Hierarchy For All Packages
Package Hierarchies:- com.compomics.cli.enzymes,
- com.compomics.cli.fasta,
- com.compomics.cli.identification_parameters,
- com.compomics.cli.modifications,
- com.compomics.cli.peptide_mapper,
- com.compomics.scripts_marc,
- com.compomics.software,
- com.compomics.software.autoupdater,
- com.compomics.software.cli,
- com.compomics.software.dialogs,
- com.compomics.software.log,
- com.compomics.software.settings,
- com.compomics.software.settings.gui,
- com.compomics.util,
- com.compomics.util.db,
- com.compomics.util.db.components,
- com.compomics.util.db.interfaces,
- com.compomics.util.db.object,
- com.compomics.util.db.object.objects,
- com.compomics.util.enumeration,
- com.compomics.util.examples,
- com.compomics.util.exceptions,
- com.compomics.util.exceptions.exception_handlers,
- com.compomics.util.experiment,
- com.compomics.util.experiment.biology.aminoacids,
- com.compomics.util.experiment.biology.aminoacids.impl,
- com.compomics.util.experiment.biology.aminoacids.sequence,
- com.compomics.util.experiment.biology.atoms,
- com.compomics.util.experiment.biology.atoms.impl,
- com.compomics.util.experiment.biology.enzymes,
- com.compomics.util.experiment.biology.genes,
- com.compomics.util.experiment.biology.genes.ensembl,
- com.compomics.util.experiment.biology.genes.go,
- com.compomics.util.experiment.biology.ions,
- com.compomics.util.experiment.biology.ions.impl,
- com.compomics.util.experiment.biology.modifications,
- com.compomics.util.experiment.biology.proteins,
- com.compomics.util.experiment.biology.taxonomy,
- com.compomics.util.experiment.biology.taxonomy.mappings,
- com.compomics.util.experiment.biology.variants,
- com.compomics.util.experiment.biology.variants.amino_acids,
- com.compomics.util.experiment.filtering,
- com.compomics.util.experiment.identification,
- com.compomics.util.experiment.identification.amino_acid_tags,
- com.compomics.util.experiment.identification.features,
- com.compomics.util.experiment.identification.filtering,
- com.compomics.util.experiment.identification.filtering.items,
- com.compomics.util.experiment.identification.identification_parameters,
- com.compomics.util.experiment.identification.matches,
- com.compomics.util.experiment.identification.matches_iterators,
- com.compomics.util.experiment.identification.modification,
- com.compomics.util.experiment.identification.modification.mapping,
- com.compomics.util.experiment.identification.modification.scores,
- com.compomics.util.experiment.identification.peptide_fragmentation,
- com.compomics.util.experiment.identification.peptide_fragmentation.models,
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration,
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features,
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic,
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_generation,
- com.compomics.util.experiment.identification.peptide_inference,
- com.compomics.util.experiment.identification.peptide_shaker,
- com.compomics.util.experiment.identification.protein_inference,
- com.compomics.util.experiment.identification.protein_inference.fm_index,
- com.compomics.util.experiment.identification.protein_sequences,
- com.compomics.util.experiment.identification.protein_sequences.digestion,
- com.compomics.util.experiment.identification.protein_sequences.digestion.iterators,
- com.compomics.util.experiment.identification.psm_scoring,
- com.compomics.util.experiment.identification.psm_scoring.psm_scores,
- com.compomics.util.experiment.identification.spectrum_annotation,
- com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators,
- com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators,
- com.compomics.util.experiment.identification.spectrum_assumptions,
- com.compomics.util.experiment.identification.utils,
- com.compomics.util.experiment.identification.validation,
- com.compomics.util.experiment.io.biology.protein,
- com.compomics.util.experiment.io.biology.protein.converters,
- com.compomics.util.experiment.io.biology.protein.iterators,
- com.compomics.util.experiment.io.identification,
- com.compomics.util.experiment.io.identification.idfilereaders,
- com.compomics.util.experiment.io.identification.writers,
- com.compomics.util.experiment.io.mass_spectrometry,
- com.compomics.util.experiment.io.mass_spectrometry.apl,
- com.compomics.util.experiment.io.mass_spectrometry.cms,
- com.compomics.util.experiment.io.mass_spectrometry.mgf,
- com.compomics.util.experiment.io.mass_spectrometry.ms2,
- com.compomics.util.experiment.io.mass_spectrometry.mzml,
- com.compomics.util.experiment.io.parameters,
- com.compomics.util.experiment.io.temp,
- com.compomics.util.experiment.mass_spectrometry,
- com.compomics.util.experiment.mass_spectrometry.indexes,
- com.compomics.util.experiment.mass_spectrometry.proteowizard,
- com.compomics.util.experiment.mass_spectrometry.spectra,
- com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser,
- com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.gui,
- com.compomics.util.experiment.mass_spectrometry.utils,
- com.compomics.util.experiment.normalization,
- com.compomics.util.experiment.patient,
- com.compomics.util.experiment.personalization,
- com.compomics.util.experiment.quantification,
- com.compomics.util.experiment.quantification.reporterion,
- com.compomics.util.experiment.quantification.spectrumcounting,
- com.compomics.util.experiment.refinement_parameters,
- com.compomics.util.experiment.units,
- com.compomics.util.general,
- com.compomics.util.general.servlet,
- com.compomics.util.gui,
- com.compomics.util.gui.atoms,
- com.compomics.util.gui.enzymes,
- com.compomics.util.gui.error_handlers,
- com.compomics.util.gui.error_handlers.notification,
- com.compomics.util.gui.events,
- com.compomics.util.gui.export.graphics,
- com.compomics.util.gui.export.report,
- com.compomics.util.gui.file_handling,
- com.compomics.util.gui.filtering,
- com.compomics.util.gui.genes,
- com.compomics.util.gui.interfaces,
- com.compomics.util.gui.isotopic_calculator,
- com.compomics.util.gui.modification,
- com.compomics.util.gui.parameters,
- com.compomics.util.gui.parameters.identification,
- com.compomics.util.gui.parameters.identification.advanced,
- com.compomics.util.gui.parameters.identification.algorithm,
- com.compomics.util.gui.parameters.identification.pride,
- com.compomics.util.gui.parameters.identification.search,
- com.compomics.util.gui.parameters.proteowizard,
- com.compomics.util.gui.parameters.tools,
- com.compomics.util.gui.protein,
- com.compomics.util.gui.renderers,
- com.compomics.util.gui.spectrum,
- com.compomics.util.gui.tablemodels,
- com.compomics.util.gui.utils,
- com.compomics.util.gui.utils.user_choice,
- com.compomics.util.gui.utils.user_choice.list_choosers,
- com.compomics.util.gui.variants.aa_substitutions,
- com.compomics.util.gui.waiting.waitinghandlers,
- com.compomics.util.interfaces,
- com.compomics.util.io,
- com.compomics.util.io.compression,
- com.compomics.util.io.compression.SectionGzWriter,
- com.compomics.util.io.export,
- com.compomics.util.io.export.styles,
- com.compomics.util.io.export.writers,
- com.compomics.util.io.export.xml,
- com.compomics.util.io.file,
- com.compomics.util.io.file.filefilters,
- com.compomics.util.io.flat,
- com.compomics.util.io.flat.readers,
- com.compomics.util.io.ftp,
- com.compomics.util.io.json,
- com.compomics.util.io.json.adapter,
- com.compomics.util.io.json.marshallers,
- com.compomics.util.junit,
- com.compomics.util.math,
- com.compomics.util.math.clustering,
- com.compomics.util.math.clustering.settings,
- com.compomics.util.math.matrix,
- com.compomics.util.math.roc,
- com.compomics.util.math.statistics,
- com.compomics.util.math.statistics.distributions,
- com.compomics.util.math.statistics.linear_regression,
- com.compomics.util.math.statistics.linear_regression.filters,
- com.compomics.util.math.statistics.linear_regression.regressions,
- com.compomics.util.memory,
- com.compomics.util.messages,
- com.compomics.util.nucleotide,
- com.compomics.util.parameters,
- com.compomics.util.parameters.identification,
- com.compomics.util.parameters.identification.advanced,
- com.compomics.util.parameters.identification.search,
- com.compomics.util.parameters.identification.tool_specific,
- com.compomics.util.parameters.peptide_shaker,
- com.compomics.util.parameters.quantification.spectrum_counting,
- com.compomics.util.parameters.searchgui,
- com.compomics.util.parameters.tools,
- com.compomics.util.pdbfinder,
- com.compomics.util.pdbfinder.das.readers,
- com.compomics.util.pdbfinder.pdb,
- com.compomics.util.pride,
- com.compomics.util.pride.prideobjects,
- com.compomics.util.pride.prideobjects.webservice,
- com.compomics.util.pride.prideobjects.webservice.file,
- com.compomics.util.pride.prideobjects.webservice.query,
- com.compomics.util.pride.validation,
- com.compomics.util.protein,
- com.compomics.util.sun,
- com.compomics.util.threading,
- com.compomics.util.waiting
Class Hierarchy
- java.lang.Object
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AAIdentityFeature (implements com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.Ms2pipFeature)
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAIdentityFeatureAbsolute
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAIdentityFeatureRelative
- com.compomics.util.experiment.identification.protein_sequences.AaOccurrence
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AAPropertyFeature (implements com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.Ms2pipFeature, com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.SingleAAPropertyFeature)
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyFeatureAbsolute
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyFeatureRelative
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature (implements com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.Ms2pipFeature, com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.MultipleAAPropertyFeature)
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AASequenceFeature (implements com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.Ms2pipFeature, com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.SingleAAPropertyFeature)
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ComplementaryIonAminoAcidFeature
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ForwardIonAminoAcidFeature
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideAminoAcidFeature
- com.compomics.util.protein.AASequenceImpl (implements com.compomics.util.interfaces.Sequence)
- com.compomics.cli.identification_parameters.AbstractIdentificationParametersCli (implements java.util.concurrent.Callable<V>)
- com.compomics.cli.identification_parameters.IdentificationParametersCLI
- javax.swing.table.AbstractTableModel (implements java.io.Serializable, javax.swing.table.TableModel)
- com.compomics.util.db.DBResultSet
- javax.swing.table.DefaultTableModel (implements java.io.Serializable)
- com.compomics.util.gui.variants.aa_substitutions.AaSubstitutionMatrixTableModel
- com.compomics.util.gui.spectrum.IonLabelColorTableModel
- com.compomics.util.gui.tablemodels.SelfUpdatingTableModel
- com.compomics.util.sun.TableMap (implements javax.swing.event.TableModelListener)
- com.compomics.util.sun.TableSorter
- com.compomics.util.experiment.identification.protein_inference.fm_index.AccessionMetaData (implements java.io.Serializable)
- com.compomics.util.gui.renderers.AlignedTableCellRenderer (implements javax.swing.table.TableCellRenderer)
- com.compomics.util.pdbfinder.das.readers.AlignmentBlock
- com.compomics.util.experiment.identification.protein_sequences.AmbiguousSequenceIterator
- com.compomics.util.experiment.biology.variants.AminoAcidSubstitution
- com.compomics.util.experiment.io.identification.idfilereaders.AndromedaIdfileReader (implements com.compomics.util.experiment.io.identification.IdfileReader)
- com.compomics.util.experiment.io.mass_spectrometry.apl.AplFileWriter (implements java.lang.AutoCloseable)
- com.compomics.util.ArrayUtil
- com.compomics.util.examples.BareBonesBrowserLaunch
- com.compomics.util.math.BasicMathFunctions
- com.compomics.util.math.BigFunctions
- com.compomics.util.math.BigMathUtils
- com.compomics.util.BinaryArrayImpl
- com.compomics.util.math.statistics.linear_regression.filters.BinningFilter
- com.compomics.util.math.statistics.distributions.BinomialDistribution (implements com.compomics.util.math.statistics.Distribution)
- com.compomics.util.experiment.biology.taxonomy.mappings.BiomartMapping
- com.compomics.util.experiment.biology.ions.Charge
- com.compomics.software.log.CliLogger (implements java.lang.AutoCloseable)
- com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileIterator (implements com.compomics.util.experiment.io.mass_spectrometry.MsFileIterator)
- com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader (implements com.compomics.util.experiment.mass_spectrometry.SpectrumProvider)
- com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileUtils
- com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileWriter (implements java.lang.AutoCloseable)
- com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFolder
- com.compomics.util.db.ColumnTypeConverter
- com.compomics.util.general.CommandLineParser
- com.compomics.software.cli.CommandLineUtils
- com.compomics.software.cli.CommandParameter
- com.compomics.software.autoupdater.CompareVersionNumbers (implements java.util.Comparator<T>)
- com.compomics.util.CompareVersionNumbers (implements java.util.Comparator<T>)
- com.compomics.software.CompomicsWrapper
- java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
- java.awt.Container
- javax.swing.JComponent (implements java.io.Serializable)
- javax.swing.JLabel (implements javax.accessibility.Accessible, javax.swing.SwingConstants)
- javax.swing.plaf.basic.BasicComboBoxRenderer (implements javax.swing.ListCellRenderer<E>, java.io.Serializable)
- com.compomics.util.gui.renderers.ToolTipComboBoxRenderer
- javax.swing.DefaultListCellRenderer (implements javax.swing.ListCellRenderer<E>, java.io.Serializable)
- com.compomics.util.gui.renderers.AlignedListCellRenderer
- javax.swing.table.DefaultTableCellRenderer (implements java.io.Serializable, javax.swing.table.TableCellRenderer)
- com.compomics.util.gui.renderers.ByteArrayRenderer
- com.compomics.util.gui.renderers.TimestampRenderer
- com.compomics.util.gui.renderers.GraphicsPanelTableCellRenderer (implements javax.swing.table.TableCellRenderer)
- javax.swing.plaf.basic.BasicComboBoxRenderer (implements javax.swing.ListCellRenderer<E>, java.io.Serializable)
- javax.swing.JPanel (implements javax.accessibility.Accessible)
- com.compomics.util.gui.atoms.AtomPanel
- com.compomics.util.gui.spectrum.GraphicsPanel
- com.compomics.util.gui.spectrum.ChromatogramPanel
- com.compomics.util.gui.spectrum.IsotopicDistributionPanel
- com.compomics.util.gui.spectrum.SpectrumPanel
- com.compomics.util.gui.spectrum.IntensityHistogram
- com.compomics.util.gui.JLabelAndComponentPanel
- com.compomics.util.gui.spectrum.MassErrorBubblePlot
- com.compomics.util.gui.spectrum.MassErrorPlot
- com.compomics.util.gui.spectrum.SequenceFragmentationPanel
- com.compomics.util.gui.protein.SequenceModificationPanel
- com.compomics.util.gui.VennDiagramPanel
- javax.swing.JTable (implements javax.accessibility.Accessible, javax.swing.event.CellEditorListener, javax.swing.event.ListSelectionListener, javax.swing.event.RowSorterListener, javax.swing.Scrollable, javax.swing.event.TableColumnModelListener, javax.swing.event.TableModelListener)
- com.compomics.util.AlternateRowColoursJTable
- com.compomics.util.gui.JTableForDB
- com.compomics.util.gui.spectrum.FragmentIonTable
- com.compomics.util.gui.modification.ModificationTable
- com.compomics.util.AlternateRowColoursJTable
- javax.swing.JLabel (implements javax.accessibility.Accessible, javax.swing.SwingConstants)
- java.awt.Window (implements javax.accessibility.Accessible)
- java.awt.Dialog
- javax.swing.JDialog (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
- com.compomics.util.gui.AaMass
- com.compomics.util.gui.AminoAcidPatternDialog
- com.compomics.util.gui.parameters.identification.algorithm.AndromedaParametersDialog (implements com.compomics.util.gui.parameters.identification.AlgorithmParametersDialog)
- com.compomics.util.gui.parameters.identification.advanced.AnnotationParametersDialog
- com.compomics.util.gui.atoms.AtomChainDialog
- com.compomics.util.gui.parameters.identification.advanced.BackgroundSpeciesDialog
- com.compomics.util.gui.error_handlers.BugReport
- com.compomics.util.gui.parameters.identification.algorithm.CometParametersDialog (implements com.compomics.util.gui.parameters.identification.AlgorithmParametersDialog)
- com.compomics.util.gui.utils.ConnectionDialog
- com.compomics.util.gui.utils.DateChooser
- com.compomics.util.gui.parameters.identification.algorithm.DirecTagParametersDialog (implements com.compomics.util.gui.parameters.identification.AlgorithmParametersDialog)
- com.compomics.util.gui.parameters.identification.pride.EnzymeParametersDialog
- com.compomics.util.gui.enzymes.EnzymesDialog
- com.compomics.util.gui.ExportFormatSelectionDialog
- com.compomics.util.gui.export.graphics.ExportGraphicsDialog
- com.compomics.util.gui.protein.FastaParametersDialog
- com.compomics.util.gui.file_handling.FileDisplayDialog
- com.compomics.util.gui.file_handling.FileSelectionDialog
- com.compomics.util.gui.filtering.FilterDialog
- com.compomics.util.gui.parameters.identification.advanced.FractionParametersDialog
- com.compomics.util.gui.genes.GeneDetailsDialog
- com.compomics.util.gui.parameters.identification.advanced.GeneParametersDialog
- com.compomics.util.gui.error_handlers.HelpDialog
- com.compomics.util.gui.parameters.identification.IdentificationParametersEditionDialog
- com.compomics.util.gui.parameters.identification.IdentificationParametersNameDialog
- com.compomics.util.gui.parameters.identification.IdentificationParametersOverviewDialog
- com.compomics.software.dialogs.JavaHomeDialog
- com.compomics.software.dialogs.JavaMemoryDialog
- com.compomics.software.dialogs.JavaParametersDialog
- com.compomics.util.gui.JExceptionDialog
- com.compomics.util.gui.utils.user_choice.ListChooser
- com.compomics.util.gui.utils.user_choice.list_choosers.ModificationChooser
- com.compomics.util.gui.utils.user_choice.list_choosers.StringListChooser
- com.compomics.util.gui.parameters.identification.advanced.MatchesImportParametersDialog
- com.compomics.util.gui.parameters.identification.algorithm.MetaMorpheusParametersDialog (implements com.compomics.util.gui.parameters.identification.AlgorithmParametersDialog)
- com.compomics.util.examples.MirroredSpectraTestDialog
- com.compomics.util.gui.modification.ModificationDialog
- com.compomics.util.gui.parameters.identification.advanced.ModificationLocalizationParametersDialog
- com.compomics.util.gui.modification.ModificationsDialog
- com.compomics.util.gui.parameters.identification.algorithm.MsAmandaParametersDialog (implements com.compomics.util.gui.parameters.identification.AlgorithmParametersDialog)
- com.compomics.util.gui.parameters.proteowizard.MsConvertParametersDialog
- com.compomics.util.gui.parameters.identification.algorithm.MsgfParametersDialog (implements com.compomics.util.gui.parameters.identification.AlgorithmParametersDialog)
- com.compomics.util.gui.parameters.identification.algorithm.MyriMatchParametersDialog (implements com.compomics.util.gui.parameters.identification.AlgorithmParametersDialog)
- com.compomics.util.gui.enzymes.NewEnzymeDialog
- com.compomics.util.gui.error_handlers.notification.NotesDialog
- com.compomics.util.gui.error_handlers.notification.NotificationDialog
- com.compomics.util.gui.parameters.identification.algorithm.NovorParametersDialog (implements com.compomics.util.gui.parameters.identification.AlgorithmParametersDialog)
- com.compomics.util.gui.parameters.identification.algorithm.OmssaParametersDialog (implements com.compomics.util.gui.parameters.identification.AlgorithmParametersDialog)
- com.compomics.software.settings.gui.PathParametersDialog
- com.compomics.util.gui.parameters.identification.algorithm.PepNovoParametersDialog (implements com.compomics.util.gui.parameters.identification.AlgorithmParametersDialog)
- com.compomics.software.dialogs.PeptideShakerSetupDialog
- com.compomics.util.gui.parameters.identification.advanced.PeptideVariantsParametersDialog
- com.compomics.util.gui.parameters.identification.algorithm.PNovoParametersDialog (implements com.compomics.util.gui.parameters.identification.AlgorithmParametersDialog)
- com.compomics.util.gui.PrivacyParametersDialog
- com.compomics.util.gui.parameters.tools.ProcessingParametersDialog
- com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog
- com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX (implements com.compomics.util.waiting.WaitingHandler)
- com.compomics.util.gui.parameters.identification.advanced.ProteinInferenceParametersDialog
- com.compomics.software.dialogs.ProteoWizardSetupDialog
- com.compomics.util.gui.parameters.identification.advanced.PsmScoringParametersDialog
- com.compomics.util.gui.export.report.ReportEditor
- com.compomics.software.dialogs.ReporterSetupDialog
- com.compomics.util.gui.SampleSelection
- com.compomics.software.dialogs.SearchGuiSetupDialog
- com.compomics.util.gui.parameters.identification.search.SearchParametersDialog
- com.compomics.util.gui.parameters.identification.search.SequenceDbDetailsDialog
- com.compomics.util.gui.parameters.identification.advanced.SequenceMatchingParametersDialog
- com.compomics.util.gui.parameters.SparklineColorsDialog
- com.compomics.util.gui.genes.SpeciesDialog
- com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.gui.ThermoRawFileParserParametersDialog
- com.compomics.util.gui.parameters.identification.algorithm.TideParametersDialog (implements com.compomics.util.gui.parameters.identification.AlgorithmParametersDialog)
- com.compomics.util.gui.parameters.identification.advanced.ValidationParametersDialog
- com.compomics.util.gui.parameters.identification.advanced.ValidationQCParametersDialog
- com.compomics.util.gui.VennDiagramDialog
- com.compomics.util.gui.VennDiagramLegendLocationDialog
- com.compomics.util.gui.VisibleTableColumnsDialog
- com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog (implements com.compomics.util.waiting.WaitingHandler)
- com.compomics.util.gui.parameters.identification.algorithm.XTandemParametersDialog (implements com.compomics.util.gui.parameters.identification.AlgorithmParametersDialog)
- com.compomics.util.gui.XYPlotFiltersDialog
- com.compomics.util.gui.XYPlottingDialog (implements com.compomics.util.gui.VisibleTableColumnsDialogParent)
- javax.swing.JDialog (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
- java.awt.Frame (implements java.awt.MenuContainer)
- javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
- com.compomics.util.gui.DummyFrame
- com.compomics.util.gui.FlamableJFrame (implements com.compomics.util.interfaces.Flamable)
- com.compomics.util.examples.HelpWindow
- com.compomics.util.gui.isotopic_calculator.IsotopeDistributionGui
- com.compomics.util.gui.JFrameForBytes
- com.compomics.util.examples.UtilitiesDemo
- javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
- java.awt.Dialog
- javax.swing.JComponent (implements java.io.Serializable)
- java.awt.Container
- com.compomics.util.experiment.Constants
- com.compomics.util.db.components.Constructors
- com.compomics.util.experiment.io.identification.idfilereaders.CossIdfileReader (implements com.compomics.util.experiment.io.identification.IdfileReader)
- com.compomics.util.pdbfinder.das.readers.DasAlignment
- com.compomics.util.pdbfinder.das.readers.DasAnnotationServerAlingmentReader
- com.compomics.util.pdbfinder.das.readers.DasAnnotationServerResultReader
- com.compomics.util.pdbfinder.das.readers.DasFeature
- com.compomics.util.math.roc.DataRoc (implements com.compomics.util.math.statistics.ROC)
- com.compomics.util.db.DBAccessor
- com.compomics.util.db.DBAccessorGenerator
- com.compomics.util.db.DBMetaData
- com.compomics.util.db.object.DbMutex
- com.compomics.util.experiment.io.biology.protein.converters.DecoyConverter
- com.compomics.util.general.DefaultOutputLoggerImplementation (implements com.compomics.util.interfaces.Logger)
- com.compomics.util.gui.spectrum.DefaultSpectrumAnnotation (implements com.compomics.util.gui.interfaces.SpectrumAnnotation)
- com.compomics.util.io.export.styles.DefaultStyle (implements com.compomics.util.io.export.WorkbookStyle)
- com.compomics.util.db.components.DeleteableCode
- com.compomics.util.experiment.biology.variants.amino_acids.Deletion (implements com.compomics.util.experiment.biology.variants.Variant)
- com.compomics.util.experiment.io.identification.idfilereaders.DirecTagIdfileReader (implements com.compomics.util.experiment.io.identification.IdfileReader)
- com.compomics.util.math.roc.DistributionRoc (implements com.compomics.util.math.statistics.ROC)
- com.compomics.util.math.matrix.DoubleMatrix
- com.compomics.software.autoupdater.DownloadLatestZipFromRepo
- com.compomics.scripts_marc.Dummy
- com.compomics.util.experiment.io.parameters.DummyParameters (implements com.compomics.util.experiment.io.parameters.MarshallableParameter)
- com.compomics.util.waiting.Duration
- com.compomics.util.gui.utils.EmptyCollections
- com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblGenomesSpecies
- com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblSpecies
- com.compomics.util.experiment.biology.genes.ensembl.EnsemblVersion
- com.compomics.util.protein.Enzyme (implements java.lang.Cloneable)
- com.compomics.util.protein.DualEnzyme
- com.compomics.util.protein.RegExEnzyme
- com.compomics.util.experiment.biology.enzymes.EnzymeFactory
- com.compomics.cli.enzymes.EnzymesCLI
- com.compomics.cli.enzymes.EnzymesCLIInputBean
- com.compomics.util.exceptions.ExceptionHandler
- com.compomics.util.exceptions.exception_handlers.CommandLineExceptionHandler
- com.compomics.util.exceptions.exception_handlers.FrameExceptionHandler
- com.compomics.util.exceptions.exception_handlers.WaitingDialogExceptionHandler
- com.compomics.util.experiment.personalization.ExperimentObject (implements java.io.Serializable)
- com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
- com.compomics.util.experiment.identification.Advocate
- com.compomics.util.experiment.biology.aminoacids.AminoAcid
- com.compomics.util.experiment.biology.aminoacids.impl.Alanine
- com.compomics.util.experiment.biology.aminoacids.impl.Arginine
- com.compomics.util.experiment.biology.aminoacids.impl.Asparagine
- com.compomics.util.experiment.biology.aminoacids.impl.AsparticAcid
- com.compomics.util.experiment.biology.aminoacids.impl.B
- com.compomics.util.experiment.biology.aminoacids.impl.Cysteine
- com.compomics.util.experiment.biology.aminoacids.impl.GlutamicAcid
- com.compomics.util.experiment.biology.aminoacids.impl.Glutamine
- com.compomics.util.experiment.biology.aminoacids.impl.Glycine
- com.compomics.util.experiment.biology.aminoacids.impl.Histidine
- com.compomics.util.experiment.biology.aminoacids.impl.Isoleucine
- com.compomics.util.experiment.biology.aminoacids.impl.J
- com.compomics.util.experiment.biology.aminoacids.impl.Leucine
- com.compomics.util.experiment.biology.aminoacids.impl.Lysine
- com.compomics.util.experiment.biology.aminoacids.impl.Methionine
- com.compomics.util.experiment.biology.aminoacids.impl.Phenylalanine
- com.compomics.util.experiment.biology.aminoacids.impl.Proline
- com.compomics.util.experiment.biology.aminoacids.impl.Pyrrolysine
- com.compomics.util.experiment.biology.aminoacids.impl.Selenocysteine
- com.compomics.util.experiment.biology.aminoacids.impl.Serine
- com.compomics.util.experiment.biology.aminoacids.impl.Threonine
- com.compomics.util.experiment.biology.aminoacids.impl.Tryptophan
- com.compomics.util.experiment.biology.aminoacids.impl.Tyrosine
- com.compomics.util.experiment.biology.aminoacids.impl.Valine
- com.compomics.util.experiment.biology.aminoacids.impl.X
- com.compomics.util.experiment.biology.aminoacids.impl.Z
- com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern
- com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence (implements com.compomics.util.experiment.identification.amino_acid_tags.TagComponent)
- com.compomics.util.parameters.identification.tool_specific.AndromedaParameters (implements com.compomics.util.gui.parameters.identification.IdentificationAlgorithmParameter)
- com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters
- com.compomics.util.experiment.biology.atoms.Atom
- com.compomics.util.experiment.biology.atoms.impl.Calcium
- com.compomics.util.experiment.biology.atoms.impl.Carbon
- com.compomics.util.experiment.biology.atoms.impl.Copper
- com.compomics.util.experiment.biology.atoms.impl.Fluorine
- com.compomics.util.experiment.biology.atoms.impl.Helium
- com.compomics.util.experiment.biology.atoms.impl.Hydrogen
- com.compomics.util.experiment.biology.atoms.impl.Iodine
- com.compomics.util.experiment.biology.atoms.impl.Iron
- com.compomics.util.experiment.biology.atoms.impl.Lithium
- com.compomics.util.experiment.biology.atoms.impl.Magnesium
- com.compomics.util.experiment.biology.atoms.impl.Nitrogen
- com.compomics.util.experiment.biology.atoms.impl.Oxygen
- com.compomics.util.experiment.biology.atoms.impl.Phosphorus
- com.compomics.util.experiment.biology.atoms.impl.Potassium
- com.compomics.util.experiment.biology.atoms.impl.Selenium
- com.compomics.util.experiment.biology.atoms.impl.Sodium
- com.compomics.util.experiment.biology.atoms.impl.Sulfur
- com.compomics.util.experiment.biology.atoms.impl.Zinc
- com.compomics.util.experiment.biology.atoms.AtomChain
- com.compomics.util.experiment.biology.atoms.AtomImpl
- com.compomics.util.db.object.objects.BlobObject
- com.compomics.util.general.BoxedObject<K>
- com.compomics.util.experiment.identification.protein_inference.fm_index.CacheElement
- com.compomics.util.parameters.identification.tool_specific.CometParameters (implements com.compomics.util.gui.parameters.identification.IdentificationAlgorithmParameter)
- com.compomics.util.pride.prideobjects.Contact (implements com.compomics.util.pride.PrideObject)
- com.compomics.util.pride.prideobjects.ContactGroup (implements com.compomics.util.pride.PrideObject)
- com.compomics.util.pride.CvTerm
- com.compomics.util.parameters.identification.search.DigestionParameters
- com.compomics.util.parameters.identification.tool_specific.DirecTagParameters (implements com.compomics.util.gui.parameters.identification.IdentificationAlgorithmParameter)
- com.compomics.util.experiment.biology.atoms.ElementaryElement
- com.compomics.util.experiment.biology.enzymes.Enzyme
- com.compomics.util.io.export.ExportScheme
- com.compomics.util.experiment.io.biology.protein.FastaParameters
- com.compomics.util.gui.filtering.FilterParameters
- com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex (implements com.compomics.util.experiment.identification.protein_inference.FastaMapper, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider, com.compomics.util.experiment.io.biology.protein.SequenceProvider)
- com.compomics.util.parameters.identification.advanced.FractionParameters
- com.compomics.util.experiment.biology.genes.GeneMaps
- com.compomics.util.parameters.identification.advanced.GeneParameters
- com.compomics.util.experiment.io.biology.protein.Header (implements java.lang.Cloneable)
- com.compomics.util.experiment.identification.Identification
- com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
- com.compomics.util.experiment.identification.IdentificationKeys
- com.compomics.util.experiment.identification.IdentificationMatch
- com.compomics.util.experiment.identification.matches.PeptideMatch
- com.compomics.util.experiment.identification.matches.ProteinMatch
- com.compomics.util.experiment.identification.matches.SpectrumMatch
- com.compomics.util.experiment.identification.IdentificationMethod
- com.compomics.util.parameters.identification.IdentificationParameters (implements com.compomics.util.experiment.io.parameters.MarshallableParameter)
- com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters
- com.compomics.util.pride.prideobjects.Instrument (implements com.compomics.util.pride.PrideObject)
- com.compomics.util.experiment.biology.ions.Ion
- com.compomics.util.experiment.biology.ions.impl.ElementaryIon
- com.compomics.util.experiment.biology.ions.impl.Glycan
- com.compomics.util.experiment.biology.ions.impl.ImmoniumIon
- com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon
- com.compomics.util.experiment.biology.ions.impl.PrecursorIon
- com.compomics.util.experiment.biology.ions.impl.RelatedIon
- com.compomics.util.experiment.biology.ions.impl.ReporterIon
- com.compomics.util.experiment.biology.ions.impl.TagFragmentIon
- com.compomics.util.experiment.identification.matches.IonMatch
- com.compomics.util.io.json.JsonMarshaller
- com.compomics.util.io.json.marshallers.IdentificationParametersMarshaller
- com.compomics.util.io.json.marshallers.PrideMarshaller
- com.compomics.util.io.json.marshallers.PTMFactoryMarshaller
- com.compomics.util.io.file.LastSelectedFolder
- com.compomics.util.experiment.identification.amino_acid_tags.MassGap (implements com.compomics.util.experiment.identification.amino_acid_tags.TagComponent)
- com.compomics.util.experiment.identification.protein_inference.fm_index.MassIndexMap
- com.compomics.util.experiment.identification.filtering.MatchFilter (implements com.compomics.util.experiment.filtering.Filter)
- com.compomics.util.experiment.identification.filtering.AssumptionFilter
- com.compomics.util.experiment.identification.filtering.PeptideFilter
- com.compomics.util.experiment.identification.filtering.ProteinFilter
- com.compomics.util.experiment.identification.filtering.PsmFilter
- com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent
- com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters (implements com.compomics.util.gui.parameters.identification.IdentificationAlgorithmParameter)
- com.compomics.util.experiment.identification.peptide_shaker.Metrics
- com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex (implements java.io.Serializable)
- com.compomics.util.experiment.biology.modifications.Modification
- com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters
- com.compomics.util.experiment.identification.matches.ModificationMatch
- com.compomics.util.parameters.identification.search.ModificationParameters
- com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
- com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters (implements com.compomics.util.gui.parameters.identification.IdentificationAlgorithmParameter)
- com.compomics.util.parameters.identification.tool_specific.MsgfParameters (implements com.compomics.util.gui.parameters.identification.IdentificationAlgorithmParameter)
- com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters (implements com.compomics.util.gui.parameters.identification.IdentificationAlgorithmParameter)
- com.compomics.util.experiment.io.identification.MzIdentMLIdfileSearchParametersConverter
- com.compomics.util.experiment.biology.ions.NeutralLoss
- com.compomics.util.experiment.identification.spectrum_annotation.NeutralLossesMap
- com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution (implements com.compomics.util.math.statistics.Distribution)
- com.compomics.util.math.statistics.distributions.NormalDistribution (implements com.compomics.util.math.statistics.Distribution)
- com.compomics.util.parameters.identification.tool_specific.NovorParameters (implements com.compomics.util.gui.parameters.identification.IdentificationAlgorithmParameter)
- com.compomics.util.parameters.identification.tool_specific.OmssaParameters (implements com.compomics.util.gui.parameters.identification.IdentificationAlgorithmParameter)
- com.compomics.util.experiment.mass_spectrometry.spectra.Peak
- com.compomics.util.experiment.refinement_parameters.PepnovoAssumptionDetails (implements com.compomics.util.experiment.personalization.UrParameter)
- com.compomics.util.experiment.io.identification.idfilereaders.PepNovoIdfileReader (implements com.compomics.util.experiment.io.identification.IdfileReader)
- com.compomics.util.parameters.identification.tool_specific.PepnovoParameters (implements com.compomics.util.gui.parameters.identification.IdentificationAlgorithmParameter)
- com.compomics.util.experiment.biology.proteins.Peptide
- com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter
- com.compomics.util.experiment.identification.matches.PeptideVariantMatches
- com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
- com.compomics.util.experiment.io.identification.idfilereaders.PNovoIdfileReader (implements com.compomics.util.experiment.io.identification.IdfileReader)
- com.compomics.util.parameters.identification.tool_specific.PNovoParameters (implements com.compomics.util.gui.parameters.identification.IdentificationAlgorithmParameter)
- com.compomics.util.experiment.mass_spectrometry.spectra.Precursor
- com.compomics.util.experiment.ProjectParameters
- com.compomics.util.experiment.biology.proteins.Protein
- com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
- com.compomics.util.pride.prideobjects.Protocol (implements com.compomics.util.pride.PrideObject)
- com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores (implements com.compomics.util.experiment.personalization.UrParameter)
- com.compomics.util.parameters.identification.advanced.PsmScoringParameters
- com.compomics.util.experiment.identification.peptide_shaker.PSParameter (implements com.compomics.util.experiment.personalization.UrParameter)
- com.compomics.util.pride.PtmToPrideMap
- com.compomics.util.experiment.quantification.Quantification
- com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
- com.compomics.util.pride.prideobjects.Reference (implements com.compomics.util.pride.PrideObject)
- com.compomics.util.pride.prideobjects.ReferenceGroup (implements com.compomics.util.pride.PrideObject)
- com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory
- com.compomics.util.pride.prideobjects.Sample (implements com.compomics.util.pride.PrideObject)
- com.compomics.util.parameters.identification.search.SearchParameters (implements com.compomics.util.experiment.io.parameters.MarshallableParameter)
- com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
- com.compomics.util.experiment.identification.protein_inference.fm_index.SNPElement
- com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum
- com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
- com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
- com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption
- com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption
- com.compomics.util.experiment.identification.amino_acid_tags.Tag
- com.compomics.util.experiment.identification.protein_inference.fm_index.TagElement
- com.compomics.util.experiment.io.identification.idfilereaders.TideIdfileReader (implements com.compomics.util.experiment.io.identification.IdfileReader)
- com.compomics.util.parameters.identification.tool_specific.TideParameters (implements com.compomics.util.gui.parameters.identification.IdentificationAlgorithmParameter)
- com.compomics.util.experiment.units.UnitOfMeasurement
- com.compomics.util.parameters.UtilitiesUserParameters
- com.compomics.util.parameters.identification.advanced.ValidationQcParameters
- com.compomics.util.experiment.io.identification.idfilereaders.XTandemIdfileReader (implements com.compomics.util.experiment.io.identification.IdfileReader)
- com.compomics.util.parameters.identification.tool_specific.XtandemParameters (implements com.compomics.util.gui.parameters.identification.IdentificationAlgorithmParameter)
- com.compomics.util.Export
- com.compomics.util.io.export.ExportWriter
- com.compomics.util.io.export.writers.ExcelWriter
- com.compomics.util.io.export.writers.TextWriter
- com.compomics.util.experiment.identification.protein_sequences.digestion.ExtendedPeptide
- com.compomics.util.experiment.io.biology.protein.iterators.FastaIterator (implements com.compomics.util.experiment.io.biology.protein.ProteinIterator)
- com.compomics.cli.fasta.FastaParametersInputBean
- com.compomics.util.experiment.io.biology.protein.FastaSummary
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_generation.FeaturesGenerator
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.FeaturesMap
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.FeaturesMapManager
- com.compomics.util.messages.FeedBack
- com.compomics.util.gui.file_handling.FileAndFileFilter
- com.compomics.util.gui.file_handling.FileChooserUtil
- com.compomics.software.autoupdater.FileDAO
- com.compomics.software.autoupdater.GUIFileDAO
- com.compomics.software.autoupdater.HeadlessFileDAO
- javax.swing.filechooser.FileFilter
- com.compomics.util.io.file.filefilters.DatFileFilter
- com.compomics.util.io.file.filefilters.DtaFileFilter
- com.compomics.util.io.file.filefilters.FastaFileFilter
- com.compomics.util.io.file.FilenameExtensionFilter (implements java.io.FilenameFilter)
- com.compomics.util.io.file.filefilters.JpegFileFilter
- com.compomics.util.io.file.filefilters.MgfFileFilter
- com.compomics.util.io.file.filefilters.Ms2FileFilter
- com.compomics.util.io.file.filefilters.MzDataFileFilter
- com.compomics.util.io.file.filefilters.MzMlFileFilter
- com.compomics.util.io.file.filefilters.MzXmlFileFilter
- com.compomics.util.io.file.filefilters.OmxFileFilter
- com.compomics.util.io.file.filefilters.OutFileFilter
- com.compomics.util.io.file.filefilters.PdfFileFilter
- com.compomics.util.io.file.filefilters.PeffFileFilter
- com.compomics.util.io.file.filefilters.PepXmlFileFilter
- com.compomics.util.io.file.filefilters.PklFileFilter
- com.compomics.util.io.file.filefilters.PklSpoFileFilter
- com.compomics.util.io.file.filefilters.PkxFileFilter
- com.compomics.util.io.file.filefilters.PngFileFilter
- com.compomics.util.io.file.filefilters.ProtXmlFileFilter
- com.compomics.util.io.file.filefilters.SequestParamsFileFilter
- com.compomics.util.io.file.filefilters.SvgFileFilter
- com.compomics.util.io.file.filefilters.TiffFileFilter
- com.compomics.util.io.file.filefilters.XmlFileFilter
- com.compomics.util.io.file.filefilters.FileFilterUtils
- com.compomics.util.general.FileLoggerImplementation (implements com.compomics.util.interfaces.Logger)
- com.compomics.util.io.file.FileSystemAccessor
- com.compomics.util.pdbfinder.FindPdbForUniprotAccessions
- com.compomics.util.io.file.FolderMonitor (implements java.lang.Runnable)
- com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.FragmentAnnotator
- com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.FragmentAnnotatorNL
- com.compomics.util.gui.renderers.FragmentIonTableCellRenderer (implements javax.swing.table.TableCellRenderer)
- com.compomics.util.experiment.identification.peptide_fragmentation.FragmentItensityPredictor
- com.compomics.util.io.ftp.FTP
- com.compomics.util.io.ftp.FTPClient
- com.compomics.util.io.ftp.FTPDownloader
- com.compomics.util.experiment.biology.genes.ensembl.GeneMapping
- com.compomics.util.experiment.io.biology.protein.converters.GenericFastaConverter
- javax.servlet.GenericServlet (implements java.io.Serializable, javax.servlet.Servlet, javax.servlet.ServletConfig)
- javax.servlet.http.HttpServlet (implements java.io.Serializable)
- com.compomics.util.general.servlet.MassCalcServlet
- javax.servlet.http.HttpServlet (implements java.io.Serializable)
- com.compomics.util.db.components.GettersAndSetters
- com.compomics.util.experiment.biology.genes.go.GoDomains
- com.compomics.util.experiment.biology.genes.go.GoMapping
- com.compomics.util.gui.GuiUtilities
- com.compomics.util.io.compression.GzUtils
- com.compomics.util.experiment.io.biology.protein.iterators.HeaderIterator
- com.compomics.util.math.HistogramUtils
- com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore
- com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
- com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory
- com.compomics.cli.identification_parameters.IdentificationParametersInputBean
- com.compomics.util.experiment.io.identification.IdfileReaderFactory
- com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.ImmoniumIonAnnotator
- com.compomics.util.experiment.io.mass_spectrometry.mgf.IndexedMgfReader
- java.io.InputStream (implements java.io.Closeable)
- java.io.FilterInputStream
- com.compomics.util.io.file.MonitorableInputStream (implements com.compomics.util.interfaces.Monitorable)
- com.compomics.util.io.file.MonitorableFileInputStream
- com.compomics.util.io.file.MonitorableInputStream (implements com.compomics.util.interfaces.Monitorable)
- java.io.FilterInputStream
- com.compomics.util.experiment.biology.variants.amino_acids.Insertion (implements com.compomics.util.experiment.biology.variants.Variant)
- com.compomics.util.db.components.InstanceVariables
- com.compomics.util.experiment.io.mass_spectrometry.mzml.IntDecoder
- com.compomics.util.io.json.adapter.InterfaceAdapter<T> (implements com.google.gson.JsonDeserializer<T>, com.google.gson.JsonSerializer<T>)
- com.compomics.util.experiment.biology.ions.IonFactory
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.IonFeature (implements com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.Ms2pipFeature)
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ComplementaryIonFeature
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ForwardIonFeature
- com.compomics.util.experiment.identification.spectrum_annotation.IonMatchKeysCache
- com.compomics.util.io.IoUtil
- com.compomics.util.general.IsotopicDistribution
- com.compomics.util.general.IsotopicDistributionSpectrum (implements com.compomics.util.interfaces.SpectrumFile)
- com.compomics.util.general.IsotopicElement
- com.compomics.util.experiment.identification.protein_sequences.digestion.IteratorFactory
- com.compomics.software.autoupdater.JarFileFilter (implements java.io.FilenameFilter)
- com.compomics.util.gui.JOptionEditorPane
- com.compomics.util.math.clustering.KMeansClustering
- com.compomics.util.math.clustering.settings.KMeansClusteringSettings
- com.compomics.util.math.statistics.linear_regression.LinearRegression
- com.compomics.cli.peptide_mapper.MappingWorker (implements java.lang.Runnable)
- com.compomics.util.io.MascotEnzymeReader
- com.compomics.util.experiment.io.identification.idfilereaders.MascotIdfileReader (implements com.compomics.util.experiment.io.identification.IdfileReader)
- com.compomics.util.general.MassCalc
- com.compomics.util.experiment.identification.matches_iterators.MatchesIterator
- com.compomics.util.experiment.identification.matches_iterators.PeptideMatchesIterator
- com.compomics.util.experiment.identification.matches_iterators.ProteinMatchesIterator
- com.compomics.util.experiment.identification.matches_iterators.SpectrumMatchesIterator
- com.compomics.util.experiment.identification.modification.scores.MDScore
- com.compomics.util.math.statistics.linear_regression.regressions.MedianRegression
- com.compomics.util.memory.MemoryConsumptionStatus
- com.compomics.software.autoupdater.MetaDataXMLParser
- com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfFileIterator (implements com.compomics.util.experiment.io.mass_spectrometry.MsFileIterator)
- com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfFileUtils
- com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfFileWriter (implements java.lang.AutoCloseable)
- com.compomics.util.experiment.biology.modifications.ModificationFactory (implements com.compomics.util.experiment.biology.modifications.ModificationProvider)
- com.compomics.util.protein.ModificationFactory
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ModificationFeature (implements com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.Ms2pipFeature)
- com.compomics.util.protein.ModificationImplementation (implements java.lang.Cloneable, com.compomics.util.interfaces.Modification)
- com.compomics.util.experiment.identification.modification.mapping.ModificationLocalizationMapper
- com.compomics.util.experiment.identification.modification.mapping.ModificationMassMapper
- com.compomics.util.experiment.identification.modification.mapping.ModificationNameMapper
- com.compomics.util.gui.protein.ModificationProfile
- com.compomics.cli.modifications.ModificationsCLI
- com.compomics.cli.modifications.ModificationsCLIInputBean
- com.compomics.util.experiment.identification.modification.ModificationSiteMapping
- com.compomics.util.experiment.identification.modification.ModificationtableContent
- com.compomics.util.protein.ModificationTemplate
- com.compomics.util.experiment.identification.utils.ModificationUtils
- com.compomics.util.protein.MolecularFormula
- com.compomics.util.gui.MonitorDimension
- com.compomics.util.experiment.io.mass_spectrometry.ms2.Ms2Exporter
- com.compomics.util.experiment.io.mass_spectrometry.ms2.Ms2FileWriter
- com.compomics.util.experiment.io.identification.idfilereaders.MsAmandaIdfileReader (implements com.compomics.util.experiment.io.identification.IdfileReader)
- com.compomics.util.experiment.mass_spectrometry.proteowizard.MsConvertParameters
- com.compomics.util.experiment.io.mass_spectrometry.MsFileExporter
- com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler (implements com.compomics.util.experiment.mass_spectrometry.SpectrumProvider)
- com.compomics.scripts_marc.MsFilePerformance
- com.compomics.util.experiment.io.mass_spectrometry.mzml.MSNumpress
- com.compomics.util.experiment.identification.features.MutexMap
- com.compomics.util.experiment.io.identification.idfilereaders.MzIdentMLIdfileReader (implements com.compomics.util.experiment.io.identification.IdfileReader)
- com.compomics.util.experiment.io.mass_spectrometry.mzml.MzmlFileIterator (implements com.compomics.util.experiment.io.mass_spectrometry.MsFileIterator)
- com.compomics.util.experiment.io.mass_spectrometry.mzml.MzmlFileUtils
- com.compomics.util.experiment.biology.ions.NeutralLossCombination
- com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.NoDigestionCombinationIterator (implements com.compomics.util.experiment.identification.protein_sequences.digestion.SequenceIterator)
- com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.NoDigestionIterator (implements com.compomics.util.experiment.identification.protein_sequences.digestion.SequenceIterator)
- com.compomics.util.experiment.normalization.NormalizationFactors
- com.compomics.util.math.statistics.distributions.NormalKernelDensityEstimator
- com.compomics.util.experiment.io.identification.idfilereaders.NovorIdfileReader (implements com.compomics.util.experiment.io.identification.IdfileReader)
- com.compomics.util.nucleotide.NucleotideSequence
- com.compomics.util.nucleotide.NucleotideSequenceImpl (implements com.compomics.util.interfaces.Sequence)
- com.compomics.util.threading.ObjectMutex
- com.compomics.util.db.object.ObjectsCache
- com.compomics.util.db.object.ObjectsCache.ObjectsCacheElement
- com.compomics.util.db.object.ObjectsDB
- com.compomics.util.experiment.io.identification.idfilereaders.OnyaseIdfileReader (implements com.compomics.util.experiment.io.identification.IdfileReader)
- com.compomics.util.experiment.patient.Patient
- com.compomics.util.experiment.patient.PatientInformation
- com.compomics.util.pdbfinder.pdb.PdbBlock
- com.compomics.util.pdbfinder.pdb.PdbParameter
- com.compomics.util.experiment.identification.protein_inference.PeptideAndProteinBuilder
- com.compomics.util.experiment.identification.protein_sequences.digestion.PeptideDraft
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideFeature (implements com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.Ms2pipFeature)
- com.compomics.util.experiment.identification.peptide_inference.PeptideInference
- com.compomics.cli.peptide_mapper.PeptideMapperCLI
- com.compomics.util.experiment.identification.protein_inference.PeptideProteinMapping
- com.compomics.util.experiment.identification.utils.PeptideUtils
- com.compomics.util.experiment.io.identification.idfilereaders.PepxmlIdfileReader (implements com.compomics.util.experiment.io.identification.IdfileReader)
- com.compomics.util.db.components.PersistableCode
- com.compomics.util.experiment.identification.modification.scores.PhosphoRS
- com.compomics.util.io.PklFile
- com.compomics.util.experiment.identification.psm_scoring.psm_scores.PrecursorAccuracy
- com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.PrecursorAnnotator
- com.compomics.util.experiment.mass_spectrometry.indexes.PrecursorMap
- com.compomics.util.experiment.mass_spectrometry.indexes.PrecursorMap.PrecursorWithTitle
- com.compomics.util.pride.prideobjects.webservice.query.PrideFilter
- com.compomics.util.pride.PrideObjectsFactory
- com.compomics.util.pride.PrideWebService
- com.compomics.util.pride.validation.PrideXmlValidator
- com.compomics.util.math.statistics.linear_regression.filters.ProbabilityFilter
- com.compomics.util.parameters.tools.ProcessingParameters
- com.compomics.util.io.PropertiesManager
- com.compomics.util.protein.Protein
- com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider
- com.compomics.util.experiment.identification.protein_sequences.digestion.ProteinIteratorUtils
- com.compomics.util.gui.protein.ProteinSequencePane
- com.compomics.util.experiment.identification.utils.ProteinUtils
- com.compomics.util.experiment.identification.psm_scoring.PsmScoresEstimator
- com.compomics.util.io.PushBackStringReader
- com.compomics.util.experiment.identification.protein_inference.fm_index.Rank (implements java.io.Serializable)
- com.compomics.util.experiment.quantification.reporterion.Reagent
- com.compomics.util.experiment.mass_spectrometry.spectra.RecalibrationUtils
- com.compomics.util.gui.spectrum.ReferenceArea
- com.compomics.util.math.statistics.linear_regression.RegressionStatistics
- com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators.ReporterIonAnnotator
- com.compomics.util.experiment.quantification.reporterion.ReporterMethod
- com.compomics.util.gui.events.RescalingEvent
- com.compomics.util.db.components.RetrievableCode
- javax.swing.RowFilter<M,I>
- com.compomics.util.gui.XYPlottingDialog.SelectedValuesTableFilter
- com.compomics.util.experiment.quantification.spectrumcounting.ScalingFactorsEstimators
- com.compomics.util.experiment.identification.peptide_fragmentation.models.SequestFragmentationModel
- com.compomics.util.io.file.SerializationUtils
- com.compomics.util.io.flat.SimpleFileWriter (implements java.lang.AutoCloseable)
- com.compomics.util.io.flat.readers.SimpleGzReader (implements com.compomics.util.io.flat.SimpleFileReader)
- com.compomics.util.math.statistics.linear_regression.regressions.SimpleLinearRegression
- com.compomics.util.experiment.io.identification.writers.SimpleMzIdentMLExporter (implements java.io.Closeable)
- com.compomics.util.experiment.mass_spectrometry.SimpleNoiseDistribution
- com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.SimplePeptideAnnotator
- com.compomics.util.threading.SimpleSemaphore
- com.compomics.util.io.flat.readers.SimpleTextReader (implements com.compomics.util.io.flat.SimpleFileReader)
- com.compomics.util.io.export.xml.SimpleXmlWriter (implements java.lang.AutoCloseable)
- com.compomics.util.experiment.identification.protein_sequences.SingleProteinSequenceProvider (implements com.compomics.util.experiment.io.biology.protein.SequenceProvider)
- com.compomics.util.experiment.identification.psm_scoring.psm_scores.SnrScore
- com.compomics.util.experiment.biology.taxonomy.SpeciesFactory
- com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters
- com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.SpecificSingleEnzymeCombinationIterator (implements com.compomics.util.experiment.identification.protein_sequences.digestion.SequenceIterator)
- com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.SpecificSingleEnzymeIterator (implements com.compomics.util.experiment.identification.protein_sequences.digestion.SequenceIterator)
- com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator
- com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator
- com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.TagSpectrumAnnotator
- com.compomics.util.experiment.mass_spectrometry.indexes.SpectrumIndex
- com.compomics.util.experiment.mass_spectrometry.spectra.SpectrumUtil
- com.compomics.software.SplashScreen
- com.compomics.util.io.StartBrowser
- com.compomics.util.pdbfinder.das.readers.StartEndPosition
- com.compomics.util.io.StreamGobbler (implements java.lang.Runnable)
- com.compomics.util.StreamUtil
- com.compomics.util.experiment.biology.variants.amino_acids.Substitution (implements com.compomics.util.experiment.biology.variants.Variant)
- com.compomics.util.experiment.biology.variants.amino_acids.Swap (implements com.compomics.util.experiment.biology.variants.Variant)
- com.compomics.util.gui.utils.SwingUtils
- com.compomics.util.sun.SwingWorker
- com.compomics.util.gui.TableMouseWheelListener (implements java.awt.event.MouseWheelListener)
- com.compomics.util.gui.TableProperties
- com.compomics.util.gui.TableScrollBarListener (implements java.awt.event.AdjustmentListener)
- com.compomics.util.experiment.identification.TagFactory
- com.compomics.util.experiment.identification.utils.TagUtils
- com.compomics.util.io.compression.TarUtils
- com.compomics.util.experiment.io.mass_spectrometry.cms.TempByteArray
- com.compomics.util.experiment.io.temp.TempFilesManager
- com.compomics.util.junit.TestCaseLM
- com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.ThermoRawFileParserParameters
- java.lang.Throwable (implements java.io.Serializable)
- java.lang.Exception
- com.compomics.util.db.GeneratorException
- java.io.IOException
- com.compomics.util.io.ftp.FtpProtocolException
- com.compomics.util.io.ftp.FtpConnectionException
- com.compomics.util.io.ftp.FtpLoginException
- com.compomics.util.io.ftp.FtpProtocolException
- com.compomics.util.general.UnknownElementMassException
- java.lang.Exception
- com.compomics.software.ToolFactory
- com.compomics.util.general.Translate
- com.google.gson.TypeAdapter<T>
- com.compomics.util.io.json.adapter.ColorAdapter
- com.compomics.util.io.json.adapter.FileAdapter
- com.compomics.util.experiment.identification.peptide_fragmentation.models.UniformFragmentation
- com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy
- com.compomics.util.experiment.units.Units
- com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.UnspecificCombinationIterator (implements com.compomics.util.experiment.identification.protein_sequences.digestion.SequenceIterator)
- com.compomics.util.experiment.identification.protein_sequences.digestion.iterators.UnspecificIterator (implements com.compomics.util.experiment.identification.protein_sequences.digestion.SequenceIterator)
- com.compomics.util.db.components.UpdateableCode
- com.compomics.util.Util
- com.compomics.util.gui.UtilitiesGUIDefaults
- com.compomics.software.settings.UtilitiesPathParameters
- com.compomics.util.math.VennDiagram
- com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl (implements com.compomics.util.waiting.WaitingHandler)
- com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerDummy (implements com.compomics.util.waiting.WaitingHandler)
- com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree (implements java.io.Serializable)
- com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree.HuffmanNode (implements java.lang.Comparable<T>)
- com.compomics.software.autoupdater.WebDAO
- com.compomics.util.io.compression.SectionGzWriter.WriterBySection (implements java.lang.AutoCloseable)
- com.compomics.util.pride.validation.XMLValidationErrorHandler (implements org.xml.sax.ErrorHandler)
- com.compomics.util.XYZDataPoint
- java.util.zip.ZipFile (implements java.io.Closeable)
- java.util.jar.JarFile
- com.compomics.software.autoupdater.MavenJarFile
- java.util.jar.JarFile
- com.compomics.util.io.compression.ZipUtils
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AAIdentityFeature (implements com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.Ms2pipFeature)
Interface Hierarchy
- com.compomics.util.gui.parameters.identification.AlgorithmParametersDialog
- java.lang.AutoCloseable
- com.compomics.util.experiment.io.identification.IdfileReader
- com.compomics.util.experiment.io.mass_spectrometry.MsFileIterator
- com.compomics.util.io.flat.SimpleFileReader
- com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
- java.lang.Comparable<T>
- com.compomics.util.interfaces.Modification
- com.compomics.util.interfaces.SpectrumFile
- com.compomics.util.interfaces.Connectable
- com.compomics.util.db.interfaces.DBElement
- com.compomics.util.db.interfaces.Deleteable
- com.compomics.util.math.statistics.Distribution
- com.compomics.util.io.export.ExportFactory
- com.compomics.util.io.export.ExportFeature
- com.compomics.util.experiment.identification.protein_inference.FastaMapper
- com.compomics.util.experiment.filtering.Filter
- com.compomics.util.experiment.filtering.FilterItem
- com.compomics.util.interfaces.Flamable
- com.compomics.util.gui.parameters.identification.IdentificationAlgorithmParameter
- com.compomics.software.dialogs.JavaHomeOrMemoryDialogParent
- com.compomics.util.interfaces.Logger
- com.compomics.util.experiment.io.parameters.MarshallableParameter
- com.compomics.util.experiment.biology.modifications.ModificationProvider
- com.compomics.util.interfaces.Monitorable
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.Ms2pipFeature
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.MultipleAAPropertyFeature
- com.compomics.util.gui.error_handlers.notification.NotificationDialogParent
- com.compomics.software.settings.PathKey
- com.compomics.util.db.interfaces.Persistable
- com.compomics.util.interfaces.PickUp
- com.compomics.util.pride.PrideObject
- com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider
- com.compomics.util.experiment.io.biology.protein.ProteinIterator
- com.compomics.util.db.interfaces.Retrievable
- com.compomics.util.math.statistics.ROC
- com.compomics.util.interfaces.Sequence
- com.compomics.util.experiment.identification.protein_sequences.digestion.SequenceIterator
- com.compomics.util.experiment.io.biology.protein.SequenceProvider
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.SingleAAPropertyFeature
- com.compomics.util.gui.interfaces.SpectrumAnnotation
- com.compomics.util.gui.interfaces.SpectrumPanelListener
- com.compomics.util.interfaces.TableValueWrapper
- com.compomics.util.experiment.identification.amino_acid_tags.TagComponent
- com.compomics.util.db.interfaces.Updateable
- com.compomics.util.experiment.personalization.UrParameter
- com.compomics.util.experiment.biology.variants.Variant
- com.compomics.util.gui.VisibleTableColumnsDialogParent
- com.compomics.util.waiting.WaitingActionListener
- com.compomics.util.waiting.WaitingHandler
- com.compomics.util.io.export.WorkbookStyle
Enum Hierarchy
- java.lang.Object
- java.lang.Enum<E> (implements java.lang.Comparable<T>, java.lang.constant.Constable, java.io.Serializable)
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.AAPropertyRelationshipFeature.Relationship
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.AASequenceFeature.Function
- com.compomics.util.experiment.identification.Advocate.AdvocateType
- com.compomics.util.experiment.biology.aminoacids.AminoAcid.Property
- com.compomics.util.parameters.identification.tool_specific.AndromedaParameters.AndromedaDecoyMode
- com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters.IntensityThresholdType
- com.compomics.util.experiment.identification.filtering.items.AssumptionFilterItem (implements com.compomics.util.experiment.filtering.FilterItem)
- com.compomics.util.parameters.identification.tool_specific.CometParameters.CometOutputFormat
- com.compomics.util.enumeration.CompomicsTools
- com.compomics.util.math.roc.DataRoc.RocInterpolation
- com.compomics.util.parameters.identification.search.DigestionParameters.CleavageParameter
- com.compomics.util.parameters.identification.search.DigestionParameters.Specificity
- com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblGenomesSpecies.EnsemblGenomeDivision
- com.compomics.cli.enzymes.EnzymesCLIParams
- com.compomics.util.io.export.ExportFormat
- com.compomics.cli.fasta.FastaParametersCLIParams
- com.compomics.util.messages.FeedBack.FeedBackType
- com.compomics.util.pride.prideobjects.webservice.file.FileType
- com.compomics.util.experiment.filtering.FilterItemComparator
- com.compomics.util.experiment.mass_spectrometry.FragmentationMethod
- com.compomics.util.gui.spectrum.GraphicsPanel.DrawingStyle
- com.compomics.util.gui.spectrum.GraphicsPanel.GraphicsPanelType
- com.compomics.util.experiment.identification.features.IdentificationFeaturesCache.ObjectType
- com.compomics.util.experiment.identification.IdentificationMatch.MatchType
- com.compomics.cli.identification_parameters.IdentificationParametersCLIParams
- com.compomics.util.enumeration.ImageType
- com.compomics.util.experiment.biology.ions.Ion.IonType
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic.IonFeature.Property
- com.compomics.util.experiment.identification.matches.IonMatch.MzErrorType
- com.compomics.util.experiment.io.parameters.MarshallableParameter.Type
- com.compomics.util.experiment.identification.filtering.MatchFilter.FilterType
- com.compomics.util.experiment.identification.validation.MatchValidationLevel
- com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters.MetaMorpheusDecoyType
- com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters.MetaMorpheusDissociationType
- com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters.MetaMorpheusFragmentationTerminusType
- com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters.MetaMorpheusInitiatorMethionineBehaviorType
- com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters.MetaMorpheusMassDiffAcceptorType
- com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters.MetaMorpheusSearchType
- com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters.MetaMorpheusToleranceType
- com.compomics.util.experiment.units.MetricsPrefix
- com.compomics.util.experiment.biology.modifications.ModificationCategory
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.ModificationFeature.Property
- com.compomics.util.experiment.identification.modification.ModificationLocalizationScore
- com.compomics.cli.modifications.ModificationsCLIParams
- com.compomics.util.experiment.biology.modifications.ModificationType
- com.compomics.util.enumeration.MolecularElement
- com.compomics.util.experiment.io.mass_spectrometry.MsFileExporter.Format
- com.compomics.util.experiment.io.identification.idfilereaders.MzIdentMLIdfileReader.RawValueConversionType
- com.compomics.util.experiment.io.identification.MzIdentMLVersion
- com.compomics.util.experiment.io.mass_spectrometry.mzml.MzmlFileIterator.Precision
- com.compomics.util.enumeration.OperatingSystemEnum
- com.compomics.util.parameters.searchgui.OutputParameters
- com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.PeptideFeature.Property
- com.compomics.util.experiment.identification.filtering.items.PeptideFilterItem (implements com.compomics.util.experiment.filtering.FilterItem)
- com.compomics.util.experiment.identification.peptide_fragmentation.PeptideFragmentationModel
- com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters.VariantType
- com.compomics.util.pride.prideobjects.webservice.query.PrideFilterType
- com.compomics.util.pride.prideobjects.webservice.PrideQuery
- com.compomics.util.parameters.tools.ProcessingParameters.ProcessingType
- com.compomics.util.parameters.peptide_shaker.ProjectType
- com.compomics.util.experiment.io.biology.protein.ProteinDatabase
- com.compomics.util.experiment.identification.filtering.items.ProteinFilterItem (implements com.compomics.util.experiment.filtering.FilterItem)
- com.compomics.util.experiment.mass_spectrometry.proteowizard.ProteoWizardFilter
- com.compomics.util.experiment.mass_spectrometry.proteowizard.ProteoWizardMsFormat
- com.compomics.util.experiment.identification.filtering.items.PsmFilterItem (implements com.compomics.util.experiment.filtering.FilterItem)
- com.compomics.util.experiment.identification.psm_scoring.PsmScore
- com.compomics.util.experiment.quantification.Quantification.QuantificationMethod
- com.compomics.util.parameters.identification.search.SearchParameters.MassAccuracyType
- com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters.MatchingType
- com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.SimplePeptideAnnotator.IonSeries
- com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator.TiesResolution
- com.compomics.util.experiment.quantification.spectrumcounting.SpectrumCountingMethod
- com.compomics.util.experiment.mass_spectrometry.utils.StandardMasses
- com.compomics.util.experiment.units.StandardUnit
- com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.ThermoRawFileParserOutputFormat
- com.compomics.software.settings.UtilitiesPathParameters.UtilitiesPathKey (implements com.compomics.software.settings.PathKey)
- com.compomics.util.gui.VennDiagramPanel.VennDiagramType
- com.compomics.util.gui.XYPlottingDialog.PlottingDialogPlotType
- java.lang.Enum<E> (implements java.lang.Comparable<T>, java.lang.constant.Constable, java.io.Serializable)