern AminoAcidPatternDialog AndromedaIdfileReader AnnotationPreferences Arginine AScore Asparagine AsparticAcid Atom B BareBonesBrowserLaunch BasicMathFunctions BinaryArrayImpl BugReport ByteArrayRenderer Carbon Charge ChromatogramPanel ColumnTypeConverter CommandLineParser CommandLineUtils CompareVersionNumbers CompareVersionNumbers CompomicsTools CompomicsWrapper Connectable ConnectionDialog Constructors Contact ContactGroup CorrectionFactor CvTerm Cysteine DasAlignment DasAnnotationServerAlingmentReader DasAnnotationServerResultReader DasFeature DateChooser DatFileFilter DBAccessor DBAccessorGenerator DBElement DBMetaData DBResultSet DefaultOutputLoggerImplementation DefaultSpectrumAnnotation Deleteable DeleteableCode DownloadLatestZipFromRepo DtaFileFilter DualEnzyme DummyFrame ElementaryElement ElementaryIon Enzyme Enzyme EnzymeFactory EnzymeSelectionDialog ExceptionHandler ExperimentIO ExperimentObject Export ExportGraphicsDialog ExportGraphicsDialogParent FastaFileFilter FastaIndex FeedBack FeedBack.FeedBackType FileDAO FileFilterUtils FileLoggerImplementation FilenameExtensionFilter FileSelectionDialog FileSystemAccessor FindPdbForUniprotAccessions Flamable FlamableJFrame FolderMonitor FragmentIonTable FragmentIonTableCellRenderer FTP FTPClient FtpConnectionException FtpLoginException FtpProtocolException GeneDetailsDialog GeneFactory GenePreferences GeneratorException GettersAndSetters GlutamicAcid Glutamine Glycine Glycon GlyconFactory GOFactory GraphicsPanel GraphicsPanel.DrawingStyle GraphicsPanel.GraphicsPanelType GraphicsPanelTableCellRenderer GUIFileDAO GuiUtilities Header Header.DatabaseType HeadlessFileDAO HelpDialog HelpWindow Histidine Hydrogen Identification IdentificationDB IdentificationMatch IdentificationMatch.MatchType IdentificationMethod IdentificationParametersReader IdfileReader IdfileReaderFactory IdFilter ImageType ImmoniumIon ImportSettingsDialog InstanceVariables Instrument IntensityHistogram Ion Ion.IonType IonFactory IonLabelColorTableModel IonMatch Isoleucine IsotopeDistributionGui IsotopicDistribution IsotopicDistributionPanel IsotopicDistributionSpectrum IsotopicElement J JarFileFilter JavaOptionsDialog JavaOptionsDialogParent JExceptionDialog JFrameForBytes JLabelAndComponentPanel JpegFileFilter JTableForDB Leucine Logger Lysine MascotEnzymeReader MascotScore MassCalc MassCalcServlet MassErrorBubblePlot MassErrorPlot MavenJarFile MDScore MetaDataXMLParser Methionine MgfFileFilter MgfIndex MgfReader MirroredSpectraTestDialog Modification ModificationFactory ModificationImplementation ModificationMatch ModificationProfile ModificationProfile ModificationsDialog ModificationTemplate MolecularElement MolecularFormula Monitorable MonitorableFileInputStream MonitorableInputStream MonitorDimension MS1Spectrum Ms2FileFilter Ms2Identification MsExperiment MSnSpectrum Mutation MutationFactory MzDataFileFilter MzMlFileFilter MzXmlFileFilter NeutralLoss NeutralLossesMap Nitrogen Node NucleotideSequence NucleotideSequenceImpl ObjectsCache ObjectsDB OmxFileFilter OperatingSystemEnum OutFileFilter Oxygen PdbBlock PdbParameter PdfFileFilter Peak PeffFileFilter Peptide PeptideAssumption PeptideAssumptionDetails PeptideFragmentIon PeptideMatch PeptideQuantification PeptideShakerSetupDialog PepXmlFileFilter Persistable PersistableCode Phenylalanine Phosphorus PickUp PklFile PklFileFilter PklSpoFileFilter PkxFileFilter PngFileFilter PostProcessor Precursor PrecursorIon PrideObject PrideObjectsFactory PrideXmlValidator ProcessingPreferences ProcessingPreferencesDialog ProgressDialog ProgressDialogX Proline PropertiesManager Protein Protein ProteinMatch ProteinMatch.MatchingType ProteinQuantification ProteinSequencePane ProteinTree ProteinTreeComponentsFactory ProteomicAnalysis Protocol ProtXmlFileFilter PsmQuantification PsmScores PTM PtmDialog PtmDialogParent PTMFactory PTMScoringPreferences PtmSiteMapping PtmtableContent PtmToPrideMap PushBackStringReader Pyrrolysine Quantification Quantification.QuantificationMethod QuantificationDB QuantificationMatch QuantificationMatch.MatchType Ratio Reference ReferenceArea ReferenceGroup RegExEnzyme RelimsSetupDialog ReporterIon ReporterIonQuantification ReporterMethod ReporterMethodFactory ReporterSetupDialog RescalingEvent Retrievable RetrievableCode Sample Sample SampleAnalysisSet SampleSelection SearchEngine SearchGuiSetupDialog SearchParameters SearchParameters.PrecursorAccuracyType SearchParametersCLIParams SearchParametersInputBean SearchParametersInputBean.ToolType SearchSettingsDialog SearchSettingsDialogParent Selenocysteine SelfUpdatingTableModel Sequence SequenceDbDetailsDialog SequenceFactory SequenceFragmentationPanel SequenceModificationPanel SequestParamsFileFilter SerializationUtils Serine SpeciesDialog Spectrum SpectrumAnnotation SpectrumAnnotator SpectrumCounting SpectrumCounting.SpectrumCountingMethod SpectrumFactory SpectrumFile SpectrumMatch SpectrumPanel SpectrumPanelListener SplashScreen StartBrowser StartEndPosition StreamGobbler Sulfur SvgFileFilter SwingWorker TableMap TableSorter TableValueWrapper TagFactory TarUtils TestCaseLM Threonine TiffFileFilter TimestampRenderer ToolFactory ToolTipComboBoxRenderer Translate Tryptophan Tyrosine UnknownElementMassException Updateable UpdateableCode UrParameter Util UtilitiesDemo UtilitiesGUIDefaults UtilitiesUserPreferences Valine VennDiagramDialog VennDiagramDialog.VennDiagramType VennDiagramLegendLocationDialog VisibleTableColumnsDialog VisibleTableColumnsDialogParent WaitingActionListener WaitingDialog WaitingHandler WaitingHandlerCLIImpl WebDAO X XmlFileFilter XMLValidationErrorHandler XYPlotFiltersDialog XYPlottingDialog XYZDataPoint Z