All Classes

AASequenceImpl Advocate AdvocateFactory Alanine AlignedListCellRenderer AlignedTableCellRenderer AlignmentBlock AlternateRowColoursJTable AminoAcid AminoAcidPattern AminoAcidPatternDialog And AndromedaIdfileReader AnnotationPreferences Arginine Asparagine AsparticAcid Atom B BareBonesBrowserLaunch BasicMathFunctions BinaryArrayImpl BugReport ByteArrayRenderer Carbon Charge ChromatogramPanel ColumnTypeConverter CombDialog CombFilter CommandLineParser CommandLineUtils 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 DtaFileFilter DualEnzyme ElementaryIon Enzyme Enzyme EnzymeFactory ExceptionHandler ExperimentIO ExperimentObject Export ExportGraphicsDialog ExportGraphicsDialogParent FastaFileFilter FastaIndex FeedBack FeedBack.FeedBackType FileFilterUtils FileLoggerImplementation FilenameExtensionFilter FileSelectionDialog FileSystemAccessor FindPdbForUniprotAccessions FingerprintDialog FingerprintPattern Flamable FlamableJFrame FolderMonitor FragmentIonTable FragmentIonTableCellRenderer FTP FTPClient FtpConnectionException FtpLoginException FtpProtocolException GeneratorException GettersAndSetters GlutamicAcid Glutamine Glycine Glycon GlyconFactory GraphicsPanel GraphicsPanel.GraphicsPanelType GraphicsPanelTableCellRenderer GuiUtilities Header Header.DatabaseType HelpDialog HelpWindow Histidine Hydrogen Identification IdentificationDB IdentificationMatch IdentificationMatch.MatchType IdentificationMethod IdentificationParametersReader IdfileReader IdfileReaderFactory ImageType ImmoniumIon InstanceVariables Instrument IntensityHistogram Ion Ion.IonType IonFactory IonLabelColorTableModel IonMatch Isoleucine IsotopeDistributionGui IsotopicDistribution IsotopicDistributionPanel IsotopicDistributionSpectrum IsotopicElement J JExceptionDialog JFrameForBytes JLabelAndComponentPanel JpegFileFilter JTableForDB Leucine Logger Lysine MascotEnzymeReader MascotScore MassCalc MassCalcServlet MassErrorBubblePlot MassErrorPlot Methionine MgfFileFilter MgfIndex MgfReader Modification ModificationFactory ModificationImplementation ModificationMatch ModificationProfile ModificationProfile ModificationsDialog ModificationTemplate MolecularElement MolecularFormula Monitorable MonitorableFileInputStream MonitorableInputStream MonitorDimension MS1Spectrum Ms2FileFilter Ms2Identification MsExperiment MSnSpectrum MzDataFileFilter MzDialog MzFilter MzMlFileFilter MzXmlFileFilter NeutralLoss NeutralLossesMap Nitrogen NucleotideSequence NucleotideSequenceImpl ObjectsCache ObjectsDB OmxFileFilter OperatingSystemEnum Or OutFileFilter Oxygen PdbBlock PdbParameter PdfFileFilter Peak PeakDialog PeakFilter PeffFileFilter Peptide PeptideAssumption PeptideFragmentIon PeptideMatch PeptideQuantification PeptideShakerSetupDialog PepXmlFileFilter Persistable PersistableCode Phenylalanine Phosphorus PickUp PklFile PklFileFilter PklSpoFileFilter PkxFileFilter PngFileFilter PostProcessor Precursor PrecursorIon PrideObject PrideObjectsFactory ProgressDialog ProgressDialogX Proline PropertiesManager Protein Protein ProteinMatch ProteinQuantification ProteinSequencePane ProteomicAnalysis Protocol ProtXmlFileFilter PsmQuantification PsmScores PTM PtmDialog PtmDialogParent PTMFactory PTMLocationScores 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 Selenocysteine Sequence SequenceFactory SequenceFragmentationPanel SequenceModificationPanel SequestParamsFileFilter SerializationUtils Serine Spectrum SpectrumAnnotation SpectrumAnnotator SpectrumCounting SpectrumCounting.SpectrumCountingMethod SpectrumFactory SpectrumFile SpectrumFilter SpectrumMatch SpectrumPanel SpectrumPanelListener StartBrowser StartEndPosition Sulfur SvgFileFilter SwingWorker TableMap TableSorter TableValueWrapper TarUtils TestCaseLM Threonine TiffFileFilter TimestampRenderer ToolFactory ToolTipComboBoxRenderer Translate Tryptophan TypeSelection Tyrosine UnknownElementMassException Updateable UpdateableCode UrParameter Util UtilitiesDemo UtilitiesGUIDefaults UtilitiesUserPreferences Valine VisibleTableColumnsDialog VisibleTableColumnsDialogParent WaitingDialog WaitingHandler WaitingHandlerCLIImpl X XmlFileFilter XYPlottingDialog XYZDataPoint Z