All Classes

AASequenceImpl Advocate AdvocateFactory Alanine AlignedListCellRenderer AlignedTableCellRenderer AlignmentBlock AlternateRowColoursJTable AminoAcid AndromedaIdfileReader AnnotationPreferences Arginine Asparagine AsparticAcid Atom B BareBonesBrowserLaunch BasicMathFunctions BinaryArrayImpl ByteArrayRenderer Carbon Charge ChromatogramPanel ColumnTypeConverter CommandLineParser CompomicsTools Connectable ConnectionDialog Constructors Contact CorrectionFactor CvTerm Cysteine DasAlignment DasAnnotationServerAlingmentReader DasAnnotationServerResultReader DasFeature DateChooser DatFileFilter DBAccessor DBAccessorGenerator DBElement DBMetaData DBResultSet DefaultOutputLoggerImplementation DefaultSpectrumAnnotation Deleteable DeleteableCode DtaFileFilter DualEnzyme ElementaryIon Enzyme Enzyme EnzymeFactory ExperimentIO ExperimentObject Export FastaFileFilter FastaIndex FileFilterUtils FileLoggerImplementation FilenameExtensionFilter FileSystemAccessor FindPdbForUniprotAccessions Flamable FlamableJFrame FolderMonitor FragmentIonTable FragmentIonTableCellRenderer FTP FTPClient FtpConnectionException FtpLoginException FtpProtocolException GeneratorException GettersAndSetters GlutamicAcid Glutamine Glycine Glycon GlyconFactory GraphicsPanel GraphicsPanel.GraphicsPanelType GraphicsPanelTableCellRenderer 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 MascotIdfileReader MascotScore MassCalc MassCalcServlet MassErrorBubblePlot MassErrorPlot Methionine MgfFileFilter MgfIndex MgfReader Modification ModificationFactory ModificationImplementation ModificationMatch ModificationProfile ModificationTemplate MolecularElement MolecularFormula Monitorable MonitorableFileInputStream MonitorableInputStream MonitorDimension MS1Spectrum Ms2FileFilter Ms2Identification MsExperiment MSnSpectrum MzDataFileFilter MzMlFileFilter MzXmlFileFilter NeutralLoss NeutralLossesMap Nitrogen NucleotideSequence NucleotideSequenceImpl ObjectsCache ObjectsDB OMSSAIdfileReader OmxFileFilter OperatingSystemEnum OutFileFilter Oxygen PdbBlock PdbParameter PdfFileFilter Peak PeffFileFilter Peptide PeptideAssumption PeptideFragmentIon PeptideMatch PeptideQuantification 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 PTM PtmDialog PtmDialogParent PTMFactory PTMLocationScores PtmtableContent PtmToPrideMap PushBackStringReader Pyrrolysine Quantification Quantification.QuantificationMethod QuantificationDB QuantificationMatch QuantificationMatch.MatchType Ratio Reference ReferenceArea RegExEnzyme ReporterIon ReporterIonQuantification ReporterMethod ReporterMethodFactory RescalingEvent Retrievable RetrievableCode Sample Sample SampleAnalysisSet SampleSelection SearchEngine Selenocysteine Sequence SequenceFactory SequenceFragmentationPanel SequenceModificationPanel SequestParamsFileFilter Serine Spectrum SpectrumAnnotation SpectrumAnnotator SpectrumCounting SpectrumCounting.SpectrumCountingMethod SpectrumFactory SpectrumFile SpectrumMatch SpectrumPanel SpectrumPanelListener StartBrowser StartEndPosition Sulfur SvgFileFilter SwingWorker TableMap TableSorter TableValueWrapper Threonine TiffFileFilter TimestampRenderer ToolTipComboBoxRenderer Translate Tryptophan Tyrosine UnknownElementMassException Updateable UpdateableCode UrParameter Util UtilitiesDemo UtilitiesGUIDefaults UtilitiesUserPreferences Valine WaitingDialog WaitingHandler WaitingHandlerCLIImpl X XmlFileFilter XTandemIdfileReader XYZDataPoint Z