Serialized Form

  • Package com.compomics.software.dialogs

    • Class com.compomics.software.dialogs.JavaHomeDialog extends JDialog implements Serializable

      • Serialized Fields

        • backgroundPanel
          JPanel backgroundPanel
        • browseButton
          JButton browseButton
        • cancelButton
          JButton cancelButton
        • javaHomeHelpJButton
          JButton javaHomeHelpJButton
        • javaHomeLabel
          JLabel javaHomeLabel
        • javaHomeOrMemoryDialogParent
          JavaHomeOrMemoryDialogParent javaHomeOrMemoryDialogParent
          Reference to the JavaHomeOrMemoryDialogParent.
        • javaHomeTxt
          JTextField javaHomeTxt
        • jSeparator1
          JSeparator jSeparator1
        • okButton
          JButton okButton
        • toolName
          String toolName
          The name of the tool, e.g., PeptideShaker.
        • welcomeDialog
          JDialog welcomeDialog
          A reference to the Welcome Dialog.
    • Class com.compomics.software.dialogs.JavaMemoryDialog extends JDialog implements Serializable

      • Serialized Fields

        • backgroundPanel
          JPanel backgroundPanel
        • cancelButton
          JButton cancelButton
        • javaHomeOrMemoryDialogParent
          JavaHomeOrMemoryDialogParent javaHomeOrMemoryDialogParent
          Reference to the JavaHomeOrMemoryDialogParent.
        • javaOptionsHelpJButton
          JButton javaOptionsHelpJButton
        • jSeparator1
          JSeparator jSeparator1
        • mbLabel
          JLabel mbLabel
        • memoryLimitLabel
          JLabel memoryLimitLabel
        • memoryTxt
          JTextField memoryTxt
        • okButton
          JButton okButton
        • toolName
          String toolName
          The name of the tool, e.g., PeptideShaker.
        • welcomeDialog
          JDialog welcomeDialog
          A reference to the Welcome Dialog.
    • Class com.compomics.software.dialogs.JavaParametersDialog extends JDialog implements Serializable

      • Serialized Fields

        • backgroundsPanel
          JPanel backgroundsPanel
        • bitLabel
          JLabel bitLabel
        • bitPanel
          JPanel bitPanel
        • bitRecommendationLabel
          JLabel bitRecommendationLabel
        • frameParent
          JFrame frameParent
          The frame parent.
        • javaHelpJLabel
          JLabel javaHelpJLabel
        • javaHomeLabel
          JLabel javaHomeLabel
        • javaHomeOrMemoryDialogParent
          JavaHomeOrMemoryDialogParent javaHomeOrMemoryDialogParent
          Reference to the JavaHomeOrMemoryDialogParent.
        • javaHomePanel
          JPanel javaHomePanel
        • memoryLabel
          JLabel memoryLabel
        • memoryPanel
          JPanel memoryPanel
        • memoryRecommendationLabel
          JLabel memoryRecommendationLabel
        • okButton
          JButton okButton
        • toolName
          String toolName
          The name of the tool, e.g., PeptideShaker.
        • versionLabel
          JLabel versionLabel
        • versionPanel
          JPanel versionPanel
        • versionRecommendationLabel1
          JLabel versionRecommendationLabel1
        • versionRecommendationLabel2
          JLabel versionRecommendationLabel2
        • welcomeDialog
          JDialog welcomeDialog
          A reference to the Welcome Dialog.
    • Class com.compomics.software.dialogs.PeptideShakerSetupDialog extends JDialog implements Serializable

      • Serialized Fields

        • backgroundPanel
          JPanel backgroundPanel
        • browseButton
          JButton browseButton
        • cancelButton
          JButton cancelButton
        • dialogCanceled
          boolean dialogCanceled
          Set to true if the dialog was canceled.
        • jLabel2
          JLabel jLabel2
        • lastSelectedFolder
          String lastSelectedFolder
          The selected folder.
        • okButton
          JButton okButton
        • parentDialog
          JDialog parentDialog
          The parent dialog. Can be null.
        • parentFrame
          JFrame parentFrame
          The parent frame. Can be null.
        • peptideShakerButton
          JButton peptideShakerButton
        • peptideShakerDownloadLinkLabel
          JLabel peptideShakerDownloadLinkLabel
        • peptideShakerDownloadPanel
          JPanel peptideShakerDownloadPanel
        • peptideShakerInfoLabel
          JLabel peptideShakerInfoLabel
        • peptideShakerInstallationPanel
          JPanel peptideShakerInstallationPanel
        • peptideShakerJarFileHelpLabel
          JLabel peptideShakerJarFileHelpLabel
        • peptideShakernstallationJTextField
          JTextField peptideShakernstallationJTextField
        • progressDialog
          ProgressDialogX progressDialog
          The progress dialog.
        • utilitiesUserParameters
          UtilitiesUserParameters utilitiesUserParameters
          The utilities preferences.
    • Class com.compomics.software.dialogs.ProteoWizardSetupDialog extends JDialog implements Serializable

      • Serialized Fields

        • backgroundPanel
          JPanel backgroundPanel
        • browseButton
          JButton browseButton
        • cancelButton
          JButton cancelButton
        • dialogCanceled
          boolean dialogCanceled
          Set to true if the dialog was canceled.
        • downloadLinkLabel
          JLabel downloadLinkLabel
        • downloadPanel
          JPanel downloadPanel
        • folderHelpLabel
          JLabel folderHelpLabel
        • iconButton
          JButton iconButton
        • infoLabel
          JLabel infoLabel
        • installationJTextField
          JTextField installationJTextField
        • installationPanel
          JPanel installationPanel
        • jLabel2
          JLabel jLabel2
        • lastSelectedFolder
          String lastSelectedFolder
          The selected folder.
        • okButton
          JButton okButton
        • utilitiesUserParameters
          UtilitiesUserParameters utilitiesUserParameters
          The utilities preferences.
    • Class com.compomics.software.dialogs.ReporterSetupDialog extends JDialog implements Serializable

      • Serialized Fields

        • backgroundPanel
          JPanel backgroundPanel
        • browseButton
          JButton browseButton
        • cancelButton
          JButton cancelButton
        • dialogCanceled
          boolean dialogCanceled
          Set to true if the dialog was canceled.
        • jLabel2
          JLabel jLabel2
        • lastSelectedFolder
          String lastSelectedFolder
          The selected folder.
        • okButton
          JButton okButton
        • reporterButton
          JButton reporterButton
        • reporterDownloadLinkLabel
          JLabel reporterDownloadLinkLabel
        • reporterDownloadPanel
          JPanel reporterDownloadPanel
        • reporterInfoLabel
          JLabel reporterInfoLabel
        • reporterInstallationJTextField
          JTextField reporterInstallationJTextField
        • reporterInstallationPanel
          JPanel reporterInstallationPanel
        • reporterJarFileHelpLabel
          JLabel reporterJarFileHelpLabel
        • utilitiesUserParameters
          UtilitiesUserParameters utilitiesUserParameters
          The utilities preferences.
    • Class com.compomics.software.dialogs.SearchGuiSetupDialog extends JDialog implements Serializable

      • Serialized Fields

        • backgroundPanel
          JPanel backgroundPanel
        • browseButton
          JButton browseButton
        • cancelButton
          JButton cancelButton
        • dialogCanceled
          boolean dialogCanceled
          Set to true if the dialog was canceled.
        • jLabel2
          JLabel jLabel2
        • lastSelectedFolder
          String lastSelectedFolder
          The selected folder.
        • okButton
          JButton okButton
        • parentDialog
          JDialog parentDialog
          The parent dialog. Can be null.
        • parentFrame
          JFrame parentFrame
          The parent frame. Can be null.
        • progressDialog
          ProgressDialogX progressDialog
          The progress dialog.
        • searchGuiButton
          JButton searchGuiButton
        • searchGuiDownloadLinkLabel
          JLabel searchGuiDownloadLinkLabel
        • searchGuiDownloadPanel
          JPanel searchGuiDownloadPanel
        • searchGuiInfoLabel
          JLabel searchGuiInfoLabel
        • searchGuiInstallationJTextField
          JTextField searchGuiInstallationJTextField
        • searchGuiInstallationPanel
          JPanel searchGuiInstallationPanel
        • searchGuiJarFileHelpLabel
          JLabel searchGuiJarFileHelpLabel
        • utilitiesUserParameters
          UtilitiesUserParameters utilitiesUserParameters
          The utilities preferences.
  • Package com.compomics.software.settings.gui

  • Package com.compomics.util

    • Class com.compomics.util.AlternateRowColoursJTable extends JTable implements Serializable

      • Serialized Fields

        • iEvenRowColor
          Color iEvenRowColor
          The background colour for the even rows. A value of 'null' means use the default background colour for JTable.
        • iUnevenRowColor
          Color iUnevenRowColor
          The background colour for the uneven rows. A value of 'null' (default here) means use the default background colour for JTable.
        • logger
          org.apache.log4j.Logger logger
  • Package com.compomics.util.db

  • Package com.compomics.util.db.object.objects

  • Package com.compomics.util.examples

    • Class com.compomics.util.examples.HelpWindow extends JFrame implements Serializable

      • Serialized Fields

    • Class com.compomics.util.examples.MirroredSpectraTestDialog extends JDialog implements Serializable

      • Serialized Fields

        • backgroundPanel
          JPanel backgroundPanel
    • Class com.compomics.util.examples.UtilitiesDemo extends JFrame implements Serializable

      • Serialized Fields

        • aIonsJCheckBox
          JCheckBox aIonsJCheckBox
        • allAnnotations
          HashMap<Integer,​Vector<SpectrumAnnotation>> allAnnotations
          A hashmap of all spectrum panel annotations.
        • allPeaksJCheckBox
          JCheckBox allPeaksJCheckBox
        • backgroundPanel
          JPanel backgroundPanel
        • bIonsJCheckBox
          JCheckBox bIonsJCheckBox
        • browseJButton
          JButton browseJButton
        • chargeOneJCheckBox
          JCheckBox chargeOneJCheckBox
        • chargeOverTwoJCheckBox
          JCheckBox chargeOverTwoJCheckBox
        • chargePeptideAJSpinner
          JSpinner chargePeptideAJSpinner
        • chargePeptideBJSpinner
          JSpinner chargePeptideBJSpinner
        • chargeTwoJCheckBox
          JCheckBox chargeTwoJCheckBox
        • chromatogramAJPanel
          JPanel chromatogramAJPanel
        • chromatogramJPanel
          JPanel chromatogramJPanel
        • chromatogramPanelHelpJLabel
          JLabel chromatogramPanelHelpJLabel
        • chromatogramPanelInfoJLabel
          JLabel chromatogramPanelInfoJLabel
        • chromatogramPanelMaxPadding
          int chromatogramPanelMaxPadding
          The maximum padding allowed in the chromatogram panels. Increase if font size on the y-axis becomes too small.
        • cIonsJCheckBox
          JCheckBox cIonsJCheckBox
        • cleanProteinSequence
          String cleanProteinSequence
          Used for the in silico digestion example.
        • currentPeffBufferedReader
          BufferedReader currentPeffBufferedReader
          The current PEFF (or FASTA) buffered reader.
        • currentSequence
          String currentSequence
          The current PEFF (or FASTA) sequence.
        • currentSequenceFile
          File currentSequenceFile
          The current PEFF (or FASTA) sequence file.
        • currentSequenceLine
          String currentSequenceLine
          The current PEFF (or FASTA) sequence line.
        • enzymesJComboBox
          JComboBox enzymesJComboBox
        • exportJButton
          JButton exportJButton
        • H2OIonsJCheckBox
          JCheckBox H2OIonsJCheckBox
        • informationJEditorPane
          JEditorPane informationJEditorPane
        • informationJPanel
          JPanel informationJPanel
        • informationJScrollPane
          JScrollPane informationJScrollPane
        • inhibitorsJTextField
          JTextField inhibitorsJTextField
        • inSilicoDigestionHelpJLabel
          JLabel inSilicoDigestionHelpJLabel
        • ionSelectionJPanel
          JPanel ionSelectionJPanel
        • isotopicDistributionAJPanel
          JPanel isotopicDistributionAJPanel
        • isotopicDistributionCalculatorHelpJLabel
          JLabel isotopicDistributionCalculatorHelpJLabel
        • isotopicDistributionCalculatorInfoJLabel
          JLabel isotopicDistributionCalculatorInfoJLabel
        • isotopicDistributionJPanel
          JPanel isotopicDistributionJPanel
        • jLabel1
          JLabel jLabel1
        • jLabel10
          JLabel jLabel10
        • jLabel11
          JLabel jLabel11
        • jLabel12
          JLabel jLabel12
        • jLabel13
          JLabel jLabel13
        • jLabel14
          JLabel jLabel14
        • jLabel15
          JLabel jLabel15
        • jLabel16
          JLabel jLabel16
        • jLabel17
          JLabel jLabel17
        • jLabel18
          JLabel jLabel18
        • jLabel19
          JLabel jLabel19
        • jLabel2
          JLabel jLabel2
        • jLabel20
          JLabel jLabel20
        • jLabel21
          JLabel jLabel21
        • jLabel24
          JLabel jLabel24
        • jLabel3
          JLabel jLabel3
        • jLabel4
          JLabel jLabel4
        • jLabel5
          JLabel jLabel5
        • jLabel6
          JLabel jLabel6
        • jLabel7
          JLabel jLabel7
        • jLabel8
          JLabel jLabel8
        • jLabel9
          JLabel jLabel9
        • jPanel1
          JPanel jPanel1
        • jPanel10
          JPanel jPanel10
        • jPanel11
          JPanel jPanel11
        • jPanel12
          JPanel jPanel12
        • jPanel2
          JPanel jPanel2
        • jPanel3
          JPanel jPanel3
        • jPanel4
          JPanel jPanel4
        • jPanel5
          JPanel jPanel5
        • jPanel6
          JPanel jPanel6
        • jPanel7
          JPanel jPanel7
        • jPanel8
          JPanel jPanel8
        • jRadioButton1
          JRadioButton jRadioButton1
        • jSeparator1
          JSeparator jSeparator1
        • jSeparator2
          JSeparator jSeparator2
        • jSeparator3
          JSeparator jSeparator3
        • jSeparator4
          JSeparator jSeparator4
        • jSeparator5
          JSeparator jSeparator5
        • jSeparator6
          JSeparator jSeparator6
        • jSeparator9
          JSeparator jSeparator9
        • jTabbedPane
          JTabbedPane jTabbedPane
        • keyValuePairs
          TreeMap<String,​String> keyValuePairs
          The map of the PEFF key value pairs.
        • linkedSpectraJCheckBox
          JCheckBox linkedSpectraJCheckBox
        • linkedSpectrumPanels
          HashMap<Integer,​SpectrumPanel> linkedSpectrumPanels
          A hashmap of both the linked spectra.
        • lowerMassJSpinner
          JSpinner lowerMassJSpinner
        • mascotEnzymeReader
          MascotEnzymeReader mascotEnzymeReader
          Used to read the enzyme details from file.
        • missedCleavagesJSpinner
          JSpinner missedCleavagesJSpinner
        • nextJButton
          JButton nextJButton
        • NH3IonsJCheckBox
          JCheckBox NH3IonsJCheckBox
        • otherIonsJCheckBox
          JCheckBox otherIonsJCheckBox
        • peffAnnotationPanel
          JPanel peffAnnotationPanel
        • peffAnnotationsColorMap
          HashMap<Integer,​Color> peffAnnotationsColorMap
          The PEFF annotations color map.
        • peffAnnotationsJTable
          JTable peffAnnotationsJTable
        • peffAnnotationsScrollPane
          JScrollPane peffAnnotationsScrollPane
        • peffAnnotationsTooltipMap
          HashMap<Integer,​String> peffAnnotationsTooltipMap
          The PEFF annotations tooltip map.
        • peffFormat
          boolean peffFormat
          If true, the format shown is PEFF, if false FASTA is assumed.
        • peffHeaderJTable
          JTable peffHeaderJTable
        • peffHeaderScrollPane
          JScrollPane peffHeaderScrollPane
        • peptideAColorJPanel
          JPanel peptideAColorJPanel
        • peptideACompositionJTextField
          JTextField peptideACompositionJTextField
        • peptideAJScrollPane
          JScrollPane peptideAJScrollPane
        • peptideAJTable
          JTable peptideAJTable
        • peptideAMzJTextField
          JTextField peptideAMzJTextField
        • peptideBColorJPanel
          JPanel peptideBColorJPanel
        • peptideBCompositionJTextField
          JTextField peptideBCompositionJTextField
        • peptideBJScrollPane
          JScrollPane peptideBJScrollPane
        • peptideBJTable
          JTable peptideBJTable
        • peptideBMzJTextField
          JTextField peptideBMzJTextField
        • peptideSequenceAJTextField
          JTextField peptideSequenceAJTextField
        • peptideSequenceBJTextField
          JTextField peptideSequenceBJTextField
        • peptidesJPanel
          JPanel peptidesJPanel
        • peptidesJTable
          JTable peptidesJTable
        • peptidesScrollPane
          JScrollPane peptidesScrollPane
        • positionJTextField
          JTextField positionJTextField
        • profileSpectrumJCheckBox
          JCheckBox profileSpectrumJCheckBox
        • proteinCoverageJScrollPane
          JScrollPane proteinCoverageJScrollPane
        • proteinDetailsScrollPane
          JScrollPane proteinDetailsScrollPane
        • proteinDigestionJLabel
          JLabel proteinDigestionJLabel
        • proteinDigestionJPanel
          JPanel proteinDigestionJPanel
        • proteinHeaderJTable
          JTable proteinHeaderJTable
        • proteinSequenceCoverageJEditorPane
          JEditorPane proteinSequenceCoverageJEditorPane
        • selectedAnnotationTypes
          HashMap<String,​Color> selectedAnnotationTypes
          The tag colors for PEFF formatting.
        • sequenceAnnotationColumnHeaderTooltips
          ArrayList<String> sequenceAnnotationColumnHeaderTooltips
          Sequence annotation column header tooltips.
        • sequenceCoverageJPanel
          JPanel sequenceCoverageJPanel
        • sequenceFileJTextField
          JTextField sequenceFileJTextField
        • sequenceJTabbedPane
          JTabbedPane sequenceJTabbedPane
        • silacLabelPeptideAJComboBox
          JComboBox silacLabelPeptideAJComboBox
        • silacLabelPeptideBJComboBox
          JComboBox silacLabelPeptideBJComboBox
        • siteJTextField
          JTextField siteJTextField
        • sparklineColor
          Color sparklineColor
          The color used for the sparkline bar chart plots.
        • spectraJPanel
          JPanel spectraJPanel
        • spectrumAJPanel
          JPanel spectrumAJPanel
        • spectrumAPanel
          SpectrumPanel spectrumAPanel
          The first spectrum panel.
        • spectrumBJPanel
          JPanel spectrumBJPanel
        • spectrumBPanel
          SpectrumPanel spectrumBPanel
          The second spectrum panel
        • spectrumJPanel
          JPanel spectrumJPanel
        • spectrumPanelHelpJLabel
          JLabel spectrumPanelHelpJLabel
        • spectrumPanelInfoJLabel
          JLabel spectrumPanelInfoJLabel
        • spectrumPanelMaxPadding
          int spectrumPanelMaxPadding
          The maximum padding allowed in the spectrum panels. Increase if font size on the y-axis becomes too small.
        • upperMassJSpinner
          JSpinner upperMassJSpinner
        • xIonsJCheckBox
          JCheckBox xIonsJCheckBox
        • yIonsJCheckBox
          JCheckBox yIonsJCheckBox
        • zIonsJCheckBox
          JCheckBox zIonsJCheckBox
  • Package com.compomics.util.experiment

  • Package com.compomics.util.experiment.biology.aminoacids

    • Class com.compomics.util.experiment.biology.aminoacids.AminoAcid extends ExperimentObject implements Serializable

      • Serialized Fields

        • aminoAcidCombinations
          char[] aminoAcidCombinations
          The amino acid combinations.
        • monoisotopicAtomChain
          AtomChain monoisotopicAtomChain
          The monoisotopic atom chain.
        • name
          String name
          Name of the amino acid.
        • singleLetterCode
          String singleLetterCode
          Single letter code of the amino acid.
        • standardGeneticCode
          String[] standardGeneticCode
          The standard genetic code.
        • subAminoAcidsWithCombination
          char[] subAminoAcidsWithCombination
          The sub amino acids with combination.
        • subAminoAcidsWithoutCombination
          char[] subAminoAcidsWithoutCombination
          The sub amino acids without combination.
        • threeLetterCode
          String threeLetterCode
          Three letter code of the amino acid.
  • Package com.compomics.util.experiment.biology.aminoacids.impl

  • Package com.compomics.util.experiment.biology.aminoacids.sequence

  • Package com.compomics.util.experiment.biology.atoms

  • Package com.compomics.util.experiment.biology.atoms.impl

  • Package com.compomics.util.experiment.biology.enzymes

  • Package com.compomics.util.experiment.biology.genes

  • Package com.compomics.util.experiment.biology.ions

    • Class com.compomics.util.experiment.biology.ions.Ion extends ExperimentObject implements Serializable

      serialVersionUID:
      -1505719074403886934L
      • Serialized Fields

        • atomChain
          AtomChain atomChain
          The atomic composition of the ion.
        • neutralLossesAsString
          String neutralLossesAsString
          Cache for the neutral losses as string.
        • theoreticMass
          Double theoreticMass
          Deprecated.
          use the double value instead.
          The theoretic mass.
        • theoreticMass1
          double theoreticMass1
          The theoretic mass.
        • type
          Ion.IonType type
          Type of ion.
    • Class com.compomics.util.experiment.biology.ions.NeutralLoss extends ExperimentObject implements Serializable

      serialVersionUID:
      5540846193082177391L
      • Serialized Fields

        • aminoAcids
          char[] aminoAcids
          Amino acids that are likely to induce this loss. Null if not a loss originating from amino acids.
        • composition
          AtomChain composition
          The composition of the ion.
        • fixed
          boolean fixed
          Boolean indicating whether the neutral loss will always be accounted for.
        • name
          String name
          The name of the neutral loss.
        • psiCvTerm
          CvTerm psiCvTerm
          The PSI MS CV term of the neutral loss, null if not set.
  • Package com.compomics.util.experiment.biology.ions.impl

  • Package com.compomics.util.experiment.biology.modifications

    • Class com.compomics.util.experiment.biology.modifications.Modification extends ExperimentObject implements Serializable

      serialVersionUID:
      -545472596243822505L
      • Serialized Fields

        • ambiguityKey
          String ambiguityKey
          The ambiguity key for ambiguous modifications.
        • atomChainAdded
          AtomChain atomChainAdded
          The composition of the molecule added. Null if not set.
        • atomChainRemoved
          AtomChain atomChainRemoved
          The composition of the molecule removed. Null if not set.
        • category
          ModificationCategory category
          The category for the modification. Null if not set.
        • mass
          Double mass
          Mass difference produced by this modification. Null if not set.
        • modificationType
          ModificationType modificationType
          The modification type.
        • name
          String name
          Name of the modification.
        • neutralLosses
          ArrayList<NeutralLoss> neutralLosses
          List of known neutral losses for this modification.
        • pattern
          AminoAcidPattern pattern
          The amino acid pattern targeted by this modification (can be set using the AminoAcidPatternDialog). Null if not set.
        • psiModCvTerm
          CvTerm psiModCvTerm
          The PSI-MOD CV term associated with this modification. Null if not set.
        • reporterIons
          ArrayList<ReporterIon> reporterIons
          List of known reporter ions for this modification.
        • shortName
          String shortName
          Short name of the modification.
        • unimodCvTerm
          CvTerm unimodCvTerm
          The Unimod CV term associated with this modification. Null if not set.
  • Package com.compomics.util.experiment.biology.proteins

  • Package com.compomics.util.experiment.biology.variants

  • Package com.compomics.util.experiment.identification

  • Package com.compomics.util.experiment.identification.amino_acid_tags

  • Package com.compomics.util.experiment.identification.features

    • Class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache extends ExperimentObject implements Serializable

      • Serialized Fields

        • currentPeptideKey
          long currentPeptideKey
          The current peptide key.
        • currentProteinKey
          long currentProteinKey
          The current protein key.
        • filtered
          boolean filtered
          Boolean indicating whether a filtering was already used. If yes, proteins might need to be unhidden.
        • largeObjectsCache
          HashMap<IdentificationFeaturesCache.ObjectType,​HashMap<Long,​Object>> largeObjectsCache
          Cache for the large objects.
        • largeObjectsInCache
          int largeObjectsInCache
          The number of large objects in cache.
        • maxSpectrumCount
          int maxSpectrumCount
          The maximum number of PSMs across all peptides of the last selected protein.
        • nValidatedPsms
          int nValidatedPsms
          The number of validated PSMs in the currently selected peptide.
        • peptideList
          long[] peptideList
          The peptide list.
        • proteinList
          long[] proteinList
          Back-up list for when proteins are hidden.
        • proteinListAfterHiding
          long[] proteinListAfterHiding
          The protein list.
        • psmList
          long[] psmList
          The PSM list.
        • readOnly
          boolean readOnly
          Indicates whether the cache is read only.
        • smallObjectsCache
          HashMap<IdentificationFeaturesCache.ObjectType,​HashMap<Long,​Object>> smallObjectsCache
          Cache for the small objects.
        • smallObjectsInCache
          int smallObjectsInCache
          The number of small objects in cache.
        • validatedProteinList
          long[] validatedProteinList
          List of the validated proteins.
  • Package com.compomics.util.experiment.identification.filtering

  • Package com.compomics.util.experiment.identification.matches

  • Package com.compomics.util.experiment.identification.peptide_shaker

    • Class com.compomics.util.experiment.identification.peptide_shaker.Metrics extends ExperimentObject implements Serializable

      • Serialized Fields

        • foundCharges
          int[] foundCharges
          The charges found in all PSMs (only the best hit per spectrum). Charges are ordered.
        • foundModifications
          TreeSet<String> foundModifications
          List of modifications found in the dataset.
        • fractionPsmMatches
          HashMap<String,​ArrayList<Long>> fractionPsmMatches
          The PSM matches for each fraction for each peptide. Key: 'fraction name'_'peptide key'. Values: arraylist of spectrum keys.
        • maxMW
          Double maxMW
          The weight of the fattest protein in the dataset.
        • maxNPeptides
          Integer maxNPeptides
          The maximal number of peptides among the proteins of the dataset.
        • maxNPsms
          Integer maxNPsms
          The maximal number of PSMs among the proteins of the dataset.
        • maxPrecursorErrorDa
          double maxPrecursorErrorDa
          The maximal peptide precursor error in Da in all PSMs (only the best peptide hit per spectrum).
        • maxPrecursorErrorPpm
          double maxPrecursorErrorPpm
          The maximal peptide precursor error in ppm in all PSMs (only the best peptide hit per spectrum).
        • maxProteinAccessionLength
          Integer maxProteinAccessionLength
          The max protein key length.
        • maxProteinAveragePrecursorIntensity
          Double maxProteinAveragePrecursorIntensity
          The maximum protein average precursor intensity.
        • maxProteinSummedPrecursorIntensity
          Double maxProteinSummedPrecursorIntensity
          The maximum protein summed precursor intensity.
        • maxSpectrumCounting
          Double maxSpectrumCounting
          The maximal spectrum counting in the proteins of the dataset.
        • maxTagPrecursorErrorDa
          double maxTagPrecursorErrorDa
          The maximal tag precursor error in Da in all PSMs (only the best tag hit per spectrum when no peptide is found).
        • maxTagPrecursorErrorPpm
          double maxTagPrecursorErrorPpm
          The maximal tag precursor error in ppm in all PSMs (only the best tag hit per spectrum when no peptide is found).
        • maxValidatedPeptidesPerFraction
          Integer maxValidatedPeptidesPerFraction
          The maximum number of peptides detected at the fraction level.
        • maxValidatedSpectraPerFraction
          Integer maxValidatedSpectraPerFraction
          The maximum number of spectra at the fraction level.
        • nConfidentProteins
          Integer nConfidentProteins
          Number of validated confident proteins.
        • nValidatedProteins
          int nValidatedProteins
          Number of validated proteins.
        • observedFractionalMassesAll
          HashMap<String,​ArrayList<Double>> observedFractionalMassesAll
          The observed molecular masses in kDa for each fraction.
        • peptideLengthDistribution
          NonSymmetricalNormalDistribution peptideLengthDistribution
          The distribution of peptide validated lengths.
        • proteinKeys
          long[] proteinKeys
          The ordered list of protein keys as estimated during the import process.
        • totalPeptidesPerFractions
          HashMap<String,​Integer> totalPeptidesPerFractions
          The total number of peptides per fraction.
        • totalSpectrumCounting
          Double totalSpectrumCounting
          The sum of all spectrum counting indexes.
        • totalSpectrumCountingMass
          Double totalSpectrumCountingMass
          The sum of all spectrum counting masses.
        • validatedTargetProteinKeys
          long[] validatedTargetProteinKeys
          The keys of the validated target protein matches.
    • Class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring extends ExperimentObject implements Serializable

      serialVersionUID:
      -3357368272501542941L
      • Serialized Fields

        • deltaScoresAtAA
          HashMap<Integer,​Double> deltaScoresAtAA
          Amino acid specific delta score. 1 is the first amino acid.
        • probabilisticScoresAtAA
          HashMap<Integer,​Double> probabilisticScoresAtAA
          Amino acid specific probabilistic score.
        • ptmLocationAtAA
          HashMap<Integer,​Integer> ptmLocationAtAA
          The retained PTM site assignment.
        • ptmName
          String ptmName
          The name of the modification of interest. 1 is the first amino acid.
    • Class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores extends ExperimentObject implements Serializable

      • Serialized Fields

        • ambiguousModificationsByModName
          HashMap<String,​HashMap<Integer,​HashSet<Integer>>> ambiguousModificationsByModName
          A map of all ambiguous modifications in a sequence indexed by modification name.
        • ambiguousModificationsByRepresentativeSite
          HashMap<Integer,​HashMap<Integer,​HashSet<String>>> ambiguousModificationsByRepresentativeSite
          A list of all ambiguous modifications in a sequence: representative site > secondary site > modification names.
        • confidentModificationsByModName
          HashMap<String,​HashSet<Integer>> confidentModificationsByModName
          A map of all confident modifications in a sequence indexed by modification name.
        • mainModificationSites
          HashMap<Integer,​HashSet<String>> mainModificationSites
          A list of all modification sites confidently localized on a sequence in a map: site > modification names.
        • modificationMap
          HashMap<String,​ModificationScoring> modificationMap
          A map containing all scores indexed by the modification of interest for a peptide or a PSM.
    • Class com.compomics.util.experiment.identification.peptide_shaker.PSParameter extends ExperimentObject implements Serializable

      serialVersionUID:
      2846587135366515967L
      • Serialized Fields

        • algorithmDeltaPEP
          double algorithmDeltaPEP
          The difference in identification algorithm level PEP with the next best peptide assumption.
        • deltaPEP
          double deltaPEP
          The difference in identification algorithm level PEP with the next best peptide assumption with sequence difference across all search engines.
        • fractionPEP
          HashMap<String,​Double> fractionPEP
          The fraction confidence map.
        • fractionScore
          HashMap<String,​Double> fractionScore
          The fraction confidence map.
        • hidden
          boolean hidden
          Boolean indicating whether this is a hidden match.
        • intermediateScores
          HashMap<Integer,​Double> intermediateScores
          Map of the intermediate scores. Score index > value
        • manualValidation
          boolean manualValidation
          Boolean indicating whether the validation confidence was manually updated.
        • matchValidationLevel
          MatchValidationLevel matchValidationLevel
          The validation level of a given match.
        • precursorIntensityAveragePerFraction
          HashMap<String,​Double> precursorIntensityAveragePerFraction
          The average precursor intensity per fraction.
        • precursorIntensityPerFraction
          HashMap<String,​ArrayList<Double>> precursorIntensityPerFraction
          The precursor intensity per fraction.
        • precursorIntensitySummedPerFraction
          HashMap<String,​Double> precursorIntensitySummedPerFraction
          The summed precursor intensity per fraction.
        • probability
          double probability
          The probability of the match.
        • proteinInferenceGroupClass
          int proteinInferenceGroupClass
          Protein groups can belong to the following groups according to the static field indexing.
        • qcFilters
          HashMap<String,​Boolean> qcFilters
          The results of the validation quality filters.
        • score
          double score
          The score of the match.
        • starred
          boolean starred
          Boolean indicating whether this is a starred match.
        • validatedPeptidesPerFraction
          HashMap<String,​Integer> validatedPeptidesPerFraction
          The number of validated peptides per fraction.
        • validatedSpectraPerFraction
          HashMap<String,​Integer> validatedSpectraPerFraction
          The number of validated spectra per fraction.
  • Package com.compomics.util.experiment.identification.protein_inference.fm_index

    • Class com.compomics.util.experiment.identification.protein_inference.fm_index.AccessionMetaData extends Object implements Serializable

      serialVersionUID:
      8320902054239025L
      • Serialized Fields

        • header
          Header header
          The header
        • headerAsString
          String headerAsString
          The header as string.
        • index
          int index
          The index.
        • indexPart
          int indexPart
          The index part.
        • trueBeginning
          int trueBeginning
          Beginning of protein sequence in the proteome.
    • Class com.compomics.util.experiment.identification.protein_inference.fm_index.CacheElement extends ExperimentObject implements Serializable

    • Class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex extends ExperimentObject implements Serializable

      • Serialized Fields

        • aaMasses
          double[] aaMasses
          List of all amino acid masses.
        • aaMassIndexes
          int[] aaMassIndexes
          List of all indexes for valid amino acid masses.
        • accessionMetaData
          HashMap<String,​AccessionMetaData> accessionMetaData
          The accessions ending positions in the index, important for getSequences function.
        • accessions
          ArrayList<String[]> accessions
          List of all accession IDs in the FASTA file.
        • allPermutations
          int[][][] allPermutations
          All permutations.
        • boundaries
          ArrayList<int[]> boundaries
          Storing the starting positions of the protein sequences.
        • BSubstitutions
          int[] BSubstitutions
          Characters that can be substituted by B.
        • cache
          HashMap<String,​CacheElement>[] cache
          List of cached intermediate tag to proteome mapping results.
        • decoyAccessions
          HashSet<String> decoyAccessions
          The decoy accessions contained in this index.
        • fmodc
          ArrayList<String> fmodc
        • fmodcaa
          ArrayList<String>[] fmodcaa
        • fmodcaaMass
          ArrayList<Double>[] fmodcaaMass
        • fmodcMass
          ArrayList<Double> fmodcMass
        • fmodcp
          ArrayList<String> fmodcp
        • fmodcpaa
          ArrayList<String>[] fmodcpaa
        • fmodcpaaMass
          ArrayList<Double>[] fmodcpaaMass
        • fmodcpMass
          ArrayList<Double> fmodcpMass
        • fmodn
          ArrayList<String> fmodn
        • fmodnaa
          ArrayList<String>[] fmodnaa
        • fmodnaaMass
          ArrayList<Double>[] fmodnaaMass
        • fmodnMass
          ArrayList<Double> fmodnMass
        • fmodnp
          ArrayList<String> fmodnp
        • fmodnpaa
          ArrayList<String>[] fmodnpaa
        • fmodnpaaMass
          ArrayList<Double>[] fmodnpaaMass
        • fmodnpMass
          ArrayList<Double> fmodnpMass
        • hasCTermDirectionModification
          boolean hasCTermDirectionModification
        • hasFixedModification_CatTerminus
          boolean hasFixedModification_CatTerminus
        • hasFixedModification_NatTerminus
          boolean hasFixedModification_NatTerminus
        • hasModificationatTerminus
          boolean hasModificationatTerminus
        • hasNTermDirectionModification
          boolean hasNTermDirectionModification
        • indexChunkSize
          int indexChunkSize
          Byte size of index chuck.
        • indexParts
          int indexParts
          Number of chunks of complete index.
        • indexStringLengths
          ArrayList<Integer> indexStringLengths
          Length of the indexed string (all concatenated protein sequences).
        • JSubstitutions
          int[] JSubstitutions
          Characters that can be substituted by J.
        • lessTablesPrimary
          ArrayList<int[]> lessTablesPrimary
          Less table for doing an update step according to the LF step.
        • lessTablesReversed
          ArrayList<int[]> lessTablesReversed
          Less table for doing an update step according to the LF step reversed.
        • longestModificationpattern
          int longestModificationpattern
          Longest modification pattern.
        • lookupMasses
          long[] lookupMasses
          Mass lookup table.
        • lookupMultiplier
          double lookupMultiplier
          Precision for the masses in lookup table.
        • massAccuracyType
          SearchParameters.MassAccuracyType massAccuracyType
          The mass accuracy type.
        • massIndexMaps
          ArrayList<MassIndexMap> massIndexMaps
          Array list for sorted masses to index mappings.
        • massTolerance
          double massTolerance
          Lookup tolerance mass.
        • maxNumberDeletions
          int maxNumberDeletions
          Number of allowed deletion operations.
        • maxNumberInsertions
          int maxNumberInsertions
          Number of allowed insertion operations.
        • maxNumberSubstitutions
          int maxNumberSubstitutions
          Number of allowed substitution operations.
        • maxNumberVariants
          int maxNumberVariants
          Number of allowed variant operations.
        • maxPTMsPerPeptide
          int maxPTMsPerPeptide
          Maximal number of PTMs per peptide.
        • maxXPerTag
          int maxXPerTag
          Maximum supported number of Xs per tag.
        • modificationFlags
          boolean[] modificationFlags
          List of all modification flags
        • modificationLabelsToId
          HashMap<String,​Integer> modificationLabelsToId
          Dictionary label to internal id
        • modificationPatternNames
          HashMap<String,​int[]> modificationPatternNames
          Mapping dictionary mod name -> (modificationPattern index, relative starting position, pattern length).
        • modificationPatterns
          ArrayList<Long[]> modificationPatterns
          List for patterns of complex modifications.
        • modifictationLabels
          String[] modifictationLabels
          List of all amino acid masses.
        • negativeModificationMass
          double negativeModificationMass
        • numMasses
          int numMasses
          List of all indexes for valid amino acid masses.
        • occurrenceTablesPrimary
          ArrayList<WaveletTree> occurrenceTablesPrimary
          Wavelet tree for storing the burrows wheeler transform.
        • occurrenceTablesReversed
          ArrayList<WaveletTree> occurrenceTablesReversed
          Wavelet tree for storing the burrows wheeler transform reversed.
        • onlyTrypticPeptides
          boolean onlyTrypticPeptides
          Flag for only considering tryptic digested peptides.
        • sampling
          int sampling
          Bit shifting for fast multiplying / dividing operations.
        • samplingMask
          int samplingMask
          Mask of fast modulo operations.
        • samplingShift
          int samplingShift
          Every 2^samplingShift suffix array entry will be sampled.
        • SNPs
          HashMap<String,​ArrayList<SNPElement>> SNPs
        • substitutionMatrix
          boolean[][] substitutionMatrix
          Allowed substitutions.
        • suffixArraysPrimary
          ArrayList<int[]> suffixArraysPrimary
          Sampled suffix array.
        • variantBitsPrimary
          ArrayList<Rank> variantBitsPrimary
        • variantBitsReversed
          ArrayList<Rank> variantBitsReversed
        • variantMatchingType
          PeptideVariantsParameters.VariantType variantMatchingType
          Either search with one maximal number of variants or use an upper limit for every variant (insertion / deletion / substitution)
        • variantsPrimary
          ArrayList<HashSet<int[]>[]> variantsPrimary
        • variantsReversed
          ArrayList<HashSet<int[]>[]> variantsReversed
        • vmodc
          ArrayList<String> vmodc
        • vmodcaa
          ArrayList<String>[] vmodcaa
        • vmodcaaMass
          ArrayList<Double>[] vmodcaaMass
        • vmodcMass
          ArrayList<Double> vmodcMass
        • vmodcp
          ArrayList<String> vmodcp
        • vmodcpaa
          ArrayList<String>[] vmodcpaa
        • vmodcpaaMass
          ArrayList<Double>[] vmodcpaaMass
        • vmodcpMass
          ArrayList<Double> vmodcpMass
        • vmodn
          ArrayList<String> vmodn
        • vmodnaa
          ArrayList<String>[] vmodnaa
        • vmodnaaMass
          ArrayList<Double>[] vmodnaaMass
        • vmodnMass
          ArrayList<Double> vmodnMass
        • vmodnp
          ArrayList<String> vmodnp
        • vmodnpaa
          ArrayList<String>[] vmodnpaa
        • vmodnpaaMass
          ArrayList<Double>[] vmodnpaaMass
        • vmodnpMass
          ArrayList<Double> vmodnpMass
        • withVariableModifications
          boolean withVariableModifications
          If true, variable modifications are included.
        • Xlookup
          long[][] Xlookup
          Lookup table for up to maxXPerTag Xs per mass tag.
        • ZSubstitutions
          int[] ZSubstitutions
          Characters that can be substituted by Z.
    • Class com.compomics.util.experiment.identification.protein_inference.fm_index.MassIndexMap extends ExperimentObject implements Serializable

      • Serialized Fields

        • indexes
          int[] indexes
        • mass
          double mass
    • Class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent extends ExperimentObject implements Serializable

      • Serialized Fields

        • allVariants
          String allVariants
          Current storing of all variant operations.
        • allXcomponents
          ArrayList<int[]> allXcomponents
          Information about all component where the Xs belong to.
        • allXMassDiffs
          HashMap<Integer,​Double> allXMassDiffs
          The all X mass differences.
        • ambiguousChar
          int ambiguousChar
          If original character was B, J, X, Z.
        • character
          int character
          Character which was chosen.
        • left
          int left
          Left index.
        • length
          int length
          Current peptide sequence length.
        • mass
          double mass
          Current mass.
        • modification
          ModificationMatch modification
          Index to the modifications list.
        • modificationPos
          int modificationPos
          List of all modifications.
        • modifications
          ArrayList<ModificationMatch> modifications
          List of all modifications.
        • numPTMs
          int numPTMs
          The number of PTMs.
        • numSpecificVariants
          int[] numSpecificVariants
          The specific variants. (0) deletion, (1) insertion, (2) substitution.
        • numVariants
          int numVariants
          List of all modifications.
        • numX
          int numX
          Current number of contained X's.
        • peptideSequence
          String peptideSequence
          Current peptide sequence.
        • peptideSequenceSearch
          String peptideSequenceSearch
          Current peptide sequence needed for search.
        • previousContent
          MatrixContent previousContent
          Index of the originating entry of a particular cell with the pattern searching matrix.
        • right
          int right
          Right index.
        • tagComponent
          int tagComponent
          Information about the component where the X belongs to.
        • variant
          char variant
          Type of edit operation, either deletion 'd', substitution 's' or insertion 'i'.
        • XMassDiff
          double XMassDiff
          The X mass difference,
    • Class com.compomics.util.experiment.identification.protein_inference.fm_index.Rank extends Object implements Serializable

      serialVersionUID:
      832090205423902L
      • Serialized Fields

        • bitfield
          long[] bitfield
          The bit field.
        • length
          int length
          The length.
        • sums
          int[] sums
          The sums.
        • sumsSecondLevel
          byte[] sumsSecondLevel
          The sums.
    • Class com.compomics.util.experiment.identification.protein_inference.fm_index.SNPElement extends ExperimentObject implements Serializable

      • Serialized Fields

        • position
          int position
        • sourceAA
          char sourceAA
        • targetAA
          char targetAA
    • Class com.compomics.util.experiment.identification.protein_inference.fm_index.TagElement extends ExperimentObject implements Serializable

      • Serialized Fields

        • isMass
          boolean isMass
        • mass
          double mass
        • modifications
          Integer[] modifications
        • sequence
          String sequence
        • xNumLimit
          int xNumLimit
    • Class com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree extends Object implements Serializable

      serialVersionUID:
      83209020542390251L
      • Serialized Fields

        • alphabetDirections
          long[] alphabetDirections
          Stored alphabet in a 128 bitfield.
        • continueLeftRangeQuery
          boolean continueLeftRangeQuery
          Continue range query for left child.
        • continueRightRangeQuery
          boolean continueRightRangeQuery
          Continue range query for right child.
        • firstChar
          int firstChar
          First character in alphabet.
        • lastChar
          int lastChar
          Last character in alphabet.
        • leftChild
          WaveletTree leftChild
          Left child of the wavelet tree.
        • leftRightMask
          int leftRightMask
          Left right mask.
        • lenText
          int lenText
          Text length.
        • less
          int[] less
          The less table.
        • rank
          Rank rank
          Instance of a rank.
        • rightChild
          WaveletTree rightChild
          Right child of the wavelet tree.
  • Package com.compomics.util.experiment.identification.spectrum_annotation

    • Class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters extends ExperimentObject implements Serializable

      • Serialized Fields

        • automaticAnnotation
          boolean automaticAnnotation
          Shall automatic annotation be used.
        • deNovoCharge
          int deNovoCharge
          The charge for the fragment ions in the de novo sequencing.
        • fragmentIonAccuracy
          double fragmentIonAccuracy
          Fragment ion accuracy used for peak matching.
        • fragmentIonPpm
          boolean fragmentIonPpm
          Indicates whether the fragment ion accuracy is in ppm.
        • intensityLimit
          double intensityLimit
          The intensity threshold to use. The type of threshold is defined according to the IntensityThreshold enum.
        • intensityThresholdType
          AnnotationParameters.IntensityThresholdType intensityThresholdType
          The type of intensity threshold.
        • neutralLossesAuto
          boolean neutralLossesAuto
          If true neutral losses will be automatically deduced from the spectrum identification assumption.
        • neutralLossesList
          ArrayList<NeutralLoss> neutralLossesList
          List of neutral losses to annotate.
        • relatedIons
          boolean relatedIons
          If true related ions will be annotated by default.
        • reporterIons
          boolean reporterIons
          If true reporter ions will be annotated by default.
        • selectedIonsMap
          HashMap<Ion.IonType,​HashSet<Integer>> selectedIonsMap
          The types of ions to annotate.
        • showAllPeaks
          boolean showAllPeaks
          If true, all peaks are shown, false displays the annotated peaks, and the non-annotated in the background.
        • showForwardIonDeNovoTags
          boolean showForwardIonDeNovoTags
          If true, the automatic forward ion de novo tags are shown.
        • showRewindIonDeNovoTags
          boolean showRewindIonDeNovoTags
          If true, the automatic rewind ion de novo tags are shown.
        • tiesResolution
          SpectrumAnnotator.TiesResolution tiesResolution
          The method to use for resolution of ties when multiple peaks can be assigned to a fragment.
        • yAxisZoomExcludesBackgroundPeaks
          boolean yAxisZoomExcludesBackgroundPeaks
          If true, the automatic y-axis zoom excludes background peaks. False includes all peaks in the auto zoom.
    • Class com.compomics.util.experiment.identification.spectrum_annotation.NeutralLossesMap extends ExperimentObject implements Serializable

      serialVersionUID:
      -4690159937753713106L
      • Serialized Fields

        • accountedNeutralLosses
          ArrayList<String> accountedNeutralLosses
          Cache for the accounted neutral losses.
        • forwardBoundaries
          HashMap<String,​Integer> forwardBoundaries
          Map indicating for each neutral loss when they should start being accounted for the forward ions (b ions for instance).
        • rewindBoundaries
          HashMap<String,​Integer> rewindBoundaries
          Map indicating for each neutral loss when they should start being accounted for the reverse ions (y ions for instance).
  • Package com.compomics.util.experiment.identification.spectrum_assumptions

  • Package com.compomics.util.experiment.io.biology.protein

    • Class com.compomics.util.experiment.io.biology.protein.FastaParameters extends ExperimentObject implements Serializable

      • Serialized Fields

        • decoyFlag
          String decoyFlag
          The flag for decoy proteins in the accession.
        • decoySuffix
          boolean decoySuffix
          Boolean indicating whether the decoy flag is a suffix or a prefix.
        • targetDecoy
          boolean targetDecoy
          Boolean indicating whether the FASTA file should be processed as target-decoy or only target.
        • targetDecoyFileNameTag
          String targetDecoyFileNameTag
          The tag added after adding decoy sequences to a FASTA file.
    • Class com.compomics.util.experiment.io.biology.protein.Header extends ExperimentObject implements Serializable

      serialVersionUID:
      7665784733371863163L
      • Serialized Fields

        • databaseType
          ProteinDatabase databaseType
          Extracted database name. As there are no standard database names, this is only an internally consistent naming scheme included to be able to later separate the databases. For example when linking to the online version of the database. The links themselves are not included as these might change outside the control of the compomics-utilities library. Note that the type is set to unknown by default, and is set to the correct type during the parsing of the header.
        • iAccession
          String iAccession
          The accession String is the unique identifier for the sequence in the respective database. Note that for NCBI, the accession number also defines a unique moment in time.
          Accession String is the second element in the abbreviated header String.
        • iAddenda
          StringBuffer iAddenda
          This StringBuffer holds all the addenda for this header.
        • iDescription
          String iDescription
          The description is a more or less elaborate description of the protein in question.
          The description is the third element (and final) in the abbreviated header String.
        • iDescriptionProteinName
          String iDescriptionProteinName
          Protein name, the protein name extracted from the protein description. For example: "GRP78_HUMAN 78 kDa glucose-regulated protein OS=Homo sapiens GN=HSPA5 PE=1 SV=2" returns "GRP78_HUMAN".
        • iDescriptionShort
          String iDescriptionShort
          A short protein description, removing all but the protein description itself. For example: "GRP78_HUMAN 78 kDa glucose-regulated protein OS=Homo sapiens GN=HSPA5 PE=1 SV=2" becomes "78 kDa glucose-regulated protein".
        • iEnd
          int iEnd
          This variable holds a possible end index for the associated sequence.
        • iForeignAccession
          String iForeignAccession
          The foreign accession String is an accession String in another database of significance. Most notably used for SwissProt accessions that are kept in the NCBI database.
          The foreign accession String is an addendum to the foreign ID String in the abbreviated header String.
        • iForeignDescription
          String iForeignDescription
          The foreign Description is a description for an entry in another DB. Most notably, the SwissProt short description for an entry that is found within NCBI.
          The foreign description is an addendum to the foreign accession String in the abbreviated header String.
        • iForeignID
          String iForeignID
          The foreign ID is the ID of another database this entry is originally from. Most notably used for SwissProt entries in NCBI.
          The foreign ID String is an addendum to the accession String in the abbreviated header String.
        • iGeneName
          String iGeneName
          The name of the gene the protein comes from. Note that this is only available for UniProt and NextProt based databases.
        • iID
          String iID
          The ID String corresponds to the String that is present as the first element following the opening '>'. It is most notably 'sw' for SwissProt, and 'gi' for NCBI.
          ID is the first element in the abbreviated header String.
        • iProteinEvidence
          Integer iProteinEvidence
          The protein evidence for the protein. Note that this is only available for UniProt-based databases.
        • iRawHeader
          String iRawHeader
          This variable holds the raw complete unformatted header. Only trailing white space is removed.
        • iRest
          String iRest
          This variable holds all unidentified parts for the Header. If the String was not (recognized as) a standard SwissProt or NCBI header, this variable holds the entire header.
        • iStart
          int iStart
          This variable holds a possible start index for the associated sequence.
        • iTaxonomy
          String iTaxonomy
          The name of the taxonomy the protein comes from. Note that this is only available for UniProt-based databases.
  • Package com.compomics.util.experiment.io.identification

  • Package com.compomics.util.experiment.io.identification.idfilereaders

  • Package com.compomics.util.experiment.io.mass_spectrometry.mgf

    • Class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex extends ExperimentObject implements Serializable

      • Serialized Fields

        • duplicatedSpectrumTitles
          HashMap<String,​Integer> duplicatedSpectrumTitles
          Map of duplicated spectrum titles and how often they are duplicated.
        • fileName
          String fileName
          The name of the indexed file.
        • indexMap
          HashMap<String,​Long> indexMap
          The map of all indexes: spectrum title > index in the file.
        • lastModified
          Long lastModified
          The last time the indexed file was modified.
        • maxCharge
          Integer maxCharge
          The maximal charge.
        • maxIntensity
          Double maxIntensity
          The maximal precursor intensity of the file.
        • maxMz
          Double maxMz
          The maximal m/z in all precursors of the file.
        • maxPeakCount
          Integer maxPeakCount
          The maximal peak count.
        • maxRT
          Double maxRT
          The maximum RT found in the spectra.
        • minRT
          Double minRT
          The minimum RT found in the spectra.
        • peakPicked
          Boolean peakPicked
          Indicates if the spectra seem to be peak picked or not. A null value indicated that the check for peak picking was not performed.
        • precursorChargesMissing
          Boolean precursorChargesMissing
          Indicates if there are spectra where the precursor charge is missing. A null value indicated that the check was not performed.
        • precursorMzMap
          HashMap<Integer,​Double> precursorMzMap
          Map of the precursor mz values.
        • spectrumCount
          Integer spectrumCount
          Returns the number of spectra in the file as counted by the begin ions tags. Null if not set.
        • spectrumNumberIndexMap
          HashMap<String,​Integer> spectrumNumberIndexMap
          A map of all the spectrum titles and which rank they have in the file, i.e., the first spectrum has rank 0, the second rank 1, etc.
        • spectrumTitles
          ArrayList<String> spectrumTitles
          List of spectrum titles.
  • Package com.compomics.util.experiment.mass_spectrometry.spectra

  • Package com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.gui

  • Package com.compomics.util.experiment.personalization

  • Package com.compomics.util.experiment.quantification

  • Package com.compomics.util.experiment.quantification.reporterion

  • Package com.compomics.util.experiment.refinement_parameters

  • Package com.compomics.util.experiment.units

  • Package com.compomics.util.general

  • Package com.compomics.util.general.servlet

  • Package com.compomics.util.gui

    • Class com.compomics.util.gui.AaMass extends JDialog implements Serializable

    • Class com.compomics.util.gui.AminoAcidPatternDialog extends JDialog implements Serializable

      • Serialized Fields

        • addJMenuItem
          JMenuItem addJMenuItem
        • backgroundPanel
          JPanel backgroundPanel
        • cancel
          boolean cancel
          A boolean indicating whether the used clicked the cancel button.
        • cancelButton
          JButton cancelButton
        • deleteSelectedRowJMenuItem
          JMenuItem deleteSelectedRowJMenuItem
        • editable
          boolean editable
          A boolean indicating whether the pattern can be edited.
        • exampleLabel
          JLabel exampleLabel
        • exampleSequence
          String exampleSequence
          The example sequence.
        • jSeparator3
          JSeparator jSeparator3
        • jSeparator4
          JSeparator jSeparator4
        • moveDownJMenuItem
          JMenuItem moveDownJMenuItem
        • moveUpJMenuItem
          JMenuItem moveUpJMenuItem
        • okButton
          JButton okButton
        • pattern
          AminoAcidPattern pattern
          The pattern displayed.
        • patternDesignPanel
          JPanel patternDesignPanel
        • patternDesignScrollPane
          JScrollPane patternDesignScrollPane
        • patternDesignTable
          JTable patternDesignTable
        • patternDesignTableToolTips
          ArrayList<String> patternDesignTableToolTips
          The pattern design table column header tooltips.
        • patternTestEditorPane
          JEditorPane patternTestEditorPane
        • patternTestJScrollPane
          JScrollPane patternTestJScrollPane
        • popupJMenu
          JPopupMenu popupJMenu
        • rightClickHelpLabel
          JLabel rightClickHelpLabel
        • testPanel
          JPanel testPanel
    • Class com.compomics.util.gui.DummyFrame extends JFrame implements Serializable

    • Class com.compomics.util.gui.ExportFormatSelectionDialog extends JDialog implements Serializable

      • Serialized Fields

        • backgroundPanel
          JPanel backgroundPanel
        • buttonGroup
          ButtonGroup buttonGroup
        • canceled
          boolean canceled
          True if the user canceled the dialog.
        • cancelJButton
          JButton cancelJButton
        • excelJRadioButton
          JRadioButton excelJRadioButton
        • exportJButton
          JButton exportJButton
        • formatTypeJPanel
          JPanel formatTypeJPanel
        • textJRadioButton
          JRadioButton textJRadioButton
    • Class com.compomics.util.gui.FlamableJFrame extends JFrame implements Serializable

      • Serialized Fields

        • logger
          org.apache.log4j.Logger logger
    • Class com.compomics.util.gui.JExceptionDialog extends JDialog implements Serializable

      • Serialized Fields

        • iMessages
          String[] iMessages
        • iThrowable
          Throwable iThrowable
        • logger
          org.apache.log4j.Logger logger
    • Class com.compomics.util.gui.JFrameForBytes extends JFrame implements Serializable

      • Serialized Fields

        • btnSave
          JButton btnSave
        • btnUnzip
          JButton btnUnzip
        • iData
          byte[] iData
          This byte[] is the data that will be shown.
        • logger
          org.apache.log4j.Logger logger
        • txtData
          JTextArea txtData
    • Class com.compomics.util.gui.JLabelAndComponentPanel extends JPanel implements Serializable

      • Serialized Fields

        • logger
          org.apache.log4j.Logger logger
    • Class com.compomics.util.gui.JTableForDB extends AlternateRowColoursJTable implements Serializable

      • Serialized Fields

        • iDateTimeFormat
          String iDateTimeFormat
          This String contains the date and time format.
        • iFrames
          Vector iFrames
          This Vector holds the references to all the tables that have been created during the life cycle.
        • logger
          org.apache.log4j.Logger logger
    • Class com.compomics.util.gui.PrivacyParametersDialog extends JDialog implements Serializable

      • Serialized Fields

        • backgroundPanel
          JPanel backgroundPanel
        • cancelButton
          JButton cancelButton
        • confidentialLabel
          JLabel confidentialLabel
        • normalIcon
          Image normalIcon
          The normal dialog icon.
        • okButton
          JButton okButton
        • openDialogHelpJButton
          JButton openDialogHelpJButton
        • settingsPanel
          JPanel settingsPanel
        • updatesCheck
          JCheckBox updatesCheck
        • utilitiesUserParameters
          UtilitiesUserParameters utilitiesUserParameters
          The user preferences.
    • Class com.compomics.util.gui.SampleSelection extends JDialog implements Serializable

      • Serialized Fields

    • Class com.compomics.util.gui.VennDiagramDialog extends JDialog implements Serializable

      • Serialized Fields

        • backgroundPanel
          JPanel backgroundPanel
        • contextMenuPlotBackgroundPanel
          JPanel contextMenuPlotBackgroundPanel
        • dataPanel
          JPanel dataPanel
        • datasetAColorJPanel
          JPanel datasetAColorJPanel
        • datasetAScrollPane
          JScrollPane datasetAScrollPane
        • datasetATextArea
          JTextArea datasetATextArea
        • datasetATextField
          JTextField datasetATextField
        • datasetBColorJPanel
          JPanel datasetBColorJPanel
        • datasetBScrollPane
          JScrollPane datasetBScrollPane
        • datasetBTextArea
          JTextArea datasetBTextArea
        • datasetBTextField
          JTextField datasetBTextField
        • datasetCColorJPanel
          JPanel datasetCColorJPanel
        • datasetCScrollPane
          JScrollPane datasetCScrollPane
        • datasetCTextArea
          JTextArea datasetCTextArea
        • datasetCTextField
          JTextField datasetCTextField
        • datasetDColorJPanel
          JPanel datasetDColorJPanel
        • datasetDScrollPane
          JScrollPane datasetDScrollPane
        • datasetDTextArea
          JTextArea datasetDTextArea
        • datasetDTextField
          JTextField datasetDTextField
        • dialogParent
          Frame dialogParent
          The dialog parent.
        • exportPlotMenuItem
          JMenuItem exportPlotMenuItem
        • fontSizeMenu
          JMenu fontSizeMenu
        • jSeparator1
          JPopupMenu.Separator jSeparator1
        • jSeparator2
          JPopupMenu.Separator jSeparator2
        • lastSelectedFolder
          LastSelectedFolder lastSelectedFolder
          The last selected folder.
        • legendCheckBoxMenuItem
          JCheckBoxMenuItem legendCheckBoxMenuItem
        • legendFontSizeMenuItem
          JMenuItem legendFontSizeMenuItem
        • legendLocationMenuItem
          JMenuItem legendLocationMenuItem
        • normalIcon
          Image normalIcon
          The normal icon for the parent dialog.
        • plotHelpJButton
          JButton plotHelpJButton
        • plotLayeredPane
          JLayeredPane plotLayeredPane
        • plotOptionsJButton
          JButton plotOptionsJButton
        • plotPopupMenu
          JPopupMenu plotPopupMenu
        • valueFontSizeMenuItem
          JMenuItem valueFontSizeMenuItem
        • vennDiagramPanel
          VennDiagramPanel vennDiagramPanel
          The Venn diagram panel.
        • waitingIcon
          Image waitingIcon
          The icon to use when busy.
        • xyPlotPanel
          JPanel xyPlotPanel
    • Class com.compomics.util.gui.VennDiagramLegendLocationDialog extends JDialog implements Serializable

      • Serialized Fields

        • backgroundPanel
          JPanel backgroundPanel
        • datasetALabel
          JLabel datasetALabel
        • datasetBLabel
          JLabel datasetBLabel
        • datasetCLabel
          JLabel datasetCLabel
        • datasetDLabel
          JLabel datasetDLabel
        • downDatasetAButton
          JButton downDatasetAButton
        • downDatasetBButton
          JButton downDatasetBButton
        • downDatasetCButton
          JButton downDatasetCButton
        • downDatasetDButton
          JButton downDatasetDButton
        • leftDatasetAButton
          JButton leftDatasetAButton
        • leftDatasetBButton
          JButton leftDatasetBButton
        • leftDatasetCButton
          JButton leftDatasetCButton
        • leftDatasetDButton
          JButton leftDatasetDButton
        • legendLocationPanel
          JPanel legendLocationPanel
        • legendShiftSize
          double legendShiftSize
          Legend shift size.
        • okButton
          JButton okButton
        • rightDatasetAButton
          JButton rightDatasetAButton
        • rightDatasetBButton
          JButton rightDatasetBButton
        • rightDatasetCButton
          JButton rightDatasetCButton
        • rightDatasetDButton
          JButton rightDatasetDButton
        • shiftSizeLabel
          JLabel shiftSizeLabel
        • shiftSizeSpinner
          JSpinner shiftSizeSpinner
        • upDatasetAButton
          JButton upDatasetAButton
        • upDatasetBButton
          JButton upDatasetBButton
        • upDatasetCButton
          JButton upDatasetCButton
        • upDatasetDButton
          JButton upDatasetDButton
        • vennDiagramDialog
          VennDiagramDialog vennDiagramDialog
          The VennDiagramDialog parent.
    • Class com.compomics.util.gui.VennDiagramPanel extends JPanel implements Serializable

      • Serialized Fields

        • chartPanel
          org.jfree.chart.ChartPanel chartPanel
          The chart panel.
        • currentVennDiagramType
          VennDiagramPanel.VennDiagramType currentVennDiagramType
          The current Venn diagram type.
        • datasetAColor
          Color datasetAColor
          The color for dataset A.
        • datasetBColor
          Color datasetBColor
          The color for dataset B.
        • datasetCColor
          Color datasetCColor
          The color for dataset C.
        • datasetDColor
          Color datasetDColor
          The color for dataset D.
        • fontSizeLegend
          int fontSizeLegend
          The font size to use for the legend.
        • fontSizeValues
          int fontSizeValues
          The font size to use for the values.
        • groupNames
          HashMap<String,​String> groupNames
          The current Venn diagram group names.
        • legendDatasetAFourWay
          no.uib.jsparklines.data.XYDataPoint legendDatasetAFourWay
          The legend location of Dataset A in a four-way Venn diagram.
        • legendDatasetAThreeWay
          no.uib.jsparklines.data.XYDataPoint legendDatasetAThreeWay
          The legend location of Dataset A in a one to three way Venn diagram.
        • legendDatasetBFourWay
          no.uib.jsparklines.data.XYDataPoint legendDatasetBFourWay
          The legend location of Dataset B in a four-way Venn diagram.
        • legendDatasetBThreeWay
          no.uib.jsparklines.data.XYDataPoint legendDatasetBThreeWay
          The legend location of Dataset B in a one to three way Venn diagram.
        • legendDatasetCFourWay
          no.uib.jsparklines.data.XYDataPoint legendDatasetCFourWay
          The legend location of Dataset C in a four-way Venn diagram.
        • legendDatasetCThreeWay
          no.uib.jsparklines.data.XYDataPoint legendDatasetCThreeWay
          The legend location of Dataset C in a one to three way Venn diagram.
        • legendDatasetDFourWay
          no.uib.jsparklines.data.XYDataPoint legendDatasetDFourWay
          The legend location of Dataset D in a four-way Venn diagram.
        • plotPanel
          JPanel plotPanel
        • showLegend
          boolean showLegend
          If true, the legend is shown.
        • tooltipToDatasetMap
          HashMap<String,​String> tooltipToDatasetMap
          Map each dataset tooltip back to the given dataset.
        • vennDiagramResults
          HashMap<String,​ArrayList<String>> vennDiagramResults
          The current Venn diagram results/data.
    • Class com.compomics.util.gui.VisibleTableColumnsDialog extends JDialog implements Serializable

      • Serialized Fields

        • backgroundPanel
          JPanel backgroundPanel
        • deselectAllMenuItem
          JMenuItem deselectAllMenuItem
        • okButton
          JButton okButton
        • selectAllMenuItem
          JMenuItem selectAllMenuItem
        • selectedColumnsTable
          JTable selectedColumnsTable
        • selectedValuesTableScrollPane
          JScrollPane selectedValuesTableScrollPane
        • selectJPopupMenu
          JPopupMenu selectJPopupMenu
        • visibleTableColumnsDialogParent
          VisibleTableColumnsDialogParent visibleTableColumnsDialogParent
          The VisibleTableColumnsDialogParent.
    • Class com.compomics.util.gui.XYPlotFiltersDialog extends JDialog implements Serializable

      • Serialized Fields

        • backgroundPanel
          JPanel backgroundPanel
        • cancelButton
          JButton cancelButton
        • filtersScrollPane
          JScrollPane filtersScrollPane
        • filtersTable
          JTable filtersTable
        • filterTypesLabel
          JLabel filterTypesLabel
        • okButton
          JButton okButton
        • xyPlottingDialog
          XYPlottingDialog xyPlottingDialog
          The XYPlottingDialog parent.
    • Class com.compomics.util.gui.XYPlottingDialog extends JDialog implements Serializable

      • Serialized Fields

        • allTableColumns
          ArrayList<TableColumn> allTableColumns
          The table columns.
        • backgroundPanel
          JPanel backgroundPanel
        • binSizeSpinner
          JSpinner binSizeSpinner
        • binsLabel
          JLabel binsLabel
        • bubbleScalingFactor
          double bubbleScalingFactor
          The bubble scaling factor in percent. 1.0 means no scaling.
        • bubbleSize
          double bubbleSize
          The bubble size.
        • bubbleSizeComboBox
          JComboBox bubbleSizeComboBox
        • bubbleSizeLabel
          JLabel bubbleSizeLabel
        • cellRenderers
          HashMap<Integer,​TableCellRenderer> cellRenderers
          The cell renderers for the table.
        • chartPanel
          org.jfree.chart.ChartPanel chartPanel
          The chart panel.
        • colorGradient
          no.uib.jsparklines.renderers.util.GradientColorCoding.ColorGradient colorGradient
          The color gradient to use.
        • colorLabel
          JLabel colorLabel
        • colorsComboBox
          JComboBox colorsComboBox
        • colummnNames
          Vector<String> colummnNames
          The column names.
        • contextMenuPlotBackgroundPanel
          JPanel contextMenuPlotBackgroundPanel
        • contextMenuSelectedValuesTableBackgroundPanel
          JPanel contextMenuSelectedValuesTableBackgroundPanel
        • dataPointToRowNumber
          HashMap<String,​Integer> dataPointToRowNumber
          The data point to model row number map.
        • densityPlotRadioButton
          JRadioButton densityPlotRadioButton
        • dialogParent
          Frame dialogParent
          The dialog parent.
        • dragButtonGroup
          ButtonGroup dragButtonGroup
        • dragEnd
          Point dragEnd
          The ending location of the mouse dragging.
        • dragSettingsPanel
          JPanel dragSettingsPanel
        • dragStart
          Point dragStart
          The starting location of the mouse dragging.
        • dragToSelectRadioButton
          JRadioButton dragToSelectRadioButton
        • dragToZoomRadioButton
          JRadioButton dragToZoomRadioButton
        • editFiltersButton
          JButton editFiltersButton
        • exportPlotMenuItem
          JMenuItem exportPlotMenuItem
        • exportSelectedValuesMenuItem
          JMenuItem exportSelectedValuesMenuItem
        • filterPanel
          JPanel filterPanel
        • filters
          HashMap<String,​String> filters
          The data filters.
        • hideColumnsMenuItem
          JMenuItem hideColumnsMenuItem
        • histogramColor
          Color histogramColor
          The color used for the bars in the histograms.
        • histogramRadioButton
          JRadioButton histogramRadioButton
        • isPlotting
          boolean isPlotting
          If true, the plot is currently being updated.
        • lastSelectedFolder
          LastSelectedFolder lastSelectedFolder
          The last selected folder.
        • logAcisPanel
          JPanel logAcisPanel
        • maxColumnWidths
          HashMap<Integer,​Integer> maxColumnWidths
          The maximum column widths for the table.
        • minColumnWidths
          HashMap<Integer,​Integer> minColumnWidths
          The minimum column widths for the table.
        • mouseDragged
          boolean mouseDragged
          If true, the mouse is currently being dragged.
        • normalIcon
          Image normalIcon
          The normal icon for the parent dialog.
        • numberOfBins
          int numberOfBins
          The number if bins for the histograms.
        • plotHelpJButton
          JButton plotHelpJButton
        • plotLayeredPane
          JLayeredPane plotLayeredPane
        • plotOptionsJButton
          JButton plotOptionsJButton
        • plotPanel
          JPanel plotPanel
        • plotPopupMenu
          JPopupMenu plotPopupMenu
        • plotTypeButtonGroup
          ButtonGroup plotTypeButtonGroup
        • plotTypePanel
          JPanel plotTypePanel
        • progressDialog
          ProgressDialogX progressDialog
          The progress dialog.
        • regressionLineCheckBoxMenuItem
          JCheckBoxMenuItem regressionLineCheckBoxMenuItem
        • rowsAfterDataFiltering
          ArrayList<Integer> rowsAfterDataFiltering
          The rows remaining after applying the data filters.
        • selectedDataPoints
          HashMap<Integer,​ArrayList<Integer>> selectedDataPoints
          The currently selected data points. The keys are the series keys, while the elements are the lists of data indexes.
        • selectedModelRows
          ArrayList<Integer> selectedModelRows
          The index of the selected rows.
        • selectedValuesLayeredPane
          JLayeredPane selectedValuesLayeredPane
        • selectedValuesPanel
          JPanel selectedValuesPanel
        • selectedValuesScrollPane
          JScrollPane selectedValuesScrollPane
        • selectedValuesTable
          JTable selectedValuesTable
        • selectedValuesTableHelpJButton
          JButton selectedValuesTableHelpJButton
        • selectedValuesTableOptionsJButton
          JButton selectedValuesTableOptionsJButton
        • selectedValuesTablePopupMenu
          JPopupMenu selectedValuesTablePopupMenu
        • selectionActive
          boolean selectionActive
          If true, selection is currently being performed.
        • showRegressionLine
          boolean showRegressionLine
          If true, the regression line is shown.
        • sizeLogCheckBox
          JCheckBox sizeLogCheckBox
        • tableModel
          TableModel tableModel
          The table model.
        • tableToolTips
          ArrayList<String> tableToolTips
          The table column header tool tips.
        • useGradientColorCoding
          boolean useGradientColorCoding
          If true, gradient color coding is used.
        • userDefinedBinSize
          boolean userDefinedBinSize
          If true, the user defined bin size will be used instead of the automatic one.
        • visibleColumns
          HashMap<Integer,​Boolean> visibleColumns
          Boolean indicators of which columns to show.
        • waitingIcon
          Image waitingIcon
          The icon to use when busy.
        • xAxisComboBox
          JComboBox xAxisComboBox
        • xAxisLabel
          JLabel xAxisLabel
        • xAxisLogCheckBox
          JCheckBox xAxisLogCheckBox
        • xAxisPanel
          JPanel xAxisPanel
        • xyPlotPanel
          JPanel xyPlotPanel
        • xyPlotRadioButton
          JRadioButton xyPlotRadioButton
        • yAxisComboBox
          JComboBox yAxisComboBox
        • yAxisLabel
          JLabel yAxisLabel
        • yAxisLogCheckBox
          JCheckBox yAxisLogCheckBox
  • Package com.compomics.util.gui.atoms

    • Class com.compomics.util.gui.atoms.AtomChainDialog extends JDialog implements Serializable

      • Serialized Fields

        • addOnly
          boolean addOnly
          If true, then only adding atoms is allowed.
        • atomChainAdded
          AtomChain atomChainAdded
          The added atom chain edited by the user.
        • atomChainRemoved
          AtomChain atomChainRemoved
          The removed atom chain edited by the user.
        • atomPanelIndex
          int atomPanelIndex
          The atom panel index.
        • backgroundPanel
          JPanel backgroundPanel
        • cancelButton
          JButton cancelButton
        • canceled
          boolean canceled
          Boolean indicating whether the user canceled the input.
        • compositionLbl
          JLabel compositionLbl
        • compositionPanel
          JPanel compositionPanel
        • compositionTxt
          JTextField compositionTxt
        • editPanel
          JPanel editPanel
        • elementsPanel
          JPanel elementsPanel
        • elementsScrollPane
          JScrollPane elementsScrollPane
        • helpJButton
          JButton helpJButton
        • MassLbl
          JLabel MassLbl
        • massTxt
          JTextField massTxt
        • okButton
          JButton okButton
        • settingUpGUI
          boolean settingUpGUI
          True if the GUI is currently being set up.
    • Class com.compomics.util.gui.atoms.AtomPanel extends JPanel implements Serializable

      • Serialized Fields

        • addLabel
          JLabel addLabel
        • atomChainDialog
          AtomChainDialog atomChainDialog
          The parent dialog.
        • atomCmb
          JComboBox atomCmb
        • isotopeCmb
          JComboBox isotopeCmb
        • isotopesMap
          HashMap<String,​Integer> isotopesMap
          Map of the isotopes as displayed: displayed string | isotope number.
        • occurenceSpinner
          JSpinner occurenceSpinner
        • panelIndex
          int panelIndex
          The panel index.
        • removeLabel
          JLabel removeLabel
  • Package com.compomics.util.gui.enzymes

    • Class com.compomics.util.gui.enzymes.EnzymesDialog extends JDialog implements Serializable

      • Serialized Fields

        • addUserEnzyme
          JButton addUserEnzyme
        • defaultEnzymesTableToolTips
          ArrayList<String> defaultEnzymesTableToolTips
          The default enzymes table column header tooltips.
        • deleteEnzymeButton
          JButton deleteEnzymeButton
        • enzymeFactory
          EnzymeFactory enzymeFactory
          The enzymes factory.
        • enzymesEditorPanel
          JPanel enzymesEditorPanel
        • enzymesHelpJButton
          JButton enzymesHelpJButton
        • enzymesPanel
          JPanel enzymesPanel
        • enzymesScrollPane
          JScrollPane enzymesScrollPane
        • enzymesTable
          JTable enzymesTable
        • exportEnzymesLabel
          JLabel exportEnzymesLabel
        • importEnzymesLabel
          JLabel importEnzymesLabel
        • notSelectedRowHtmlTagFontColor
          String notSelectedRowHtmlTagFontColor
          The color to use for the HTML tags for the rows that are not selected, in HTML color code.
        • okButton
          JButton okButton
        • resetEnzymesLabel
          JLabel resetEnzymesLabel
        • selectedRowHtmlTagFontColor
          String selectedRowHtmlTagFontColor
          The color to use for the HTML tags for the selected rows, in HTML color code.
        • userEnzymesTableToolTips
          ArrayList<String> userEnzymesTableToolTips
          The user enzymes table column header tooltips.
    • Class com.compomics.util.gui.enzymes.NewEnzymeDialog extends JDialog implements Serializable

      • Serialized Fields

        • backgroundPanel
          JPanel backgroundPanel
        • butNotAfterLabel
          JLabel butNotAfterLabel
        • butNotAfterTxt
          JTextField butNotAfterTxt
        • butNotBeforeLabel
          JLabel butNotBeforeLabel
        • butNotBeforeTxt
          JTextField butNotBeforeTxt
        • cancelButton
          JButton cancelButton
        • canceled
          boolean canceled
          Boolean indicating whether the dialog was canceled by the user.
        • cleavageRulesPanel
          JPanel cleavageRulesPanel
        • cleavesAfterLabel
          JLabel cleavesAfterLabel
        • cleavesAfterTxt
          JTextField cleavesAfterTxt
        • cleavesBeforeLabel
          JLabel cleavesBeforeLabel
        • cleavesBeforeTxt
          JTextField cleavesBeforeTxt
        • enzymeFactory
          EnzymeFactory enzymeFactory
          The enzymes factory.
        • enzymesDialog
          EnzymesDialog enzymesDialog
          The parent enzymes dialog.
        • helpJButton
          JButton helpJButton
        • nameLabel
          JLabel nameLabel
        • nameTxt
          JTextField nameTxt
        • okButton
          JButton okButton
        • psiMsAccessionJTextField
          JTextField psiMsAccessionJTextField
        • psiMsAccessionLabel
          JLabel psiMsAccessionLabel
        • psiMsLinkLabel
          JLabel psiMsLinkLabel
        • psMsMappingPanel
          JPanel psMsMappingPanel
  • Package com.compomics.util.gui.error_handlers

  • Package com.compomics.util.gui.error_handlers.notification

  • Package com.compomics.util.gui.export.graphics

  • Package com.compomics.util.gui.export.report

  • Package com.compomics.util.gui.file_handling

  • Package com.compomics.util.gui.filtering

  • Package com.compomics.util.gui.genes

    • Class com.compomics.util.gui.genes.GeneDetailsDialog extends JDialog implements Serializable

      • Serialized Fields

        • backgroundPanel
          JPanel backgroundPanel
        • chromosomeLabel
          JLabel chromosomeLabel
        • chromosomeNameTxt
          JTextField chromosomeNameTxt
        • detailsPanel
          JPanel detailsPanel
        • ensemlbIdLabel
          JLabel ensemlbIdLabel
        • geneIdTxt
          JTextField geneIdTxt
        • geneMaps
          GeneMaps geneMaps
          The gene maps.
        • geneNameLabel
          JLabel geneNameLabel
        • geneNameTxt
          JTextField geneNameTxt
        • goAnnotationLabel
          JLabel goAnnotationLabel
        • goTable
          JTable goTable
        • goTableScrollPane
          JScrollPane goTableScrollPane
        • goTermDescriptions
          ArrayList<String> goTermDescriptions
          The GO term descriptions attached to this protein match.
        • notSelectedRowHtmlTagFontColor
          String notSelectedRowHtmlTagFontColor
          The color to use for the HTML tags for the rows that are not selected, in HTML color code.
        • okButton
          JButton okButton
        • proteinAccessionColumn
          ArrayList<String> proteinAccessionColumn
          The protein accession column in the table. Only used if more than one accession.
        • proteinAccessions
          String[] proteinAccessions
          The protein accessions of this match.
        • proteinDetailsProvider
          ProteinDetailsProvider proteinDetailsProvider
          The protein details provider.
        • selectedRowHtmlTagFontColor
          String selectedRowHtmlTagFontColor
          The color to use for the HTML tags for the selected rows, in HTML color code.
    • Class com.compomics.util.gui.genes.SpeciesDialog extends JDialog implements Serializable

      • Serialized Fields

        • backgroundPanel
          JPanel backgroundPanel
          Deprecated.
        • cancelButton
          JButton cancelButton
          Deprecated.
        • canceled
          boolean canceled
          Deprecated.
          Boolean indicating whether the user canceled the editing.
        • chickenLabel
          JLabel chickenLabel
          Deprecated.
        • comma1Label
          JLabel comma1Label
          Deprecated.
        • comma2Label
          JLabel comma2Label
          Deprecated.
        • comma3Label
          JLabel comma3Label
          Deprecated.
        • comma4Label
          JLabel comma4Label
          Deprecated.
        • dialogParent
          JDialog dialogParent
          Deprecated.
          The dialog parent, if any.
        • ensemblCategoryJComboBox
          JComboBox ensemblCategoryJComboBox
          Deprecated.
        • ensemblVersionLabel
          JLabel ensemblVersionLabel
          Deprecated.
        • geneFactory
          ProteinGeneDetailsProvider geneFactory
          Deprecated.
          The gene factory.
        • humanLabel
          JLabel humanLabel
          Deprecated.
        • mouseLabel
          JLabel mouseLabel
          Deprecated.
        • normalImage
          Image normalImage
          Deprecated.
          The icon to display when processing is finished.
        • okButton
          JButton okButton
          Deprecated.
        • parentFrame
          Frame parentFrame
          Deprecated.
          The frame parent, if any.
        • popularSpeciesLabel
          JLabel popularSpeciesLabel
          Deprecated.
        • progressDialog
          ProgressDialogX progressDialog
          Deprecated.
          The progress dialog.
        • ratLabel
          JLabel ratLabel
          Deprecated.
        • selectedSpeciesList
          ArrayList<String> selectedSpeciesList
          Deprecated.
          The selected species.
        • speciesFactory
          SpeciesFactory speciesFactory
          Deprecated.
          The species factory
        • speciesJComboBox
          JComboBox speciesJComboBox
          Deprecated.
        • speciesPanel
          JPanel speciesPanel
          Deprecated.
        • speciesToTaxonMap
          HashMap<String,​Integer> speciesToTaxonMap
          Deprecated.
          A species name to taxon map.
        • unknownSpeciesLabel
          JLabel unknownSpeciesLabel
          Deprecated.
        • updateMappingsButton
          JButton updateMappingsButton
          Deprecated.
        • waitingImage
          Image waitingImage
          Deprecated.
          The icon to display when waiting.
        • zebrafishLabel
          JLabel zebrafishLabel
          Deprecated.
  • Package com.compomics.util.gui.isotopic_calculator

  • Package com.compomics.util.gui.modification

    • Class com.compomics.util.gui.modification.ModificationDialog extends JDialog implements Serializable

      • Serialized Fields

        • addNeutralLoss
          JButton addNeutralLoss
        • addReporterIon
          JButton addReporterIon
        • atomChainAdded
          AtomChain atomChainAdded
          The atom chain added by the modification.
        • atomChainRemoved
          AtomChain atomChainRemoved
          The atom chain removed by the modification.
        • backgroundPanel
          JPanel backgroundPanel
        • cancelButton
          JButton cancelButton
        • canceled
          boolean canceled
          Boolean indicating whether the edition has been canceled by the user.
        • categoryCmb
          JComboBox categoryCmb
        • categoryLabel
          JLabel categoryLabel
        • compositionLabel
          JLabel compositionLabel
        • compositionTxt
          JTextField compositionTxt
        • currentPtm
          Modification currentPtm
          The edited Modification.
        • cvTermSplitPane
          JSplitPane cvTermSplitPane
        • editable
          boolean editable
          Boolean indicating whether the user can edit the Modification or not.
        • helpJButton
          JButton helpJButton
        • massLabel
          JLabel massLabel
        • massTxt
          JTextField massTxt
        • modificationFactory
          ModificationFactory modificationFactory
          The post translational modifications factory.
        • nameLabel
          JLabel nameLabel
        • nameShortLabel
          JLabel nameShortLabel
        • nameShortTxt
          JTextField nameShortTxt
        • nameTxt
          JTextField nameTxt
        • neutralLosses
          ArrayList<NeutralLoss> neutralLosses
          The neutral losses.
        • neutralLossesAndReportIonsTabbedPane
          JTabbedPane neutralLossesAndReportIonsTabbedPane
        • neutralLossesJScrollPane
          JScrollPane neutralLossesJScrollPane
        • neutralLossesPanel
          JPanel neutralLossesPanel
        • neutralLossesTable
          JTable neutralLossesTable
        • neutralLossesTableToolTips
          ArrayList<String> neutralLossesTableToolTips
          The neutral losses table column header tooltips.
        • okButton
          JButton okButton
        • pattern
          AminoAcidPattern pattern
          The amino acid pattern of the modification
        • patternLabel
          JLabel patternLabel
        • patternTxt
          JTextField patternTxt
        • propertiesPanel
          JPanel propertiesPanel
        • psiModAccessionJTextField
          JTextField psiModAccessionJTextField
        • psiModAccessionLabel
          JLabel psiModAccessionLabel
        • psiModLabel
          JLabel psiModLabel
        • psiModLinkLabel
          JLabel psiModLinkLabel
        • psiModNameJTextField
          JTextField psiModNameJTextField
        • psiModNameLabel
          JLabel psiModNameLabel
        • psiModPanel
          JPanel psiModPanel
        • removeNeutralLoss
          JButton removeNeutralLoss
        • removerReporterIon
          JButton removerReporterIon
        • reporterIons
          ArrayList<ReporterIon> reporterIons
          The reporter ions.
        • reporterIonsAndNeutralLossesPanel
          JPanel reporterIonsAndNeutralLossesPanel
        • reporterIonsJScrollPane
          JScrollPane reporterIonsJScrollPane
        • reporterIonsPanel
          JPanel reporterIonsPanel
        • reporterIonsTable
          JTable reporterIonsTable
        • reporterIonTableToolTips
          ArrayList<String> reporterIonTableToolTips
          The reporter ion table column header tooltips.
        • typeCmb
          JComboBox typeCmb
        • typeLabel
          JLabel typeLabel
        • unimodAccessionJTextField
          JTextField unimodAccessionJTextField
        • unimodAccessionLabel
          JLabel unimodAccessionLabel
        • unimodLabel
          JLabel unimodLabel
        • unimodLinkLabel
          JLabel unimodLinkLabel
        • unimodMappingPanel
          JPanel unimodMappingPanel
        • unimodNameJTextField
          JTextField unimodNameJTextField
        • unimodNameLabel
          JLabel unimodNameLabel
        • unimodPanel
          JPanel unimodPanel
    • Class com.compomics.util.gui.modification.ModificationsDialog extends JDialog implements Serializable

      • Serialized Fields

        • addUserModification
          JButton addUserModification
        • defaultModificationsTable
          JTable defaultModificationsTable
        • defaultModsPanel
          JPanel defaultModsPanel
        • defaultModsPopupMenu
          JPopupMenu defaultModsPopupMenu
        • defaultModsScrollPane
          JScrollPane defaultModsScrollPane
        • defaultModsTableToolTips
          ArrayList<String> defaultModsTableToolTips
          The default mods table column header tooltips.
        • deleteUserModification
          JButton deleteUserModification
        • editUserModification
          JButton editUserModification
        • editUserPtmJMenuItem
          JMenuItem editUserPtmJMenuItem
        • exportDefaultModsLabel
          JLabel exportDefaultModsLabel
        • exportUserModsLabel
          JLabel exportUserModsLabel
        • findJLabel
          JLabel findJLabel
        • modificationFactory
          ModificationFactory modificationFactory
          The post translational modifications factory.
        • modificationsEditorPanel
          JPanel modificationsEditorPanel
        • modificationsHelpJButton
          JButton modificationsHelpJButton
        • modificationsSplitPane
          JSplitPane modificationsSplitPane
        • notSelectedRowHtmlTagFontColor
          String notSelectedRowHtmlTagFontColor
          The color to use for the HTML tags for the rows that are not selected, in HTML color code.
        • okButton
          JButton okButton
        • searchCurrentSelection
          int searchCurrentSelection
          The search current selection.
        • searchIndexLabel
          JLabel searchIndexLabel
        • searchInputTxt
          JTextField searchInputTxt
        • searchNextButton
          JButton searchNextButton
        • searchPossibilities
          ArrayList<Integer> searchPossibilities
          The lines of the Modifications concerned by the search.
        • searchPreviousButton
          JButton searchPreviousButton
        • searchWelcomeText
          String searchWelcomeText
          The search text to display by default.
        • selectedRowHtmlTagFontColor
          String selectedRowHtmlTagFontColor
          The color to use for the HTML tags for the selected rows, in HTML color code.
        • sparklineColor
          Color sparklineColor
          The color used for the sparkline bar chart plots.
        • userModificationsTable
          JTable userModificationsTable
        • userModsPanel
          JPanel userModsPanel
        • userModsPopupMenu
          JPopupMenu userModsPopupMenu
        • userModsScrollPane
          JScrollPane userModsScrollPane
        • userModsTableToolTips
          ArrayList<String> userModsTableToolTips
          The user mods table column header tooltips.
        • viewDefaultModsJMenuItem
          JMenuItem viewDefaultModsJMenuItem
    • Class com.compomics.util.gui.modification.ModificationTable extends JTable implements Serializable

      • Serialized Fields

        • annotationParameters
          AnnotationParameters annotationParameters
          The annotation parameters.
        • areaChart
          boolean areaChart
          If true, area charts are used, false results in bar charts.
        • identification
          Identification identification
          The identification object.
        • maxAreaChartValue
          double maxAreaChartValue
          The max value for the area charts.
        • modification
          Modification modification
          The PTM to analyze.
        • modificationParameters
          ModificationParameters modificationParameters
          The modification parameters.
        • modificationSequenceMatchingParameters
          SequenceMatchingParameters modificationSequenceMatchingParameters
          The modification sequence matching parameters.
        • modificationSites
          ArrayList<Integer> modificationSites
          A list of the modification site indexes.
        • nModifications
          int nModifications
          Number of PTMs.
        • peptideMatch
          PeptideMatch peptideMatch
          The peptide match.
        • sequenceProvider
          SequenceProvider sequenceProvider
          The protein sequence provider.
        • spectrumProvider
          SpectrumProvider spectrumProvider
          The spectrum provider.
        • tooltips
          ArrayList<String> tooltips
          The table tooltips.
  • Package com.compomics.util.gui.parameters

    • Class com.compomics.util.gui.parameters.SparklineColorsDialog extends JDialog implements Serializable

      • Serialized Fields

        • backgroundPanel
          JPanel backgroundPanel
        • doubtfulColorLabel
          JLabel doubtfulColorLabel
        • doubtfulColorPanel
          JPanel doubtfulColorPanel
        • falsePositiveColorLabel
          JLabel falsePositiveColorLabel
        • falsePositiveColorPanel
          JPanel falsePositiveColorPanel
        • mirroredPeakColorLabel3
          JLabel mirroredPeakColorLabel3
        • mirroredPeakColorPanel2
          JPanel mirroredPeakColorPanel2
        • notFoundColorLabel
          JLabel notFoundColorLabel
        • notFoundColorPanel
          JPanel notFoundColorPanel
        • notValidatedColorLabel
          JLabel notValidatedColorLabel
        • notValidatedColorPanel
          JPanel notValidatedColorPanel
        • okButton
          JButton okButton
        • possibleColorLabel
          JLabel possibleColorLabel
        • possibleColorPanel
          JPanel possibleColorPanel
        • sparklineColorsPanel
          JPanel sparklineColorsPanel
        • utilitiesUserParameters
          UtilitiesUserParameters utilitiesUserParameters
          The utilities user parameters object.
        • validatedColorLabel
          JLabel validatedColorLabel
        • validatedColorPanel
          JPanel validatedColorPanel
  • Package com.compomics.util.gui.parameters.identification

  • Package com.compomics.util.gui.parameters.identification.advanced

  • Package com.compomics.util.gui.parameters.identification.algorithm

    • Class com.compomics.util.gui.parameters.identification.algorithm.AndromedaParametersDialog extends JDialog implements Serializable

      • Serialized Fields

        • advancedSettingsWarningLabel
          JLabel advancedSettingsWarningLabel
        • ammoniaLossCmb
          JComboBox ammoniaLossCmb
        • ammoniaLossLabel
          JLabel ammoniaLossLabel
        • backgroundPanel
          JPanel backgroundPanel
        • cancelled
          boolean cancelled
          Boolean indicating whether the used canceled the editing.
        • closeButton
          JButton closeButton
        • decoyModeCmb
          JComboBox decoyModeCmb
        • decoyModeLabel
          JLabel decoyModeLabel
        • editable
          boolean editable
          Boolean indicating whether the settings can be edited by the user.
        • empiricalCorrectionCombo
          JComboBox empiricalCorrectionCombo
        • empiricalCorrectionLabel
          JLabel empiricalCorrectionLabel
        • equalILCombo
          JComboBox equalILCombo
        • equalILLabel
          JLabel equalILLabel
        • fragmentAllCmb
          JComboBox fragmentAllCmb
        • fragmentAllLabel
          JLabel fragmentAllLabel
        • fragMethodCmb
          JComboBox fragMethodCmb
        • fragMethodLabel
          JLabel fragMethodLabel
        • higherChargeCombo
          JComboBox higherChargeCombo
        • higherChargeLabel
          JLabel higherChargeLabel
        • maxCombinationsLabel
          JLabel maxCombinationsLabel
        • maxCombinationsTxt
          JTextField maxCombinationsTxt
        • maxPepLengthNoEnzymeTxt
          JTextField maxPepLengthNoEnzymeTxt
        • maxPeptideMassLabel
          JLabel maxPeptideMassLabel
        • maxPeptideMassTxt
          JTextField maxPeptideMassTxt
        • maxPtmsLabel
          JLabel maxPtmsLabel
        • maxPtmsTxt
          JTextField maxPtmsTxt
        • minPepLengthNoEnzymeTxt
          JTextField minPepLengthNoEnzymeTxt
        • neutralLossesCmb
          JComboBox neutralLossesCmb
        • neutralLossesLabel
          JLabel neutralLossesLabel
        • numberMatchesLabel
          JLabel numberMatchesLabel
        • numberMatchesTxt
          JTextField numberMatchesTxt
        • okButton
          JButton okButton
        • openDialogHelpJButton
          JButton openDialogHelpJButton
        • peptideLengthNoEnzymeDividerLabel
          JLabel peptideLengthNoEnzymeDividerLabel
        • peptideLengthNoEnzymeLabel
          JLabel peptideLengthNoEnzymeLabel
        • settingsInnerPanel
          JPanel settingsInnerPanel
        • settingsPanel
          JPanel settingsPanel
        • settingsScrollPane
          JScrollPane settingsScrollPane
        • topPeaksLabel
          JLabel topPeaksLabel
        • topPeaksTxt
          JTextField topPeaksTxt
        • topPeaksWindowLabel
          JLabel topPeaksWindowLabel
        • topPeaksWindowTxt
          JTextField topPeaksWindowTxt
        • waterLossCombo
          JComboBox waterLossCombo
        • waterLossLabel
          JLabel waterLossLabel
    • Class com.compomics.util.gui.parameters.identification.algorithm.CometParametersDialog extends JDialog implements Serializable

      • Serialized Fields

        • advancedSettingsWarningLabel
          JLabel advancedSettingsWarningLabel
        • backgroundPanel
          JPanel backgroundPanel
        • batchSizeLabel
          JLabel batchSizeLabel
        • batchSizeTxt
          JTextField batchSizeTxt
        • cancelled
          boolean cancelled
          Boolean indicating whether the used canceled the editing.
        • clearMzRangeDividerLabel
          JLabel clearMzRangeDividerLabel
        • clearMzRangeLabel
          JLabel clearMzRangeLabel
        • clearMzRangeLowerTxt
          JTextField clearMzRangeLowerTxt
        • clearMzRangeUpperTxt
          JTextField clearMzRangeUpperTxt
        • closeButton
          JButton closeButton
        • correlationScoreTypeCmb
          JComboBox correlationScoreTypeCmb
        • correlationScoreTypeLabel
          JLabel correlationScoreTypeLabel
        • editable
          boolean editable
          Boolean indicating whether the settings can be edited by the user.
        • enzymeTypeCmb
          JComboBox enzymeTypeCmb
        • enzymeTypeLabel
          JLabel enzymeTypeLabel
        • fragmentBinOffsetLabel
          JLabel fragmentBinOffsetLabel
        • fragmentBinOffsetTxt
          JTextField fragmentBinOffsetTxt
        • fragmentIonsPanel
          JPanel fragmentIonsPanel
        • isotopeCorrectionCmb
          JComboBox isotopeCorrectionCmb
        • isotopeCorrectionLabel
          JLabel isotopeCorrectionLabel
        • maxFragmentChargeLabel
          JLabel maxFragmentChargeLabel
        • maxFragmentChargeTxt
          JTextField maxFragmentChargeTxt
        • maxPepLengthTxt
          JTextField maxPepLengthTxt
        • maxPrecursorMassTxt
          JTextField maxPrecursorMassTxt
        • maxPtmsLabel
          JLabel maxPtmsLabel
        • maxPtmsTxt
          JTextField maxPtmsTxt
        • minPeakIntensityLbl
          JLabel minPeakIntensityLbl
        • minPeakIntensityTxt
          JTextField minPeakIntensityTxt
        • minPeaksLbl
          JLabel minPeaksLbl
        • minPeaksTxt
          JTextField minPeaksTxt
        • minPepLengthTxt
          JTextField minPepLengthTxt
        • minPrecursorMassTxt
          JTextField minPrecursorMassTxt
        • numberMatchesLabel
          JLabel numberMatchesLabel
        • numberMatchesTxt
          JTextField numberMatchesTxt
        • okButton
          JButton okButton
        • openDialogHelpJButton
          JButton openDialogHelpJButton
        • outputFormatCmb
          JComboBox outputFormatCmb
        • outputPanel
          JPanel outputPanel
        • outputPepXmlLabel
          JLabel outputPepXmlLabel
        • peptideLengthDividerLabel
          JLabel peptideLengthDividerLabel
        • peptideLengthLabel
          JLabel peptideLengthLabel
        • precursorMassDividerLabel
          JLabel precursorMassDividerLabel
        • precursorMassLabel
          JLabel precursorMassLabel
        • printExpecScoreLabel
          JLabel printExpecScoreLabel
        • printExpectScoreCmb
          JComboBox printExpectScoreCmb
        • removeMethionineCmb
          JComboBox removeMethionineCmb
        • removeMethionineLabel
          JLabel removeMethionineLabel
        • removePrecursorPeakCombo
          JComboBox removePrecursorPeakCombo
        • removePrecursorPeakLabel
          JLabel removePrecursorPeakLabel
        • removePrecursorPeakToleranceLbl
          JLabel removePrecursorPeakToleranceLbl
        • removePrecursorPeakToleranceTxt
          JTextField removePrecursorPeakToleranceTxt
        • requireVariablePtmCmb
          JComboBox requireVariablePtmCmb
        • requireVariablePtmLabel
          JLabel requireVariablePtmLabel
        • searchSettingsPanel
          JPanel searchSettingsPanel
        • spectrumProcessingPanel
          JPanel spectrumProcessingPanel
        • tabbedPane
          JTabbedPane tabbedPane
    • Class com.compomics.util.gui.parameters.identification.algorithm.DirecTagParametersDialog extends JDialog implements Serializable

      • Serialized Fields

        • adjustPrecursorMassCmb
          JComboBox adjustPrecursorMassCmb
        • adjustPrecursorMassLabel
          JLabel adjustPrecursorMassLabel
        • backgroundPanel
          JPanel backgroundPanel
        • cancelButton
          JButton cancelButton
        • canceled
          boolean canceled
          True if the dialog was canceled by the user.
        • complementScoreWeightLabel
          JLabel complementScoreWeightLabel
        • complementScoreWeightTextField
          JTextField complementScoreWeightTextField
        • complementToleranceLabel
          JLabel complementToleranceLabel
        • complementToleranceTextField
          JTextField complementToleranceTextField
        • deisotopingModeLabel
          JLabel deisotopingModeLabel
        • deisptopingModeTextField
          JTextField deisptopingModeTextField
        • directTagPanel
          JPanel directTagPanel
        • duplicateSpectraLabel
          JLabel duplicateSpectraLabel
        • duplicateSpectraPerChargeCmb
          JComboBox duplicateSpectraPerChargeCmb
        • editable
          boolean editable
          Boolean indicating whether the settings can be edited by the user.
        • intensityScoreWeightLabel
          JLabel intensityScoreWeightLabel
        • intensityScoreWeightTextField
          JTextField intensityScoreWeightTextField
        • isotopeToleranceLabel
          JLabel isotopeToleranceLabel
        • isotopeToleranceTextField
          JTextField isotopeToleranceTextField
        • maxPeakCountLabel
          JLabel maxPeakCountLabel
        • maxPeakCountTextField
          JTextField maxPeakCountTextField
        • maxPrecursorAdjustmentLabel
          JLabel maxPrecursorAdjustmentLabel
        • maxPrecursorAdjustmentTextField
          JTextField maxPrecursorAdjustmentTextField
        • maxTagCountLabel
          JLabel maxTagCountLabel
        • maxTagCountSpinner
          JSpinner maxTagCountSpinner
        • minPrecursorAdjustmentLabel
          JLabel minPrecursorAdjustmentLabel
        • minPrecursorAdjustmentTextField
          JTextField minPrecursorAdjustmentTextField
        • mzFidelityScoreWeightLabel
          JLabel mzFidelityScoreWeightLabel
        • mzFidelityScoreWeightTextField
          JTextField mzFidelityScoreWeightTextField
        • numberOfChargeStatesLabel
          JLabel numberOfChargeStatesLabel
        • numberOfChargeStatesTextField
          JTextField numberOfChargeStatesTextField
        • numberOfIntensityClassesLabel
          JLabel numberOfIntensityClassesLabel
        • numberOfIntensityClassesTextField
          JTextField numberOfIntensityClassesTextField
        • numVariableModsLabel
          JLabel numVariableModsLabel
        • numVariableModsTextField
          JTextField numVariableModsTextField
        • okButton
          JButton okButton
        • openDialogHelpJButton
          JButton openDialogHelpJButton
        • outputSuffixLabel
          JLabel outputSuffixLabel
        • outputSuffixTextField
          JTextField outputSuffixTextField
        • precursorAdjustmentStepLabel
          JLabel precursorAdjustmentStepLabel
        • precursorAdjustmentStepTextField
          JTextField precursorAdjustmentStepTextField
        • tagLengthLabel
          JLabel tagLengthLabel
        • tagLengthTextField
          JTextField tagLengthTextField
        • ticCutoffLabel
          JLabel ticCutoffLabel
        • ticCutoffTextField
          JTextField ticCutoffTextField
        • useSpectrumChargeStateCmb
          JComboBox useSpectrumChargeStateCmb
        • useSpectrumChargeStateLabel
          JLabel useSpectrumChargeStateLabel
    • Class com.compomics.util.gui.parameters.identification.algorithm.MetaMorpheusParametersDialog extends JDialog implements Serializable

      • Serialized Fields

        • advancedSettingsWarningLabel
          JLabel advancedSettingsWarningLabel
        • backgroundPanel
          JPanel backgroundPanel
        • cancelled
          boolean cancelled
          Boolean indicating whether the used canceled the editing.
        • closeButton
          JButton closeButton
        • deconvIntRatioLbl
          JLabel deconvIntRatioLbl
        • deconvIntRatioTxt
          JTextField deconvIntRatioTxt
        • deconvMassToleranceLbl
          JLabel deconvMassToleranceLbl
        • deconvMassToleranceTxt
          JTextField deconvMassToleranceTxt
        • deconvMassToleranceTypeCmb
          JComboBox deconvMassToleranceTypeCmb
        • deconvMassToleranceTypeLbl
          JLabel deconvMassToleranceTypeLbl
        • decoyTypeCmb
          JComboBox decoyTypeCmb
        • decoyTypeLbl
          JLabel decoyTypeLbl
        • deisotopingPanel
          JPanel deisotopingPanel
        • dissociationTypeCombo
          JComboBox dissociationTypeCombo
        • dissociationTypeLbl
          JLabel dissociationTypeLbl
        • doPrecDeconvCmb
          JComboBox doPrecDeconvCmb
        • doPrecDeconvLbl
          JLabel doPrecDeconvLbl
        • editable
          boolean editable
          Boolean indicating whether the settings can be edited by the user.
        • excludeOneHitWondersCmb
          JComboBox excludeOneHitWondersCmb
        • excludeOneHitWondersLbl
          JLabel excludeOneHitWondersLbl
        • fragmentationTerminusCmb
          JComboBox fragmentationTerminusCmb
        • fragmentationTerminusLbl
          JLabel fragmentationTerminusLbl
        • gptmPanel
          JPanel gptmPanel
        • gPtmScrollPane
          JScrollPane gPtmScrollPane
        • gPtmTable
          JTable gPtmTable
        • inSilicoDigestionPanel
          JPanel inSilicoDigestionPanel
        • intitiatorMethBehaviorCombo
          JComboBox intitiatorMethBehaviorCombo
        • intitiatorMethBehaviorLabel
          JLabel intitiatorMethBehaviorLabel
        • jSeparator1
          JSeparator jSeparator1
        • massDiffAcceptorTypeCmb
          JComboBox massDiffAcceptorTypeCmb
        • massDiffAcceptorTypeLbl
          JLabel massDiffAcceptorTypeLbl
        • maxFragmentSizeLbl
          JLabel maxFragmentSizeLbl
        • maxFragmentSizeTxt
          JTextField maxFragmentSizeTxt
        • maxHetroVariantsLbl
          JLabel maxHetroVariantsLbl
        • maxHetroVariantsTxt
          JTextField maxHetroVariantsTxt
        • maxModIsoformsLbl
          JLabel maxModIsoformsLbl
        • maxModIsoformsTxt
          JTextField maxModIsoformsTxt
        • maxNumModPeptideLbl
          JLabel maxNumModPeptideLbl
        • maxNumModPeptideTxt
          JTextField maxNumModPeptideTxt
        • maxPepLengthTxt
          JTextField maxPepLengthTxt
        • minAllowedIntensityRatioToBasePeakLbl
          JLabel minAllowedIntensityRatioToBasePeakLbl
        • minAllowedIntensityRatioToBasePeakTxt
          JTextField minAllowedIntensityRatioToBasePeakTxt
        • minPepLengthTxt
          JTextField minPepLengthTxt
        • minVariantDepthLabel
          JLabel minVariantDepthLabel
        • minVariantDepthTxt
          JTextField minVariantDepthTxt
        • modifiedPeptidesAreDifferentCmb
          JComboBox modifiedPeptidesAreDifferentCmb
        • modifiedPeptidesAreDifferentLbl
          JLabel modifiedPeptidesAreDifferentLbl
        • normalizePeaksAcrossAllWindowsCmb
          JComboBox normalizePeaksAcrossAllWindowsCmb
        • normalizePeaksAcrossAllWindowsLbl
          JLabel normalizePeaksAcrossAllWindowsLbl
        • numberOfPartitionsLbl
          JLabel numberOfPartitionsLbl
        • numberOfPartitionsTxt
          JTextField numberOfPartitionsTxt
        • numberOfWindowsLbl
          JLabel numberOfWindowsLbl
        • numberOfWindowsTxt
          JTextField numberOfWindowsTxt
        • numPeaksPerWindowLbl
          JLabel numPeaksPerWindowLbl
        • numPeaksPerWindowTxt
          JTextField numPeaksPerWindowTxt
        • okButton
          JButton okButton
        • openDialogHelpJButton
          JButton openDialogHelpJButton
        • outputPanel
          JPanel outputPanel
        • peakTrimmingPanel
          JPanel peakTrimmingPanel
        • peptideLengthDividerLabel
          JLabel peptideLengthDividerLabel
        • peptideLengthJLabel
          JLabel peptideLengthJLabel
        • proteinGroupingPanel
          JPanel proteinGroupingPanel
        • runGptmLbl
          JLabel runGptmLbl
        • runGtpmCmb
          JComboBox runGtpmCmb
        • scoreCutoffLabel
          JLabel scoreCutoffLabel
        • scoreCutoffTxt
          JTextField scoreCutoffTxt
        • searchPanel
          JPanel searchPanel
        • searchTargetComboBox
          JComboBox searchTargetComboBox
        • searchTargetLabel
          JLabel searchTargetLabel
        • searchTypeCombo
          JComboBox searchTypeCombo
        • searchTypeLabel
          JLabel searchTypeLabel
        • tabbedPane
          JTabbedPane tabbedPane
        • trimMs1Cmb
          JComboBox trimMs1Cmb
        • trimMs1Lbl
          JLabel trimMs1Lbl
        • trimMsMsCmb
          JComboBox trimMsMsCmb
        • trimMsMsLbl
          JLabel trimMsMsLbl
        • useDeltaScoreCmb
          JComboBox useDeltaScoreCmb
        • useDeltaScoreLbl
          JLabel useDeltaScoreLbl
        • useProvidedPrecCmb
          JComboBox useProvidedPrecCmb
        • useProvidedPrecLabel
          JLabel useProvidedPrecLabel
        • windowWidthThompsonLbl
          JLabel windowWidthThompsonLbl
        • windowWidthThompsonTxt
          JTextField windowWidthThompsonTxt
        • writeMzidCmb
          JComboBox writeMzidCmb
        • writeMzidLbl
          JLabel writeMzidLbl
        • writePepXmlCmb
          JComboBox writePepXmlCmb
        • writePepXmlLbl
          JLabel writePepXmlLbl
    • Class com.compomics.util.gui.parameters.identification.algorithm.MsAmandaParametersDialog extends JDialog implements Serializable

      • Serialized Fields

        • advancedSearchSettingsPanel
          JPanel advancedSearchSettingsPanel
        • advancedSettingsWarningLabel
          JLabel advancedSettingsWarningLabel
        • backgroundPanel
          JPanel backgroundPanel
        • cancelled
          boolean cancelled
          Boolean indicating whether the used canceled the editing.
        • closeButton
          JButton closeButton
        • decoyDatabaseCmb
          JComboBox decoyDatabaseCmb
        • decoyDatabaseLabel
          JLabel decoyDatabaseLabel
        • editable
          boolean editable
          Boolean indicating whether the settings can be edited by the user.
        • instrumentCmb
          JComboBox instrumentCmb
        • instrumentLabel
          JLabel instrumentLabel
        • maxModPerPeptideCmb
          JComboBox maxModPerPeptideCmb
        • maxModPerPeptideLabel
          JLabel maxModPerPeptideLabel
        • maxNeutralLossesPerPeptideCmb
          JComboBox maxNeutralLossesPerPeptideCmb
        • maxNeutralLossesPerPeptideLabel
          JLabel maxNeutralLossesPerPeptideLabel
        • maxPeptideLengthTxt
          JTextField maxPeptideLengthTxt
        • maxPotentialModSitePerPeptideCmb
          JComboBox maxPotentialModSitePerPeptideCmb
        • maxPotentialModSitePerPeptideLabel
          JLabel maxPotentialModSitePerPeptideLabel
        • maxProteinsLoadedLabel
          JLabel maxProteinsLoadedLabel
        • maxProteinsLoadedTxt
          JTextField maxProteinsLoadedTxt
        • maxPtmNeutalLossesPerPeptideCmb
          JComboBox maxPtmNeutalLossesPerPeptideCmb
        • maxPtmNeutalLossesPerPeptideLabel
          JLabel maxPtmNeutalLossesPerPeptideLabel
        • maxRankLabel
          JLabel maxRankLabel
        • maxRankTxt
          JTextField maxRankTxt
        • maxSpectraLoadedLabel
          JLabel maxSpectraLoadedLabel
        • maxSpectraLoadedTxt
          JTextField maxSpectraLoadedTxt
        • maxVariableModPerPeptideCmb
          JComboBox maxVariableModPerPeptideCmb
        • maxVariableModPerPeptideLabel
          JLabel maxVariableModPerPeptideLabel
        • minPeptideLengthTxt
          JTextField minPeptideLengthTxt
        • monoIsotopicCmb
          JComboBox monoIsotopicCmb
        • monoIsotopicLabel
          JLabel monoIsotopicLabel
        • okButton
          JButton okButton
        • openDialogHelpJButton
          JButton openDialogHelpJButton
        • outputFormatCmb
          JComboBox outputFormatCmb
        • outputFormatLabel
          JLabel outputFormatLabel
        • peptideLengthDividerLabel
          JLabel peptideLengthDividerLabel
        • peptideLengthLabel
          JLabel peptideLengthLabel
        • performDeisotopingCmb
          JComboBox performDeisotopingCmb
        • performDeisotopingLabel
          JLabel performDeisotopingLabel
        • rankTargetAndDecoySeparatelyCmb
          JComboBox rankTargetAndDecoySeparatelyCmb
        • rankTargetAndDecoySeparatelyLabel
          JLabel rankTargetAndDecoySeparatelyLabel
    • Class com.compomics.util.gui.parameters.identification.algorithm.MsgfParametersDialog extends JDialog implements Serializable

      • Serialized Fields

        • additionalOutputCmb
          JComboBox additionalOutputCmb
        • additionalOutputLabel
          JLabel additionalOutputLabel
        • advancedSearchSettingsPanel
          JPanel advancedSearchSettingsPanel
        • advancedSettingsWarningLabel
          JLabel advancedSettingsWarningLabel
        • backgroundPanel
          JPanel backgroundPanel
        • cancelled
          boolean cancelled
          Boolean indicating whether the used canceled the editing.
        • closeButton
          JButton closeButton
        • decoyDatabaseCmb
          JComboBox decoyDatabaseCmb
        • decoyDatabaseLabel
          JLabel decoyDatabaseLabel
        • editable
          boolean editable
          Boolean indicating whether the settings can be edited by the user.
        • fragmentationMethodCmb
          JComboBox fragmentationMethodCmb
        • fragmentationMethodLabel
          JLabel fragmentationMethodLabel
        • instrumentCmb
          JComboBox instrumentCmb
        • instrumentLabel
          JLabel instrumentLabel
        • maxPepLengthTxt
          JTextField maxPepLengthTxt
        • maxPtmsLabel
          JLabel maxPtmsLabel
        • maxPtmsTxt
          JTextField maxPtmsTxt
        • minPepLengthTxt
          JTextField minPepLengthTxt
        • numberMatchesLabel
          JLabel numberMatchesLabel
        • numberMatchesTxt
          JTextField numberMatchesTxt
        • numberOfTasksLabel
          JLabel numberOfTasksLabel
        • numberOfTasksTxt
          JTextField numberOfTasksTxt
        • numberTerminiLabel
          JLabel numberTerminiLabel
        • okButton
          JButton okButton
        • openDialogHelpJButton
          JButton openDialogHelpJButton
        • peptideLengthDividerLabel
          JLabel peptideLengthDividerLabel
        • peptideLengthLabel
          JLabel peptideLengthLabel
        • protocolCmb
          JComboBox protocolCmb
        • protocolLabel
          JLabel protocolLabel
        • terminiCmb
          JComboBox terminiCmb
    • Class com.compomics.util.gui.parameters.identification.algorithm.MyriMatchParametersDialog extends JDialog implements Serializable

      • Serialized Fields

        • advancedSearchSettingsPanel
          JPanel advancedSearchSettingsPanel
        • advancedSettingsPanel
          JPanel advancedSettingsPanel
        • advancedSettingsWarningLabel
          JLabel advancedSettingsWarningLabel
        • backgroundPanel
          JPanel backgroundPanel
        • cancelled
          boolean cancelled
          Boolean indicating whether the used canceled the editing.
        • classSizeMultiplierLabel
          JLabel classSizeMultiplierLabel
        • classSizeMultiplierTxt
          JTextField classSizeMultiplierTxt
        • closeButton
          JButton closeButton
        • computeXCorrCmb
          JComboBox computeXCorrCmb
        • computeXCorrlLabel
          JLabel computeXCorrlLabel
        • editable
          boolean editable
          Boolean indicating whether the settings can be edited by the user.
        • fragmentationMethodCmb
          JComboBox fragmentationMethodCmb
        • fragmentationMethodLabel
          JLabel fragmentationMethodLabel
        • maxPeakCountLabel
          JLabel maxPeakCountLabel
        • maxPeakCountTxt
          JTextField maxPeakCountTxt
        • maxPepLengthTxt
          JTextField maxPepLengthTxt
        • maxPrecursorMassTxt
          JTextField maxPrecursorMassTxt
        • maxPtmsLabel
          JLabel maxPtmsLabel
        • maxPtmsTxt
          JTextField maxPtmsTxt
        • minPepLengthTxt
          JTextField minPepLengthTxt
        • minPrecursorMassTxt
          JTextField minPrecursorMassTxt
        • numbBatchesLabel
          JLabel numbBatchesLabel
        • numbBatchesTxt
          JTextField numbBatchesTxt
        • numberMatchesLabel
          JLabel numberMatchesLabel
        • numberMatchesTxt
          JTextField numberMatchesTxt
        • numberTerminiLabel
          JLabel numberTerminiLabel
        • numIntensityClassesLabel
          JLabel numIntensityClassesLabel
        • numIntensityClassesTxt
          JTextField numIntensityClassesTxt
        • okButton
          JButton okButton
        • openDialogHelpJButton
          JButton openDialogHelpJButton
        • outputFormatCmb
          JComboBox outputFormatCmb
        • outputFormatLabel
          JLabel outputFormatLabel
        • peptideLengthDividerLabel
          JLabel peptideLengthDividerLabel
        • peptideLengthLabel
          JLabel peptideLengthLabel
        • precursorMassDividerLabel
          JLabel precursorMassDividerLabel
        • precursorMassLabel
          JLabel precursorMassLabel
        • scrollPane
          JScrollPane scrollPane
        • terminiCmb
          JComboBox terminiCmb
        • ticCutoffPercentageLabel
          JLabel ticCutoffPercentageLabel
        • ticCutoffPercentageTxt
          JTextField ticCutoffPercentageTxt
        • useSmartPlusThreeModelCmb
          JComboBox useSmartPlusThreeModelCmb
        • useSmartPlusThreeModelLabel
          JLabel useSmartPlusThreeModelLabel
    • Class com.compomics.util.gui.parameters.identification.algorithm.NovorParametersDialog extends JDialog implements Serializable

      • Serialized Fields

        • backgroundPanel
          JPanel backgroundPanel
        • cancelButton
          JButton cancelButton
        • canceled
          boolean canceled
          True if the dialog was canceled by the user.
        • editable
          boolean editable
          Boolean indicating whether the settings can be edited by the user.
        • fragmentationMethodCmb
          JComboBox fragmentationMethodCmb
        • fragmentationMethodLabel
          JLabel fragmentationMethodLabel
        • massAnalyzerCmb
          JComboBox massAnalyzerCmb
        • massAnalyzerLabel
          JLabel massAnalyzerLabel
        • novorPanel
          JPanel novorPanel
        • okButton
          JButton okButton
        • openDialogHelpJButton
          JButton openDialogHelpJButton
    • Class com.compomics.util.gui.parameters.identification.algorithm.OmssaParametersDialog extends JDialog implements Serializable

      • Serialized Fields

        • advancedSearchSettingsPanel
          JPanel advancedSearchSettingsPanel
        • advancedSettingsWarningLabel
          JLabel advancedSettingsWarningLabel
        • backgroundPanel
          JPanel backgroundPanel
        • cancelled
          boolean cancelled
          Boolean indicating whether the used canceled the editing.
        • chargeEstimationCombo
          JComboBox chargeEstimationCombo
        • chargeReductionLabel
          JLabel chargeReductionLabel
        • cleaveNterminalMethionineCmb
          JComboBox cleaveNterminalMethionineCmb
        • cleaveNterminalMethionineLbl
          JLabel cleaveNterminalMethionineLbl
        • closeButton
          JButton closeButton
        • consecutiveIonProbabilityLbl
          JLabel consecutiveIonProbabilityLbl
        • consecutiveIonProbabilityTxt
          JTextField consecutiveIonProbabilityTxt
        • correlationCorrectionScoreCmb
          JComboBox correlationCorrectionScoreCmb
        • correlationCorrectionScoreLbl
          JLabel correlationCorrectionScoreLbl
        • cTermIonsCmb
          JComboBox cTermIonsCmb
        • cTermIonsLbl
          JLabel cTermIonsLbl
        • databaseProcessingPanel
          JPanel databaseProcessingPanel
        • doublyChargedNPeaksLbl
          JLabel doublyChargedNPeaksLbl
        • doublyChargedNpeaksTxt
          JTextField doublyChargedNpeaksTxt
        • doublyChargedWindowWidthLbl
          JLabel doublyChargedWindowWidthLbl
        • doublyChargedWindowWidthTxt
          JTextField doublyChargedWindowWidthTxt
        • editable
          boolean editable
          Boolean indicating whether the settings can be edited by the user.
        • eliminatePrecursorCombo
          JComboBox eliminatePrecursorCombo
        • eValueLbl
          JLabel eValueLbl
        • forwardIonsFirstCmb
          JComboBox forwardIonsFirstCmb
        • forwardIonsFirstLbl
          JLabel forwardIonsFirstLbl
        • fractionChargeLbl
          JLabel fractionChargeLbl
        • fractionChargeTxt
          JTextField fractionChargeTxt
        • highIntensityLbl
          JLabel highIntensityLbl
        • highIntensityTxt
          JTextField highIntensityTxt
        • hitListLbl
          JLabel hitListLbl
        • hitlistTxt
          JTextField hitlistTxt
        • intensityIncrementLbl
          JLabel intensityIncrementLbl
        • intensityIncrementTxt
          JTextField intensityIncrementTxt
        • iterativeReplaceEvalueLbl
          JLabel iterativeReplaceEvalueLbl
        • iterativeReplaceEvalueTxt
          JTextField iterativeReplaceEvalueTxt
        • iterativeSearchSettingsPanel
          JPanel iterativeSearchSettingsPanel
        • iterativeSequenceEvalueLbl
          JLabel iterativeSequenceEvalueLbl
        • iterativeSequenceEvalueTxt
          JTextField iterativeSequenceEvalueTxt
        • iterativeSpectraEvalueLbl
          JLabel iterativeSpectraEvalueLbl
        • iterativeSpectraEvalueTxt
          JTextField iterativeSpectraEvalueTxt
        • jSeparator1
          JSeparator jSeparator1
        • lowIntensityLbl
          JLabel lowIntensityLbl
        • lowIntensityTxt
          JTextField lowIntensityTxt
        • maxEvalueTxt
          JTextField maxEvalueTxt
        • maxFragmentChargeLbl
          JLabel maxFragmentChargeLbl
        • maxFragmentChargeTxt
          JTextField maxFragmentChargeTxt
        • maxFragmentsPerSeriesLbl
          JLabel maxFragmentsPerSeriesLbl
        • maxFragmentsPerSeriesTxt
          JTextField maxFragmentsPerSeriesTxt
        • maxLaddersLbl
          JLabel maxLaddersLbl
        • maxLaddersTxt
          JTextField maxLaddersTxt
        • maxPepLengthTxt
          JTextField maxPepLengthTxt
        • minAnnotatedMostIntensePeaksLbl
          JLabel minAnnotatedMostIntensePeaksLbl
        • minAnnotatedMostIntensePeaksTxt
          JTextField minAnnotatedMostIntensePeaksTxt
        • minAnnotatedPeaksLbl
          JLabel minAnnotatedPeaksLbl
        • minAnnotatedPeaksTxt
          JTextField minAnnotatedPeaksTxt
        • minPepLengthTxt
          JTextField minPepLengthTxt
        • minPrecChargeMultipleChargedFragmentsTxt
          JTextField minPrecChargeMultipleChargedFragmentsTxt
        • minPrecPerSpectrumLbl
          JLabel minPrecPerSpectrumLbl
        • minPrecPerSpectrumTxt
          JTextField minPrecPerSpectrumTxt
        • minPrecursorChargeConsideredMultiplyChargedFragmentsJLabel
          JLabel minPrecursorChargeConsideredMultiplyChargedFragmentsJLabel
        • neutronLbl
          JLabel neutronLbl
        • neutronTxt
          JTextField neutronTxt
        • nHitsPerSpectrumPerChargeLbl
          JLabel nHitsPerSpectrumPerChargeLbl
        • nHitsPerSpectrumPerChargeTxt
          JTextField nHitsPerSpectrumPerChargeTxt
        • nPeaksLbl
          JLabel nPeaksLbl
        • nPeaksTxt
          JTextField nPeaksTxt
        • okButton
          JButton okButton
        • omssaOutputFormatComboBox
          JComboBox omssaOutputFormatComboBox
        • omssaOutputFormatLabel
          JLabel omssaOutputFormatLabel
        • openDialogHelpJButton
          JButton openDialogHelpJButton
        • outputParametersPanel
          JPanel outputParametersPanel
        • peptideLengthDividerLabel1
          JLabel peptideLengthDividerLabel1
        • peptideLengthJLabel
          JLabel peptideLengthJLabel
        • plusOneChargeAutomaticLbl
          JLabel plusOneChargeAutomaticLbl
        • plusOneChargeCmb
          JComboBox plusOneChargeCmb
        • precursorChargeEstimationLabel
          JLabel precursorChargeEstimationLabel
        • precursorMassScalingLabel
          JLabel precursorMassScalingLabel
        • precursorScalingCombo
          JComboBox precursorScalingCombo
        • searchPositiveIonsCmb
          JComboBox searchPositiveIonsCmb
        • searchPositiveIonsLbl
          JLabel searchPositiveIonsLbl
        • searchSettingsPanel
          JPanel searchSettingsPanel
        • searchSettingsScrollPane
          JScrollPane searchSettingsScrollPane
        • semiEnzymaticParametersPanel
          JPanel semiEnzymaticParametersPanel
        • sequenceMappingCmb
          JComboBox sequenceMappingCmb
        • sequenceMappingLbl
          JLabel sequenceMappingLbl
        • singlyChargedNPeaksLbl
          JLabel singlyChargedNPeaksLbl
        • singlyChargedNpeaksTxt
          JTextField singlyChargedNpeaksTxt
        • singlyChargedWindowWidthLbl
          JLabel singlyChargedWindowWidthLbl
        • singlyChargedWindowWidthTxt
          JTextField singlyChargedWindowWidthTxt
        • spectrumProcessingPanel
          JPanel spectrumProcessingPanel
        • tabbedPane
          JTabbedPane tabbedPane
    • Class com.compomics.util.gui.parameters.identification.algorithm.PepNovoParametersDialog extends JDialog implements Serializable

      • Serialized Fields

        • backgroundPanel
          JPanel backgroundPanel
        • cancelButton
          JButton cancelButton
        • canceled
          boolean canceled
          True if the dialog was canceled by the user.
        • correctPrecursorMassCmb
          JComboBox correctPrecursorMassCmb
        • correctPrecursorMassLabel
          JLabel correctPrecursorMassLabel
        • editable
          boolean editable
          Boolean indicating whether the settings can be edited by the user.
        • estimateChargeCmb
          JComboBox estimateChargeCmb
        • estimateChargeLabel
          JLabel estimateChargeLabel
        • hitListLengthLabel
          JLabel hitListLengthLabel
        • hitListLengthSpinner
          JSpinner hitListLengthSpinner
        • okButton
          JButton okButton
        • openDialogHelpJButton
          JButton openDialogHelpJButton
        • pepNovoPanel
          JPanel pepNovoPanel
    • Class com.compomics.util.gui.parameters.identification.algorithm.PNovoParametersDialog extends JDialog implements Serializable

      • Serialized Fields

        • activationTypeCmb
          JComboBox activationTypeCmb
        • activationTypeLabel
          JLabel activationTypeLabel
        • backgroundPanel
          JPanel backgroundPanel
        • cancelButton
          JButton cancelButton
        • canceled
          boolean canceled
          True if the dialog was canceled by the user.
        • editable
          boolean editable
          Boolean indicating whether the settings can be edited by the user.
        • maxPrecursorMassLabel
          JLabel maxPrecursorMassLabel
        • maxPrecursorMassTextField
          JTextField maxPrecursorMassTextField
        • minPrecursorMassLabel
          JLabel minPrecursorMassLabel
        • minPrecursorMassTextField
          JTextField minPrecursorMassTextField
        • okButton
          JButton okButton
        • openDialogHelpJButton
          JButton openDialogHelpJButton
        • pNovoPanel
          JPanel pNovoPanel
    • Class com.compomics.util.gui.parameters.identification.algorithm.TideParametersDialog extends JDialog implements Serializable

      • Serialized Fields

        • advancedSettingsWarningLabel
          JLabel advancedSettingsWarningLabel
        • backgroundPanel
          JPanel backgroundPanel
        • cancelled
          boolean cancelled
          Boolean indicating whether the used canceled the editing.
        • chargesCombo
          JComboBox chargesCombo
        • chargesLabel
          JLabel chargesLabel
        • closeButton
          JButton closeButton
        • decoyFormatCombo
          JComboBox decoyFormatCombo
        • decoyformatLabel
          JLabel decoyformatLabel
        • decoySeedLabel
          JLabel decoySeedLabel
        • decoySeedTxt
          JTextField decoySeedTxt
        • editable
          boolean editable
          Boolean indicating whether the settings can be edited by the user.
        • enzymeTypeCmb
          JComboBox enzymeTypeCmb
        • enzymeTypeLabel
          JLabel enzymeTypeLabel
        • exactPvalueCombo
          JComboBox exactPvalueCombo
        • exactPvalueLabel
          JLabel exactPvalueLabel
        • indexPanel
          JPanel indexPanel
        • keepTerminalAaCombo
          JComboBox keepTerminalAaCombo
        • keepTerminalAaLabel
          JLabel keepTerminalAaLabel
        • maxPepLengthTxt
          JTextField maxPepLengthTxt
        • maxPrecursorMassTxt
          JTextField maxPrecursorMassTxt
        • maxPtmsLabel
          JLabel maxPtmsLabel
        • maxPtmsTxt
          JTextField maxPtmsTxt
        • maxSpectrumMzTxt
          JTextField maxSpectrumMzTxt
        • maxVariablePtmsPerTypeLabel
          JLabel maxVariablePtmsPerTypeLabel
        • maxVariablePtmsPerTypeTxt
          JTextField maxVariablePtmsPerTypeTxt
        • minPeaksLbl
          JLabel minPeaksLbl
        • minPeaksTxt
          JTextField minPeaksTxt
        • minPepLengthTxt
          JTextField minPepLengthTxt
        • minPrecursorMassTxt
          JTextField minPrecursorMassTxt
        • minSpectrumMzTxt
          JTextField minSpectrumMzTxt
        • monoPrecursorCmb
          JComboBox monoPrecursorCmb
        • monoPrecursorLabel
          JLabel monoPrecursorLabel
        • mzBinOffsetLabel
          JLabel mzBinOffsetLabel
        • mzBinOffsetTxt
          JTextField mzBinOffsetTxt
        • mzBinWidthLabel
          JLabel mzBinWidthLabel
        • mzBinWidthTxt
          JTextField mzBinWidthTxt
        • numberMatchesLabel
          JLabel numberMatchesLabel
        • numberMatchesTxt
          JTextField numberMatchesTxt
        • okButton
          JButton okButton
        • openDialogHelpJButton
          JButton openDialogHelpJButton
        • outputFormatCombo
          JComboBox outputFormatCombo
        • outputFormatLabel
          JLabel outputFormatLabel
        • peptideLengthDividerLabel
          JLabel peptideLengthDividerLabel
        • peptideLengthLabel
          JLabel peptideLengthLabel
        • peptideListCmb
          JComboBox peptideListCmb
        • peptideListLabel
          JLabel peptideListLabel
        • precursorMassDividerLabel
          JLabel precursorMassDividerLabel
        • precursorMassLabel
          JLabel precursorMassLabel
        • removeMethionineCmb
          JComboBox removeMethionineCmb
        • removeMethionineLabel
          JLabel removeMethionineLabel
        • removePrecursorPeakCombo
          JComboBox removePrecursorPeakCombo
        • removePrecursorPeakLabel
          JLabel removePrecursorPeakLabel
        • removePrecursorPeakToleranceLbl
          JLabel removePrecursorPeakToleranceLbl
        • removePrecursorPeakToleranceTxt
          JTextField removePrecursorPeakToleranceTxt
        • removeTempFoldersCmb
          JComboBox removeTempFoldersCmb
        • removeTempFoldersLabel
          JLabel removeTempFoldersLabel
        • searchPanel
          JPanel searchPanel
        • spectrumMzDividerLabel
          JLabel spectrumMzDividerLabel
        • spectrumMzLabel
          JLabel spectrumMzLabel
        • spScoreCombo
          JComboBox spScoreCombo
        • spScoreLabel
          JLabel spScoreLabel
        • tabbedPane
          JTabbedPane tabbedPane
        • useFlankingCmb
          JComboBox useFlankingCmb
        • useFlankingLabel
          JLabel useFlankingLabel
        • useNeutralLossCmb
          JComboBox useNeutralLossCmb
        • useNeutralLossLabel
          JLabel useNeutralLossLabel
    • Class com.compomics.util.gui.parameters.identification.algorithm.XTandemParametersDialog extends JDialog implements Serializable

      • Serialized Fields

        • advancedSearchSettingsPanel
          JPanel advancedSearchSettingsPanel
        • advancedSettingsWarningLabel
          JLabel advancedSettingsWarningLabel
        • backgroundPanel
          JPanel backgroundPanel
        • cancelled
          boolean cancelled
          Boolean indicating whether the used canceled the editing.
        • closeButton
          JButton closeButton
        • dynamicRangeLbl
          JLabel dynamicRangeLbl
        • dynamicRangeTxt
          JTextField dynamicRangeTxt
        • editable
          boolean editable
          Boolean indicating whether the settings can be edited by the user.
        • eValueLbl
          JLabel eValueLbl
        • eValueTxt
          JTextField eValueTxt
        • fragmentIonMassAccuracyInDa
          double fragmentIonMassAccuracyInDa
          The fragment ion mass accuracy.
        • jSeparator1
          JSeparator jSeparator1
        • maxEValueRefineTxt
          JTextField maxEValueRefineTxt
        • maxEValueRefinmentLbl
          JLabel maxEValueRefinmentLbl
        • minFragmentMzTxt
          JTextField minFragmentMzTxt
        • minFragMzLbl
          JLabel minFragMzLbl
        • minPeaksLbl
          JLabel minPeaksLbl
        • minPeaksTxt
          JTextField minPeaksTxt
        • minPrecMassLbl
          JLabel minPrecMassLbl
        • minPrecMassTxt
          JTextField minPrecMassTxt
        • modificationComplexityLbl
          JLabel modificationComplexityLbl
        • modificationComplexityTxt
          JTextField modificationComplexityTxt
        • modificationFactory
          ModificationFactory modificationFactory
          The post translational modifications factory.
        • modificationProfile
          ModificationParameters modificationProfile
          The modification profile used for the search.
        • modificationsJScrollPane
          JScrollPane modificationsJScrollPane
        • modificationsTable
          JTable modificationsTable
        • modificationTableToolTips
          ArrayList<String> modificationTableToolTips
          The modification table column header tooltips.
        • modProfileChanged
          boolean modProfileChanged
          Boolean indicating whether the modification profile has been changed. Note that it only checks if the user has made changed to the selection, not if the end result is different or not.
        • noiseSuppressionCmb
          JComboBox noiseSuppressionCmb
        • noiseSuppressionLabel
          JLabel noiseSuppressionLabel
        • nPeaksLbl
          JLabel nPeaksLbl
        • nPeaksTxt
          JTextField nPeaksTxt
        • okButton
          JButton okButton
        • openDialogHelpJButton
          JButton openDialogHelpJButton
        • openModificationSettingsJButton
          JButton openModificationSettingsJButton
        • outputHistogramsCmb
          JComboBox outputHistogramsCmb
        • outputHistogramsLabel
          JLabel outputHistogramsLabel
        • outputProteinsCmb
          JComboBox outputProteinsCmb
        • outputProteinsLabel
          JLabel outputProteinsLabel
        • outputResultsCmb
          JComboBox outputResultsCmb
        • outputResultsLabel
          JLabel outputResultsLabel
        • outputSequencesCmb
          JComboBox outputSequencesCmb
        • outputSequencesLabel
          JLabel outputSequencesLabel
        • outputSettingsPanel
          JPanel outputSettingsPanel
        • outputSpectraCmb
          JComboBox outputSpectraCmb
        • outputSpectraLabel
          JLabel outputSpectraLabel
        • parentMonoisotopicMassIsotopeErrorCmb
          JComboBox parentMonoisotopicMassIsotopeErrorCmb
        • parentMonoisotopicMassIsotopeErrorLabel
          JLabel parentMonoisotopicMassIsotopeErrorLabel
        • pointMutationLabel
          JLabel pointMutationLabel
        • pointMutationsCmb
          JComboBox pointMutationsCmb
        • potentialModificationsCmb
          JComboBox potentialModificationsCmb
        • quickAcetylCmb
          JComboBox quickAcetylCmb
        • quickAcetylLabel
          JLabel quickAcetylLabel
        • quickPyroCmb
          JComboBox quickPyroCmb
        • quickPyroLabel
          JLabel quickPyroLabel
        • refinementCmb
          JComboBox refinementCmb
        • refinementLabel
          JLabel refinementLabel
        • refinementModificationsJPanel
          JPanel refinementModificationsJPanel
        • refinementModificationsLabel
          JLabel refinementModificationsLabel
        • refinementSettingsPanel
          JPanel refinementSettingsPanel
        • semiEnzymaticCmb
          JComboBox semiEnzymaticCmb
        • semiEnzymaticLabel
          JLabel semiEnzymaticLabel
        • skylinePathValueLbl
          JLabel skylinePathValueLbl
        • skylineTxt
          JTextField skylineTxt
        • snapsCmb
          JComboBox snapsCmb
        • snapsLabel
          JLabel snapsLabel
        • spectrumImportSettingsPanel
          JPanel spectrumImportSettingsPanel
        • spectrumSynthesisCmb
          JComboBox spectrumSynthesisCmb
        • spectrumSynthesisLabel
          JLabel spectrumSynthesisLabel
        • stpBiasCmb
          JComboBox stpBiasCmb
        • stpBiasLabel
          JLabel stpBiasLabel
        • tabbedPane
          JTabbedPane tabbedPane
        • unanticipatedCleavageCmb
          JComboBox unanticipatedCleavageCmb
        • unanticipatedCleavageLabel
          JLabel unanticipatedCleavageLabel
        • usePotentialModsLabel
          JLabel usePotentialModsLabel
  • Package com.compomics.util.gui.parameters.identification.pride

  • Package com.compomics.util.gui.parameters.identification.search

    • Class com.compomics.util.gui.parameters.identification.search.SearchParametersDialog extends JDialog implements Serializable

      • Serialized Fields

        • addFixedModification
          JButton addFixedModification
        • addVariableModification
          JButton addVariableModification
        • availableModsPanel
          JPanel availableModsPanel
        • backgroundPanel
          JPanel backgroundPanel
        • cancelButton
          JButton cancelButton
        • canceled
          boolean canceled
          Boolean indicating whether the cancel button was pressed.
        • currentPtmSearchString
          String currentPtmSearchString
          The current Modification search string.
        • digestionCmb
          JComboBox digestionCmb
        • digestionLabel
          JLabel digestionLabel
        • editable
          boolean editable
          Boolean indicating whether the settings can be edited by the user.
        • enzymeFactory
          EnzymeFactory enzymeFactory
          The enzyme factory.
        • enzymeLabel
          JLabel enzymeLabel
        • enzymesCmb
          JComboBox enzymesCmb
        • fixedModificationsLabel
          JLabel fixedModificationsLabel
        • fixedModsJScrollPane
          JScrollPane fixedModsJScrollPane
        • fixedModsPanel
          JPanel fixedModsPanel
        • fixedModsTable
          JTable fixedModsTable
        • forwardIons
          String[] forwardIons
          Convenience array for forward ion type selection.
        • fragmentIon1Cmb
          JComboBox fragmentIon1Cmb
        • fragmentIon2Cmb
          JComboBox fragmentIon2Cmb
        • fragmentIonAccuracyTxt
          JTextField fragmentIonAccuracyTxt
        • fragmentIonLbl
          JLabel fragmentIonLbl
        • fragmentIonType1Lbl
          JLabel fragmentIonType1Lbl
        • fragmentIonUnit
          JComboBox fragmentIonUnit
        • isotopeMaxTxt
          JTextField isotopeMaxTxt
        • isotopeMinTxt
          JTextField isotopeMinTxt
        • isotopeRangeLabel
          JLabel isotopeRangeLabel
        • isotopesLbl
          JLabel isotopesLbl
        • keyPressedCounter
          int keyPressedCounter
          Counts the number of times the users has pressed a key on the keyboard in the search field.
        • lastSelectedFolder
          LastSelectedFolder lastSelectedFolder
          The last selected folder to use.
        • maxMissedCleavagesLabel
          JLabel maxMissedCleavagesLabel
        • maxMissedCleavagesTxt
          JTextField maxMissedCleavagesTxt
        • maxPrecursorChargeTxt
          JTextField maxPrecursorChargeTxt
        • minPrecursorChargeTxt
          JTextField minPrecursorChargeTxt
        • modificationFactory
          ModificationFactory modificationFactory
          The post translational modifications factory.
        • modificationsJScrollPane
          JScrollPane modificationsJScrollPane
        • modificationsLayeredPane
          JLayeredPane modificationsLayeredPane
        • modificationsListCombo
          JComboBox modificationsListCombo
        • modificationsPanel
          JPanel modificationsPanel
        • modificationsTable
          JTable modificationsTable
        • modificationTableToolTips
          ArrayList<String> modificationTableToolTips
          The modification table column header tooltips.
        • modificationTypesSplitPane
          JSplitPane modificationTypesSplitPane
        • normalIcon
          Image normalIcon
          The normal dialog icon.
        • okButton
          JButton okButton
        • openDialogHelpJButton1
          JButton openDialogHelpJButton1
        • openModificationSettingsJButton
          JButton openModificationSettingsJButton
        • parentFrame
          Frame parentFrame
          The dialog parent frame.
        • precursorChargeLbl
          JLabel precursorChargeLbl
        • precursorChargeRangeLabel
          JLabel precursorChargeRangeLabel
        • precursorIonAccuracyTxt
          JTextField precursorIonAccuracyTxt
        • precursorIonLbl
          JLabel precursorIonLbl
        • precursorIonUnit
          JComboBox precursorIonUnit
        • proteaseAndFragmentationPanel
          JPanel proteaseAndFragmentationPanel
        • refMass
          Double refMass
          Reference mass for the conversion of the fragment ion tolerance from ppm to Dalton.
        • removeFixedModification
          JButton removeFixedModification
        • removeVariableModification
          JButton removeVariableModification
        • rewindIons
          String[] rewindIons
          Convenience array for rewind ion type selection.
        • searchParameters
          SearchParameters searchParameters
        • specificityComboBox
          JComboBox specificityComboBox
        • specificityLabel
          JLabel specificityLabel
        • utilitiesUserParameters
          UtilitiesUserParameters utilitiesUserParameters
          The utilities user parameters.
        • variableModificationsLabel
          JLabel variableModificationsLabel
        • variableModsJScrollPane
          JScrollPane variableModsJScrollPane
        • variableModsPanel
          JPanel variableModsPanel
        • variableModsTable
          JTable variableModsTable
        • waitingIcon
          Image waitingIcon
          The waiting dialog icon.
        • waitingTime
          int waitingTime
          The time to wait between keys typed before updating the search.
    • Class com.compomics.util.gui.parameters.identification.search.SequenceDbDetailsDialog extends JDialog implements Serializable

      • Serialized Fields

        • accessionsSample
          ArrayList<String> accessionsSample
          Accessions of the sampled proteins.
        • accessionsSpinner
          JSpinner accessionsSpinner
        • backgroundPanel
          JPanel backgroundPanel
        • browseButton
          JButton browseButton
        • cancelButton
          JButton cancelButton
        • canceled
          boolean canceled
          Boolean indicating whether the database selection was canceled by the user.
        • databaseHelpSettingsJLabel
          JLabel databaseHelpSettingsJLabel
        • databaseInformationPanel
          JPanel databaseInformationPanel
        • dbEditable
          boolean dbEditable
          Boolean indicating whether the database can be changed.
        • dbNameTxt
          JTextField dbNameTxt
        • decoyButton
          JButton decoyButton
        • editFastaParametersJLabel
          JLabel editFastaParametersJLabel
        • fastaParameters
          FastaParameters fastaParameters
          The parameters used to parse the FASTA file.
        • fastaSummary
          FastaSummary fastaSummary
          Summary information on the FASTA file content.
        • fileLabel
          JLabel fileLabel
        • fileTxt
          JTextField fileTxt
        • headersSample
          HashMap<String,​Header> headersSample
          Sample of protein headers from the database.
        • lastModifiedLabel
          JLabel lastModifiedLabel
        • lastModifiedTxt
          JTextField lastModifiedTxt
        • lastSelectedFolder
          LastSelectedFolder lastSelectedFolder
          The last selected folder.
        • nameLabel
          JLabel nameLabel
        • normalImange
          Image normalImange
          The normal icon.
        • okButton
          JButton okButton
        • parentFrame
          Frame parentFrame
          The parent frame.
        • previewPanel
          JPanel previewPanel
        • proteinIterator
          FastaIterator proteinIterator
          A protein iterator to fill the sample.
        • proteinLabel
          JLabel proteinLabel
        • proteinsSample
          HashMap<String,​Protein> proteinsSample
          Sample of proteins from the database.
        • proteinTxt
          JTextArea proteinTxt
        • proteinYxtScrollPane
          JScrollPane proteinYxtScrollPane
        • selectedFastaFile
          String selectedFastaFile
          The selected FASTA file.
        • sizeLabel
          JLabel sizeLabel
        • sizeTxt
          JTextField sizeTxt
        • speciesJTextField
          JTextField speciesJTextField
        • speciesLabel
          JLabel speciesLabel
        • targetDecoyTxt
          JLabel targetDecoyTxt
        • typeJTextField
          JTextField typeJTextField
        • typeLabel
          JLabel typeLabel
        • utilitiesUserParameters
          UtilitiesUserParameters utilitiesUserParameters
          The utilities user parameters.
        • versionLabel
          JLabel versionLabel
        • versionTxt
          JTextField versionTxt
        • waitingImage
          Image waitingImage
          The icon to display when waiting.
  • Package com.compomics.util.gui.parameters.proteowizard

  • Package com.compomics.util.gui.parameters.tools

    • Class com.compomics.util.gui.parameters.tools.ProcessingParametersDialog extends JDialog implements Serializable

      • Serialized Fields

        • backgroundPanel
          JPanel backgroundPanel
        • cancelButton
          JButton cancelButton
        • canceled
          boolean canceled
          Boolean indicating whether the user canceled the editing.
        • editable
          boolean editable
          Boolean indicating whether the processing and identification parameters should be edited upon clicking on OK.
        • nThreadsSpinner
          JSpinner nThreadsSpinner
        • okButton
          JButton okButton
        • performanceLbl
          JLabel performanceLbl
        • performancePanel
          JPanel performancePanel
        • processingTypeCmb
          JComboBox processingTypeCmb
        • processingTypeLbl
          JLabel processingTypeLbl
        • processingTypePanel
          JPanel processingTypePanel
  • Package com.compomics.util.gui.protein

    • Class com.compomics.util.gui.protein.FastaParametersDialog extends JDialog implements Serializable

      • Serialized Fields

        • backgroundPanel
          JPanel backgroundPanel
        • cancelButton
          JButton cancelButton
        • canceled
          boolean canceled
          Boolean indicating whether the user canceled the editing.
        • decoyFlagTxt
          JTextField decoyFlagTxt
        • decoySuffixLabel
          JLabel decoySuffixLabel
        • decoyTagLabel
          JLabel decoyTagLabel
        • decoyTypeComboBox
          JComboBox<String> decoyTypeComboBox
        • decoyTypeLabel
          JLabel decoyTypeLabel
        • editable
          boolean editable
          Boolean indicating whether the settings can be edited by the user.
        • fastaSuffixTxt
          JTextField fastaSuffixTxt
        • fileProcessingPanel
          JPanel fileProcessingPanel
        • helpJButton
          JButton helpJButton
        • okButton
          JButton okButton
        • parentFrame
          Frame parentFrame
          The parent frame.
        • targetDecoyComboBox
          JComboBox<String> targetDecoyComboBox
        • targetDecoyLabel
          JLabel targetDecoyLabel
    • Class com.compomics.util.gui.protein.SequenceModificationPanel extends JPanel implements Serializable

      • Serialized Fields

        • fragmentIonRectangles
          HashMap<String,​Rectangle> fragmentIonRectangles
          A map of the rectangles used to draw each profile peak. This map is later used for the tooltip for each peak.
        • iBarWidth
          int iBarWidth
          The width of the bars.
        • iBaseFont
          Font iBaseFont
          The font to use.
        • iHorizontalSpace
          int iHorizontalSpace
          The horizontal space.
        • iMaxBarHeight
          double iMaxBarHeight
          The maximum bar height.
        • iSequenceComponents
          String[] iSequenceComponents
          Elementary data for composing the Panel.
        • isModifiedSequence
          boolean isModifiedSequence
          This boolean holds whether or not the given sequence is a modified sequence or a normal peptide sequence. Normal: KENNY Modified: NH2-K<Ace>ENNY-COOH
        • iXStart
          int iXStart
          The x-axis start position.
        • iYStart
          int iYStart
          The y-axis start position.
        • profiles
          ArrayList<ModificationProfile> profiles
          The list of modification profiles.
        • score1Name
          String score1Name
          The name of the score above of the sequence.
        • score2Name
          String score2Name
          The name of the score under of the sequence.
  • Package com.compomics.util.gui.renderers

  • Package com.compomics.util.gui.spectrum

    • Class com.compomics.util.gui.spectrum.ChromatogramPanel extends GraphicsPanel implements Serializable

      • Serialized Fields

        • iChromatogramColor
          Color iChromatogramColor
          Color in which the profileChromatogram polyline is rendered. Defaults to gray.
        • iChromatogramPointColor
          Color iChromatogramPointColor
          Color in which the data points and peaks are rendered. Defaults to black.
    • Class com.compomics.util.gui.spectrum.FragmentIonTable extends JTable implements Serializable

      • Serialized Fields

        • allAnnotations
          ArrayList<IonMatch[]> allAnnotations
          The spectrum annotations map.
        • allSpectra
          ArrayList<Spectrum> allSpectra
          The list of spectra. Needed for intensity normalization.
        • currentFragmentIonTypes
          HashSet<Integer> currentFragmentIonTypes
          The list of currently selected fragment ion types.
        • currentPeptide
          Peptide currentPeptide
          The current peptide.
        • modificationParameters
          ModificationParameters modificationParameters
          The modification parameters.
        • modificationSequenceMatchingParameters
          SequenceMatchingParameters modificationSequenceMatchingParameters
          The modification sequence matching parameters.
        • neutralLosses
          NeutralLossesMap neutralLosses
          The list of the currently selected neutral loss types.
        • peptideSequence
          String peptideSequence
          The current peptide sequence.
        • sequenceProvider
          SequenceProvider sequenceProvider
          The protein sequence provider.
        • singleCharge
          boolean singleCharge
          If true, singly charge ions are included in the table.
        • tooltips
          ArrayList<String> tooltips
          The table tooltips.
        • twoCharges
          boolean twoCharges
          If true, doubly charged ions are included in the table.
    • Class com.compomics.util.gui.spectrum.GraphicsPanel extends JPanel implements Serializable

      • Serialized Fields

        • alphaLevel
          float alphaLevel
          The opacity of the spectra. 0 means completely see-through, 1 means opaque.
        • ANNOTATED_STATUS
          int ANNOTATED_STATUS
          This status indicates that annotation (if present) will be displayed, while limiting the user to zooming in/out.
        • annotateHighestPeak
          boolean annotateHighestPeak
          If more than one peak is within the accuracy range of an annotation setting this to true will always select the most intense of possible peaks. Setting this variable to false will instead select the most accurate peak.
        • backgroundPeakWidth
          float backgroundPeakWidth
          The width used for the background peaks.
        • currentGraphicsPanelType
          GraphicsPanel.GraphicsPanelType currentGraphicsPanelType
          Sets the current GraphicsPanel type, default to centroid spectrum.
        • currentPadding
          int currentPadding
          The current padding (distance between the axes and the border of the panel).
        • dataSetCounter
          int dataSetCounter
          The number of datasets currently displayed in the panel.
        • dataSetCounterMirroredSpectra
          int dataSetCounterMirroredSpectra
          The number of mirrored datasets currently displayed in the panel.
        • deltaMassWindow
          double deltaMassWindow
          The size of the window to use when searching for matches in the known masses list when the user hovers over a second data point after clicking a previous data point.
        • iAnnotations
          Vector iAnnotations
          The Vector that holds a set of Annotation instances.
        • iAnnotationsMirroredSpectra
          Vector iAnnotationsMirroredSpectra
          The Vector that holds a set of Annotation instances for the mirrored spectra.
        • iAnnotationYAxisThreshold
          double iAnnotationYAxisThreshold
          The percent non-inclusive, minimal y-axis value (compared to the highest point in the spectrum) a point should have before being eligible for annotation. Default is '0.0'.
        • iAreaUnderCurveColor
          ArrayList<Color> iAreaUnderCurveColor
          Colors in which the chromatogram polyline is rendered. Indexed by dataset.
        • iAreaUnderCurveColorMirroredSpectra
          ArrayList<Color> iAreaUnderCurveColorMirroredSpectra
          Colors in which the chromatogram polyline is rendered for the mirrored spectra. Indexed by dataset.
        • iClicked
          boolean iClicked
          Boolean that indicates whether a point has been marked by clicking.
        • iClickedDataSetIndex
          int iClickedDataSetIndex
          Int that indicates which dataset contains the clicked point.
        • iClickedDataSetIndexMirrored
          int iClickedDataSetIndexMirrored
          Int that indicates which dataset contains the clicked point in the mirrored spectra.
        • iClickedIndex
          int iClickedIndex
          Int that indicates which point was clicked.
        • iClickedIndexMirrored
          int iClickedIndexMirrored
          Int that indicates which point was clicked in the mirrored spectra.
        • iClickedList
          Vector iClickedList
          The Vector that holds all points clicked up to now.
        • iClickedListDatasetIndices
          Vector iClickedListDatasetIndices
          The Vector that holds the dataset indices of all points clicked up to now.
        • iClickedListDatasetIndicesMirrored
          Vector iClickedListDatasetIndicesMirrored
          The Vector that holds the dataset indices of all points clicked up to now in the mirrored spectra.
        • iClickedListMirrored
          Vector iClickedListMirrored
          The Vector that holds all points clicked up to now in the mirrored spectra.
        • iClickedMirrored
          boolean iClickedMirrored
          Boolean that indicates whether a point has been marked by clicking in the mirrored spectra.
        • iCurrentDrawStyle
          GraphicsPanel.DrawingStyle iCurrentDrawStyle
          This variable holds the current drawing style.
        • iDataPointAndLineColor
          ArrayList<Color> iDataPointAndLineColor
          Colors in which the data points and peaks are rendered. Indexed by dataset.
        • iDataPointAndLineColorMirroredSpectra
          ArrayList<Color> iDataPointAndLineColorMirroredSpectra
          Colors in which the data points and peaks are rendered for the mirrored spectra. Indexed by dataset.
        • iDotRadius
          int iDotRadius
          This variable holds the dot radius; only used when drawing style is DOTS style.
        • iDragged
          boolean iDragged
          This boolean is set to 'true' when dragging is performed.
        • iDragXLoc
          int iDragXLoc
          The current dragging location.
        • iEndXLoc
          int iEndXLoc
          When the mouse is dragged, this represents the X-coordinate of the ending location.
        • iFilename
          String iFilename
          The spectrum or chromatogram filename.
        • iFilenameColor
          Color iFilenameColor
          This is the color the filename should be presented in.
        • iFilenameMirrorredSpectrum
          String iFilenameMirrorredSpectrum
          The spectrum or chromatogram filename for the mirrored spectrum or chromatogram.
        • iHighLight
          boolean iHighLight
          Boolean that will be 'true' when a point needs highlighting.
        • iHighLightDatasetIndex
          int iHighLightDatasetIndex
          Index of the dataset containing the point that needs to be highlighted.
        • iHighLightDatasetIndexMirrored
          int iHighLightDatasetIndexMirrored
          Index of the dataset containing the point that needs to be highlighted in the mirrored spectra.
        • iHighLightIndex
          int iHighLightIndex
          Index of the point that needs to be highlighted.
        • iHighLightIndexMirrored
          int iHighLightIndexMirrored
          Index of the point that needs to be highlighted in the mirrored spectra.
        • iHighLightMirrored
          boolean iHighLightMirrored
          Boolean that will be 'true' when a point needs highlighting in the mirrored spectra.
        • iMinDrag
          int iMinDrag
          Minimal dragging distance in pixels.
        • iMSLevel
          int iMSLevel
          The ms level of the current spectrum. O is assumed to mean no ms level given.
        • INTERACTIVE_STATUS
          int INTERACTIVE_STATUS
          This status indicates that no annotation will be displayed, but the user will have a fully functional interface (point clicking, selecting, sequencing etc.)
        • iPointDetectionTolerance
          int iPointDetectionTolerance
          The deviation (both left and right) allowed for point highlighting detection.
        • iPointSize
          Integer iPointSize
          Size for the point on a polygon.
        • iPrecursorCharge
          String iPrecursorCharge
          This String holds the charge for the precursor.
        • iPrecursorChargeMirorredSpectrum
          String iPrecursorChargeMirorredSpectrum
          This String holds the charge for the precursor for the mirrored spectrum.
        • iPrecursorMZ
          double iPrecursorMZ
          This variable holds the precursor M/Z.
        • iPrecursorMZMirroredSpectrum
          double iPrecursorMZMirroredSpectrum
          This variable holds the precursor M/Z for the mirrored spectrum.
        • iSpecPanelListeners
          ArrayList iSpecPanelListeners
          The list of SpectrumPanelListeners.
        • iStartXLoc
          int iStartXLoc
          When the mouse is dragged, this represents the X-coordinate of the starting location.
        • iStartYLoc
          int iStartYLoc
          When the mouse is dragged, this represents the Y-coordinate of the starting location.
        • iStoredSequence
          Vector iStoredSequence
          The Vector that holds a set of stored points from a previously established list.
        • iStoredSequenceDatasetIndices
          Vector iStoredSequenceDatasetIndices
          The Vector that holds the dataset indices of stored points from a previously established list.
        • iStoredSequenceDatasetIndicesMirrored
          Vector iStoredSequenceDatasetIndicesMirrored
          The Vector that holds the dataset indices of stored points from a previously established list in the mirrored spectra.
        • iStoredSequenceMirrored
          Vector iStoredSequenceMirrored
          The Vector that holds a set of stored points from a previously established list in the mirrored spectra.
        • iTopPadding
          int iTopPadding
          Effective distance from the panel top border to 5 pixels above the top of the highest point (or y-tick mark).
        • iXAxisData
          ArrayList<double[]> iXAxisData
          All the x-axis data points. Indexed by dataset (one double[] per dataset). First dataset is the first double[], second dataset is the second double[] etc.Should at all times be sorted from high to low.
        • iXAxisDataInPixels
          ArrayList<int[]> iXAxisDataInPixels
          This array will hold the x-coordinates in pixels for all the x-axis values. Link is through index. Again indexed by dataset (one double[] per dataset).
        • iXAxisDataInPixelsMirroredSpectrum
          ArrayList<int[]> iXAxisDataInPixelsMirroredSpectrum
          This array will hold the x-coordinates in pixels for all the x-axis values of the mirrored spectrum. Link is through index. Again indexed by dataset (one double[] per dataset).
        • iXAxisDataMirroredSpectrum
          ArrayList<double[]> iXAxisDataMirroredSpectrum
          All the x-axis data points for the mirrored spectrum. Indexed by dataset (one double[] per dataset). First dataset is the first double[], second dataset is the second double[] etc.Should at all times be sorted from high to low.
        • iXAxisLabel
          String iXAxisLabel
          The label (and unit between brackets, if available) for the x-axis. Defaults to "m/z".
        • iXAxisMax
          double iXAxisMax
          The maximum x-axis value to display.
        • iXAxisMin
          double iXAxisMin
          The minimum x-axis value to display.
        • iXAxisStartAtZero
          boolean iXAxisStartAtZero
          This boolean is set to 'true' if the x-axis should start at zero.
        • iXPadding
          int iXPadding
          Effective distance from the x-axis to the panel border.
        • iXScaleUnit
          double iXScaleUnit
          Scale unit for the X axis.
        • iXUnit
          int iXUnit
          Graphical unit for the X axis.
        • iYAxisData
          ArrayList<double[]> iYAxisData
          All the y-axis values. Indexed by dataset (one double[] per dataset). First dataset is the first double[], second dataset is the second double[] etc. Y-axis values are related to the x-axis values by the table index. So the first y-axis value of the first dataset is the value for the first x-axis value in the first dataset etc.
        • iYAxisDataInPixels
          ArrayList<int[]> iYAxisDataInPixels
          This array will hold the y-coordinates in pixels for all the y-axis values. Link is through index. Again indexed by dataset (one double[] per dataset).
        • iYAxisDataInPixelsMirroredSpectrum
          ArrayList<int[]> iYAxisDataInPixelsMirroredSpectrum
          This array will hold the y-coordinates in pixels for all the y-axis values of the mirrored spectrum. Link is through index. Again indexed by dataset (one double[] per dataset).
        • iYAxisDataMirroredSpectrum
          ArrayList<double[]> iYAxisDataMirroredSpectrum
          All the y-axis values for the mirrored spectra. Indexed by dataset (one double[] per dataset). First dataset is the first double[], second dataset is the second double[] etc. Y-axis values are related to the x-axis values by the table index. So the first y-axis value of the first dataset is the value for the first x-axis value in the first dataset etc.
        • iYAxisLabel
          String iYAxisLabel
          The label (and unit between brackets, if available) for the y-axis. Defaults to "Int".
        • iYAxisMax
          double iYAxisMax
          The maximum y-axis value to display.
        • iYAxisMin
          double iYAxisMin
          The minimum y-axis value to display.
        • iYScaleUnit
          double iYScaleUnit
          Scale unit for the Y axis.
        • iYUnit
          int iYUnit
          Graphical unit for the Y axis.
        • maxPadding
          int maxPadding
          The maximum padding (distance between the axes and the border of the panel). Increase if font size on the y-axis becomes too small.
        • miniature
          boolean miniature
          If set to true, the y-axis is removed, the y- and x-axis tags are removed, and any annotations are hidden. All to make the graphics panel look better in a smaller version, e.g., when put into a table cell. When turning miniature mode one it is also recommended to reduce the max padding. Note that miniature and reduced max padding is set automatically by the GraphicsPanelTableCellRenderer.
        • padding
          int padding
          The padding (distance between the axes and the border of the panel).
        • peakWaterMarkColor
          Color peakWaterMarkColor
          The color to use for the non-annotated peaks when only the annotated peaks are to be shown.
        • peakWidth
          float peakWidth
          The width used for the annotated peaks.
        • referenceAreasXAxis
          HashMap<String,​ReferenceArea> referenceAreasXAxis
          A hashmap of the current x-axis reference areas. Key is the name of the reference area.
        • referenceAreasYAxis
          HashMap<String,​ReferenceArea> referenceAreasYAxis
          A hashmap of the current y-axis reference areas. Key is the name of the reference area.
        • scientificPattern
          String scientificPattern
          The number format pattern for scientific annotation.
        • scientificXAxis
          boolean scientificXAxis
          If true the x-axis will be drawn using the scientific annotation. The pattern i set in the "scientificPattern" field.
        • scientificYAxis
          boolean scientificYAxis
          If true the y-axis will be drawn using the scientific annotation. The pattern i set in the "scientificPattern" field.
        • showAllPeaks
          boolean showAllPeaks
          If false, only the annotated peaks will be shown. Note that this setting is ignored in profile mode!
        • showFileName
          boolean showFileName
          The boolean is set to 'true' if the file name is to be shown in the panel.
        • showPrecursorDetails
          boolean showPrecursorDetails
          The boolean is set to 'true' if the precursor details is to be shown in the panel.
        • showResolution
          boolean showResolution
          The boolean is set to 'true' if the resolution is to be shown in the panel.
        • subscriptAnnotationNumbers
          boolean subscriptAnnotationNumbers
          If true, all numbers in peak annotations are subscripted.
        • useMassDeltaCombinations
          boolean useMassDeltaCombinations
          If true, pairs of delta mass annotations are used when doing de novo sequencing. If false, only single delta masses are annotated.
        • xAxisZoomRangeLowerValue
          double xAxisZoomRangeLowerValue
          The lower range for the current zoom range.
        • xAxisZoomRangeUpperValue
          double xAxisZoomRangeUpperValue
          The upper range for the current zoom range.
        • xTagCount
          int xTagCount
          The number of X-axis tags.
        • yAxisZoomExcludesBackgroundPeaks
          boolean yAxisZoomExcludesBackgroundPeaks
          If true, the automatic y-axis zoom excludes the background peaks. False includes all peaks in the zoom.
        • yDataIsPositive
          boolean yDataIsPositive
          If set to true, all y data is assumed to be positive. This adds a white polygon under the y-axis hiding any polygon data lines that crosses (slightly) below the y-axis.
        • yTagCount
          int yTagCount
          The number of Y-axis tags.
    • Class com.compomics.util.gui.spectrum.IntensityHistogram extends JPanel implements Serializable

      • Serialized Fields

        • chartPanel
          org.jfree.chart.ChartPanel chartPanel
          The chart panel for external access.
    • Class com.compomics.util.gui.spectrum.IonLabelColorTableModel extends DefaultTableModel implements Serializable

    • Class com.compomics.util.gui.spectrum.IsotopicDistributionPanel extends GraphicsPanel implements Serializable

      • Serialized Fields

        • aSpectrumPeakColor
          Color aSpectrumPeakColor
          The color used for the peaks. Default to red.
        • aSpectrumProfileModeLineColor
          Color aSpectrumProfileModeLineColor
          The color used for the area under the curve. Defaults to pink.
        • iElements
          HashMap<String,​MolecularFormula> iElements
          HashMap with the molecular formula for all the amino acids.
        • logger
          org.apache.log4j.Logger logger
        • peptideCharges
          ArrayList<Integer> peptideCharges
          The charges of the peptides. Indexed by dataset.
        • peptideSequences
          ArrayList<AASequenceImpl> peptideSequences
          The peptide sequences to display the isotopic distribution for.
    • Class com.compomics.util.gui.spectrum.MassErrorBubblePlot extends JPanel implements Serializable

      • Serialized Fields

        • chartPanel
          org.jfree.chart.ChartPanel chartPanel
          The chart panel.
        • currentlyUsedIonMatches
          IonMatch[] currentlyUsedIonMatches
          The array of currently used ions.
        • dataSeriesfragmentIonColors
          ArrayList<Color> dataSeriesfragmentIonColors
          The data series fragment ion colors.
        • useRelativeError
          boolean useRelativeError
          If true the relative error (ppm) is used instead of the absolute error (Da).
    • Class com.compomics.util.gui.spectrum.MassErrorPlot extends JPanel implements Serializable

      • Serialized Fields

        • annotations
          IonMatch[] annotations
          The complete list of possible spectrum annotations.
        • chartPanel
          org.jfree.chart.ChartPanel chartPanel
          The chart panel.
    • Class com.compomics.util.gui.spectrum.SequenceFragmentationPanel extends JPanel implements Serializable

      • Serialized Fields

        • bIons
          double[] bIons
          Double array on b-ions for the sequence components. If '0', no corresponding ions were given for the component. Otherwise, a double between [0:1] is stored in the array that is relative with the intensity of the most intense fragment ion.
        • fontColor
          Color fontColor
          Color for the peptide sequence.
        • forwardColor
          Color forwardColor
          Color for the forward ion
        • forwardIon
          int forwardIon
          the forward ion type (for instance B ion) as indexed by the PeptideFragmentIon static fields
        • iBarWidth
          int iBarWidth
          The width of the bars.
        • iHighlightModifications
          boolean iHighlightModifications
          If true the modification are highlighted with a background color.
        • iHorizontalSpace
          int iHorizontalSpace
          The horizontal space.
        • iIonMatches
          IonMatch[] iIonMatches
          The array of fragment ion matches.
        • iMaxBarHeight
          double iMaxBarHeight
          The maximum bar height.
        • iPeptideSequenceFont
          Font iPeptideSequenceFont
          The font to use for the peptide sequence..
        • iSequenceComponents
          String[] iSequenceComponents
          Elementary data for composing the Panel.
        • isModifiedSequence
          boolean isModifiedSequence
          This boolean holds whether or not the given sequence is a modified sequence or a normal peptide sequence. Normal: KENNY Modified: NH2-K<Ace>ENNY-COOH
        • iXStart
          int iXStart
          The x-axis start position.
        • modificationProfile
          ModificationParameters modificationProfile
          The modification profile.
        • rewindColor
          Color rewindColor
          Color for the rewind ion
        • rewindIon
          int rewindIon
          the rewind ion type (for instance B ion) as indexed by the PeptideFragmentIon static fields
        • tooltipRectangles
          HashMap<String,​Rectangle> tooltipRectangles
          A map of the rectangles that have tooltips, i.e., the fragment ion peaks and the PTM highlighting.
        • yIons
          double[] yIons
          Double array on y-ions for the sequence components. If '0', no corresponding ions were given for the component. Otherwise, a double between [0:1] is stored in the array that is relative with the intensity of the most intense fragment ion.
    • Class com.compomics.util.gui.spectrum.SpectrumPanel extends GraphicsPanel implements Serializable

      • Serialized Fields

        • spectrumPeakColor
          Color spectrumPeakColor
          The color used for the peaks. Default to red.
        • spectrumProfileModeLineColor
          Color spectrumProfileModeLineColor
          The color used for the profile mode spectra. Defaults to pink.
  • Package com.compomics.util.gui.tablemodels

    • Class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel extends DefaultTableModel implements Serializable

      • Serialized Fields

        • isScrolling
          boolean isScrolling
          When true this indicates that the user is currently scrolling in the table and that the table should not update.
        • lastColumnSorted
          int lastColumnSorted
          Indicates which column was last changed.
        • lastLoadingRunnable
          com.compomics.util.gui.tablemodels.SelfUpdatingTableModel.LoadingRunnable lastLoadingRunnable
          The last loading runnable.
        • loadingPool
          ExecutorService loadingPool
          Executor for the loading threads.
        • progressDialog
          ProgressDialogX progressDialog
          A progress dialog.
        • rowEndLoading
          int rowEndLoading
          The view end index of the rows being loaded.
        • rowStartLoading
          int rowStartLoading
          The view start index of the rows being loaded.
        • selfUpdating
          boolean selfUpdating
          If false, the table will not update automatically.
        • sortAscending
          boolean sortAscending
          If true the current sorting is ascending.
        • unsorted
          boolean unsorted
          If true the table has not yet been sorted.
        • updateMutex
          Semaphore updateMutex
          Mutex for the table update.
        • updatingPool
          ExecutorService updatingPool
          Executor for the updating threads.
        • viewIndexes
          ArrayList<Integer> viewIndexes
          List of view indexes.
  • Package com.compomics.util.gui.utils

  • Package com.compomics.util.gui.utils.user_choice

  • Package com.compomics.util.gui.utils.user_choice.list_choosers

  • Package com.compomics.util.gui.variants.aa_substitutions

  • Package com.compomics.util.gui.waiting.waitinghandlers

    • Class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog extends JDialog implements Serializable

      • Serialized Fields

        • iProgress
          JProgressBar iProgress
        • logger
          org.apache.log4j.Logger logger
    • Class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX extends JDialog implements Serializable

      • Serialized Fields

        • canceled
          boolean canceled
          Boolean indicating whether the process has been canceled.
        • displayProgress
          boolean displayProgress
          Set if the waiting handler is to show the progress for the current process or not. Useful when running subprocesses that one wants to be able to cancel but do not want to show the progress for.
        • doNothingOnClose
          boolean doNothingOnClose
          If set to true, trying to close the progress bar will be ignored. Use this option if the process being monitored can not be stopped.
          Note: replaced by unstoppable.
        • finished
          boolean finished
          Boolean indicating whether the process has been completed.
        • mutex
          SimpleSemaphore mutex
          Mutex to synchronize multiple threads.
        • normalIcon
          Image normalIcon
          The dialog/frame icon to use when done.
        • progressBar
          JProgressBar progressBar
        • unstoppable
          boolean unstoppable
          Set this to true of the process the progress bar is used for is not possible to stop, or not possible to stop nicely. If the user still tries to close the progress bar the a warning message is first shown were the user has to confirm that he/she still wants to close the progress bar.
        • waitingActionListener
          WaitingActionListener waitingActionListener
          The waiting action listener.
        • waitingHandlerParentDialog
          JDialog waitingHandlerParentDialog
          The waitingHandlerParent dialog.
        • waitingHandlerParentFrame
          Frame waitingHandlerParentFrame
          The waitingHandlerParent frame.
        • waitingIcon
          Image waitingIcon
          The dialog/frame icon to use when waiting.
    • Class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog extends JDialog implements Serializable

      • Serialized Fields

        • backgroundPanel
          JPanel backgroundPanel
        • closeDialogWhenImportCompletesCheckBox
          JCheckBox closeDialogWhenImportCompletesCheckBox
        • closeJButton
          JButton closeJButton
        • currentTipIndex
          int currentTipIndex
          The current tip index.
        • dialog
          JDialog dialog
          Needed for the shaking feature.
        • displayProgress
          boolean displayProgress
          Set if the waiting handler is to show the progress for the current process or not. Useful when running subprocesses that one wants to be able to cancel but do not want to show the progress for.
        • lastSelectedFolder
          String lastSelectedFolder
          The last selected folder
        • layeredPane
          JLayeredPane layeredPane
        • lineBreak
          String lineBreak
          The line break type.
        • naturalLocation
          Point naturalLocation
          Used in the shaking feature.
        • nextJButton
          JButton nextJButton
        • normalIcon
          Image normalIcon
          The dialog/frame icon to use when done.
        • okButton
          JButton okButton
        • primaryMutex
          SimpleSemaphore primaryMutex
          Mutex to synchronize multiple threads on the primary error bar.
        • processName
          String processName
          The name of the process we are waiting for, e.g., 'Import Data' or 'Search'.
        • processProgressPanel
          JPanel processProgressPanel
        • progressBar
          JProgressBar progressBar
        • reportScrollPane
          JScrollPane reportScrollPane
        • reportTextArea
          JTextArea reportTextArea
        • runCanceled
          boolean runCanceled
          Boolean indicating whether the process is canceled.
        • runFinished
          boolean runFinished
          Boolean indicating whether the process is finished.
        • saveReportLabel
          JLabel saveReportLabel
        • secondaryJProgressBar
          JProgressBar secondaryJProgressBar
        • secondaryMutex
          SimpleSemaphore secondaryMutex
          Mutex to synchronize multiple threads on the secondary error bar.
        • secondaryProgressBarSplitPane
          JSplitPane secondaryProgressBarSplitPane
        • shakeTimer
          Timer shakeTimer
          Timer for the shaking feature.
        • shakeWhenFinished
          boolean shakeWhenFinished
          If true, the dialog will shake when completed. Mainly a PeptideShaker feature.
        • showTipOfTheDayCheckBox
          JCheckBox showTipOfTheDayCheckBox
        • tempJProgressBar
          JProgressBar tempJProgressBar
        • textMutex
          SimpleSemaphore textMutex
          Mutex to synchronize multiple threads writing text.
        • tipOfTheDayEditorPane
          JEditorPane tipOfTheDayEditorPane
        • tipOfTheDayJPanel
          JPanel tipOfTheDayJPanel
        • tipOfTheDayLayeredPane
          JLayeredPane tipOfTheDayLayeredPane
        • tipOfTheDayScrollPane
          JScrollPane tipOfTheDayScrollPane
        • tips
          ArrayList<String> tips
          An array list of the tip of the day.
        • toolName
          String toolName
          The name of the tool using the waiting dialog. Used for the report.
        • toolVersion
          String toolVersion
          The version number of the tool using the waiting dialog. Used for the report.
        • waitingActionListener
          WaitingActionListener waitingActionListener
          The waiting action listener.
        • waitingHandlerParent
          Frame waitingHandlerParent
          The waitingHandlerParent.
        • waitingIcon
          Image waitingIcon
          The dialog/frame icon to use when waiting.
  • Package com.compomics.util.io.export

    • Class com.compomics.util.io.export.ExportScheme extends ExperimentObject implements Serializable

      serialVersionUID:
      -4712918049667194600L
      • Serialized Fields

        • editable
          boolean editable
          A boolean indicating whether the scheme can be modified.
        • exportFeaturesMap
          HashMap<String,​ArrayList<ExportFeature>> exportFeaturesMap
          Map of the features to export indexed by feature type.
        • header
          boolean header
          Boolean indicating whether column headers shall be included.
        • includeDecoy
          Boolean includeDecoy
          Indicates whether decoy matches should be included.
        • includeSectionTitles
          boolean includeSectionTitles
          Indicates whether the title of every section shall be included.
        • indexes
          boolean indexes
          Boolean indicating whether the line shall be indexed.
        • mainTitle
          String mainTitle
          The title of the report.
        • name
          String name
          The name of the scheme.
        • sectionList
          ArrayList<String> sectionList
          Ordered list of the features in that scheme.
        • separationLines
          int separationLines
          indicates how many lines shall be used to separate sections.
        • separator
          String separator
          The separator used to separate columns.
        • validatedOnly
          Boolean validatedOnly
          Indicates whether only validated matches should be included.
  • Package com.compomics.util.io.file

  • Package com.compomics.util.io.ftp

  • Package com.compomics.util.io.json

    • Class com.compomics.util.io.json.JsonMarshaller extends ExperimentObject implements Serializable

      • Serialized Fields

        • builder
          com.google.gson.GsonBuilder builder
          GsonBuilder that can be used to append interfaces so the parser knows how to handle them.
        • gson
          com.google.gson.Gson gson
          GSON parser instance to convert JSON to Java objects and back.
  • Package com.compomics.util.io.json.marshallers

  • Package com.compomics.util.math.statistics.distributions

  • Package com.compomics.util.parameters

    • Class com.compomics.util.parameters.UtilitiesUserParameters extends ExperimentObject implements Serializable

      serialVersionUID:
      -4343570286224891504L
      • Serialized Fields

        • autoUpdate
          boolean autoUpdate
          Indicates whether the tool should check for updates.
        • checkDuplicateTitles
          boolean checkDuplicateTitles
          If true, the selected spectra will be checked for duplicate spectrum titles.
        • checkMgfSize
          boolean checkMgfSize
          If true, the mgf files will be checked for size.
        • checkPeakPicking
          boolean checkPeakPicking
          If true, the selected spectra will be checked for peak picking.
        • checkSpectrumCharges
          boolean checkSpectrumCharges
          If true, the spectra will be checked for missing charges.
        • dbFolder
          String dbFolder
          The user last used database folder.
        • deNovoGuiPath
          String deNovoGuiPath
          The path to the DeNovoGUI installation (if any). Set to null if no path is provided.
        • displayedTips
          ArrayList<String> displayedTips
          The list of already displayed tips.
        • gzip
          boolean gzip
          Boolean indicating whether the output files should be gzipped.
        • includeDateInOutputName
          boolean includeDateInOutputName
          Indicates whether the date should be included in the output.
        • javaHome
          String javaHome
          The Java Home, for example, C:\Program Files\Java\jdk1.8.0_25\bin. Null if not set. Note that this setting will be ignored of a JavaHome.txt file is found.
        • lastSelectedFolder
          LastSelectedFolder lastSelectedFolder
          The last selected folder.
        • localPrideFolder
          String localPrideFolder
          The local PRIDE projects folder.
        • maxSpectrumChargeRange
          int maxSpectrumChargeRange
          The minimum charge added when the charge is missing for a given spectrum.
        • memoryParameter
          int memoryParameter
          The memory to use.
        • mgfMaxSize
          double mgfMaxSize
          If an mgf file exceeds this limit, the user will be asked for a split.
        • mgfNSpectra
          int mgfNSpectra
          Number of spectra allowed in the split file.
        • minSpectrumChargeRange
          int minSpectrumChargeRange
          The maximum charge added when the charge is missing for a given spectrum.
        • outputData
          boolean outputData
          Indicates whether data files (mgf and FASTA) should be copied in the output.
        • outputFolder
          String outputFolder
          The user last used output folder.
        • outputOption
          OutputParameters outputOption
          The way output files should be exported.
        • peptideSelected
          Color peptideSelected
          The color of the selected peptide.
        • peptideShakerPath
          String peptideShakerPath
          The path to the PeptideShaker installation (if any). Set to null if no path is provided.
        • proteoWizardPath
          String proteoWizardPath
          The path to the ProteoWizard installation (if any). Set to null if no path is provided.
        • readTweets
          ArrayList<String> readTweets
          The list of already read tweets.
        • refMass
          double refMass
          Reference mass for the conversion of the fragment ion tolerance from ppm to Dalton.
        • relimsPath
          String relimsPath
          The path to the Relims installation (if any). Set to null if no path is provided.
        • renameXTandemFile
          boolean renameXTandemFile
          If true the X! Tandem file will be renamed.
        • reporterPath
          String reporterPath
          The path to the Reporter installation (if any). Set to null if no path is provided.
        • searchGuiPath
          String searchGuiPath
          The path to the SearchGUI installation (if any). Makes it possible to start SearchGUI directly from PeptideShaker. Set to null if no path is provided.
        • sortPsmsOnRt
          boolean sortPsmsOnRt
          If true, the PSMs are sorted on retention time, false sorts on PSM score.
        • sparklineColorDoubtful
          Color sparklineColorDoubtful
          The color used for the doubtful matches in sparkline bar chart plots.
        • sparklineColorFalsePositive
          Color sparklineColorFalsePositive
          The color used for the false positive in sparkline bar chart plots.
        • sparklineColorNonValidated
          Color sparklineColorNonValidated
          The color used for the non-validated sparkline bar chart plots.
        • sparklineColorNotFound
          Color sparklineColorNotFound
          The color used for the not found sparkline bar chart plots.
        • sparklineColorPossible
          Color sparklineColorPossible
          The color used for the possible values sparkline bar chart plots.
        • sparklineColorValidated
          Color sparklineColorValidated
          The color used for the sparkline bar chart plots.
        • spectrumAnnotatedMirroredPeakColor
          Color spectrumAnnotatedMirroredPeakColor
          The color to use for the annotated mirrored peaks.
        • spectrumAnnotatedPeakColor
          Color spectrumAnnotatedPeakColor
          The color to use for the annotated peaks.
        • spectrumAnnotatedPeakWidth
          float spectrumAnnotatedPeakWidth
          The width to use for the annotated peaks.
        • spectrumBackgroundPeakColor
          Color spectrumBackgroundPeakColor
          The color to use for the background peaks.
        • spectrumBackgroundPeakWidth
          float spectrumBackgroundPeakWidth
          The width to use for the background peaks.
        • spectrumFolder
          String spectrumFolder
          The user last used spectrum folder.
  • Package com.compomics.util.parameters.identification

  • Package com.compomics.util.parameters.identification.advanced

    • Class com.compomics.util.parameters.identification.advanced.FractionParameters extends ExperimentObject implements Serializable

      • Serialized Fields

        • fractionMolecularWeightRanges
          HashMap<String,​no.uib.jsparklines.data.XYDataPoint> fractionMolecularWeightRanges
          The list of fraction molecular weights. The key is the fraction name.
        • proteinConfidenceMwPlots
          Double proteinConfidenceMwPlots
          The minimum confidence required for a protein to be included in the calculation of the average molecular weight plot in the Fractions tab of PeptideShaker.
    • Class com.compomics.util.parameters.identification.advanced.GeneParameters extends ExperimentObject implements Serializable

      • Serialized Fields

        • autoUpdate
          Boolean autoUpdate
          If true the gene mappings will auto update.
        • backgroundSpecies
          Integer backgroundSpecies
          The taxon of the species selected as background for the GO analysis.
        • useGeneMapping
          Boolean useGeneMapping
          If true the gene mappings will be used.
    • Class com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters extends ExperimentObject implements Serializable

      • Serialized Fields

        • defaultPeptideFDR
          double defaultPeptideFDR
          The default peptide FDR.
        • defaultProteinFDR
          double defaultProteinFDR
          The default protein FDR.
        • defaultPsmFDR
          double defaultPsmFDR
          The default PSM FDR.
        • validationQCPreferences
          ValidationQcParameters validationQCPreferences
          The validation quality control preferences.
    • Class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters extends ExperimentObject implements Serializable

      • Serialized Fields

        • alignNonConfidentModifications
          boolean alignNonConfidentModifications
          Boolean indicating whether the non confidently localized modification should be aligned on the confident sites.
        • dScoreThreshold
          double dScoreThreshold
          The D-score threshold.
        • probabilisticScoreCalculation
          boolean probabilisticScoreCalculation
          Boolean indicating whether a probabilistic score is to be calculated.
        • probabilisticScoreNeutralLosses
          boolean probabilisticScoreNeutralLosses
          Boolean indicating whether neutral losses shall be accounted for in the calculation of the probabilistic score.
        • probabilisticScoreThreshold
          double probabilisticScoreThreshold
          The probabilistic score threshold.
        • selectedProbabilisticScore
          ModificationLocalizationScore selectedProbabilisticScore
          The probabilistic score selected.
        • sequenceMatchingParameters
          SequenceMatchingParameters sequenceMatchingParameters
          The preferences to use when matching modifications to amino acid sequences.
    • Class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters extends ExperimentObject implements Serializable

      • Serialized Fields

        • aaSubstitutionMatrix
          AaSubstitutionMatrix aaSubstitutionMatrix
          The amino acid substitution matrix selected.
        • fixedVariants
          HashMap<String,​ArrayList<SNPElement>> fixedVariants
          SNP positions for fixed variants
        • nAaDeletions
          int nAaDeletions
          The number of amino acid deletions allowed.
        • nAaInsertions
          int nAaInsertions
          The number of amino acid insertions allowed.
        • nAaSubstitutions
          int nAaSubstitutions
          The number of amino acid substitutions allowed.
        • nAaSwap
          int nAaSwap
          The number of amino acid swap allowed.
        • nVariants
          int nVariants
          Total number of variants allowed per peptide.
        • variantType
          PeptideVariantsParameters.VariantType variantType
          Boolean indicating whether specific variant counts should be used.
    • Class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters extends ExperimentObject implements Serializable

      • Serialized Fields

        • confidenceThreshold
          double confidenceThreshold
          Confidence below which a peptide is considered absent.
        • modificationRefinement
          boolean modificationRefinement
          Refine based on terminal and pattern modifications.
        • simplifyGroupsConfidence
          boolean simplifyGroupsConfidence
          Simplify groups based on peptide confidenc level.
        • simplifyGroupsEnzymaticity
          boolean simplifyGroupsEnzymaticity
          Simplify groups based on enzymaticity.
        • simplifyGroupsEvidence
          boolean simplifyGroupsEvidence
          Simplify groups based on UniProt evidence level.
        • simplifyGroupsVariants
          boolean simplifyGroupsVariants
          Simplify groups based on variant matching.
        • simplifyProteinGroups
          boolean simplifyProteinGroups
          Simplify protein groups.
    • Class com.compomics.util.parameters.identification.advanced.PsmScoringParameters extends ExperimentObject implements Serializable

      • Serialized Fields

        • defaultScores
          HashSet<Integer> defaultScores
          The scores to use by default.
        • minDecoysInBin
          int minDecoysInBin
          The minimal number of decoys to include in a bin to set the bin size of the score histogram.
        • spectrumMatchingScores
          HashMap<Integer,​HashSet<Integer>> spectrumMatchingScores
          The scores used to score the spectrum matches for every advocate in a map: advocate index > list of score indexes.
    • Class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters extends ExperimentObject implements Serializable

      • Serialized Fields

        • enzymaticTagsOnly
          Boolean enzymaticTagsOnly
          Boolean deciding whether tags should only be mapped to enzymatic peptides.
        • limitX
          double limitX
          Limit the share of X's a match can contain, range [0.0-1.0].
        • maxPtmsPerTagPeptide
          int maxPtmsPerTagPeptide
          The maximum number of PTMs per peptide when mapping tags.
        • minAminoAcidScore
          Integer minAminoAcidScore
          The minimum amino acid score [0-100]. Used when converting Novor peptides into tags.
        • minTagLength
          Integer minTagLength
          The minimum tag length. Used when converting Novor peptides into tags.
        • sequenceMatchingType
          SequenceMatchingParameters.MatchingType sequenceMatchingType
          The amino acid matching type.
    • Class com.compomics.util.parameters.identification.advanced.ValidationQcParameters extends ExperimentObject implements Serializable

      • Serialized Fields

        • confidenceMargin
          Double confidenceMargin
          The margin in number of resolution over the confidence threshold.
        • dbSize
          boolean dbSize
          Indicates whether the database size should be checked.
        • firstDecoy
          boolean firstDecoy
          Indicates whether the number of hits before the first decoy should be checked.
        • peptideFilters
          ArrayList<Filter> peptideFilters
          List of QC filters for peptides.
        • proteinFilters
          ArrayList<Filter> proteinFilters
          List of QC filters for proteins.
        • psmFilters
          ArrayList<Filter> psmFilters
          List of QC filters for PSMs.
  • Package com.compomics.util.parameters.identification.search

  • Package com.compomics.util.parameters.identification.tool_specific

    • Class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters extends ExperimentObject implements Serializable

      serialVersionUID:
      9056661756332085205L
      • Serialized Fields

        • decoyMode
          AndromedaParameters.AndromedaDecoyMode decoyMode
          The decoy mode.
        • dependentLosses
          Boolean dependentLosses
          Boolean indicating whether neutral losses should be sequence dependent.
        • empiricalCorrection
          Boolean empiricalCorrection
          Boolean indicating whether the empirical correction should be used.
        • equalIL
          Boolean equalIL
          Boolean indicating whether I and L should be considered indistinguishable.
        • fragmentAll
          Boolean fragmentAll
          Boolean indicating whether the fragment all option should be used.
        • fragmentationMethod
          FragmentationMethod fragmentationMethod
          The fragmentation method used.
        • higherCharge
          Boolean higherCharge
          Boolean indicating whether the higher charge option should be used.
        • includeAmmonia
          Boolean includeAmmonia
          Boolean indicating whether ammonia losses should be accounted for.
        • includeWater
          Boolean includeWater
          Boolean indicating whether water losses should be accounted for.
        • maxCombinations
          Integer maxCombinations
          The maximum number of combinations.
        • maxNumberOfModifications
          Integer maxNumberOfModifications
          The maximal number of modifications.
        • maxPeptideLengthNoEnzyme
          Integer maxPeptideLengthNoEnzyme
          The maximal peptide length when no enzyme is used.
        • maxPeptideMass
          Double maxPeptideMass
          The maximal peptide mass.
        • minPeptideLengthNoEnzyme
          Integer minPeptideLengthNoEnzyme
          The minimal peptide length when no enzyme is used.
        • numberOfCandidates
          Integer numberOfCandidates
          The number of candidates to report.
        • ptmIndexes
          HashMap<Integer,​String> ptmIndexes
          Map of the Andromeda indexes used for user modifications in this search.
        • topPeaks
          Integer topPeaks
          The top peaks number.
        • topPeaksWindow
          Integer topPeaksWindow
          The top peaks window size.
    • Class com.compomics.util.parameters.identification.tool_specific.CometParameters extends ExperimentObject implements Serializable

      serialVersionUID:
      -2996752557726296967L
      • Serialized Fields

        • batchSize
          Integer batchSize
          When this parameter is set to a non-zero value, say 5000, this causes Comet to load and search about 5000 spectra at a time, looping through sets of 5000 spectra until all data have been analyzed. Set this parameter to 0 to load and search all spectra at once.
        • enzymeType
          Integer enzymeType
          The enzyme type: 1 for a semi-enzyme search, 2 for a full-enzyme search, 8 for a semi-enzyme search, unspecific cleavage on peptide's C-terminus and 9 for a semi-enzyme search, unspecific cleavage on peptide's N-terminus.
        • fragmentBinOffset
          Double fragmentBinOffset
          The fragment bin offset.
        • isotopeCorrection
          Integer isotopeCorrection
          Isotope correction setting. 0: analyzes no isotope offsets, just the given precursor mass, 1: searches 0, +1 isotope offsets, 2: searches 0, +1, +2 isotope offsets, 3: searches 0, +1, +2, +3 isotope offsets, 4: searches -8, -4, 0, +4, +8 isotope offsets (for +4/+8 stable isotope labeling).
        • lowerClearMzRange
          Double lowerClearMzRange
          Defines the lower m/z value to clear out in each MS/MS spectra.
        • maxFragmentCharge
          Integer maxFragmentCharge
          The maximum fragment charge.
        • maxPeptideLength
          Integer maxPeptideLength
          The maximal peptide length. Maximum length for Comet is 63.
        • maxPrecursorMass
          Double maxPrecursorMass
          The maximum precursor mass.
        • maxVariableMods
          Integer maxVariableMods
          The maximum number of variable modifications per peptide.
        • minPeakIntensity
          Double minPeakIntensity
          The minimum peak intensity.
        • minPeaks
          Integer minPeaks
          The minimum allowed number of peaks in a spectrum.
        • minPeptideLength
          Integer minPeptideLength
          The minimum peptide length.
        • minPrecursorMass
          Double minPrecursorMass
          The minimum precursor mass.
        • numberOfSpectrumMatches
          Integer numberOfSpectrumMatches
          The maximum number of spectrum matches.
        • printExpectScore
          Boolean printExpectScore
          A boolean flag this determines whether or not the expectation score (E-value) is reported in .out and SQT formats. Note that the E-value is always reported in pepXML output. This parameter is only relevant for results reported in .out and SQT formats.
        • removeMethionine
          Boolean removeMethionine
          This parameter controls whether Comet will automatically remove the N-terminal methionine from a sequence entry.
        • removePrecursor
          Integer removePrecursor
          Remove precursor peak. An input value of 0 will not perform any precursor removal. An input value of 1 will remove all peaks around the precursor m/z. An input value of 2 will remove all charge reduced precursor peaks as expected to be present for ETD/ECD spectra. An input value of 3 will remove the HPO3 (-80) and H3PO4 (-98) precursor phosphate neutral loss peaks.
        • removePrecursorTolerance
          Double removePrecursorTolerance
          This parameter specifies the mass tolerance (in Da) around each precursor m/z that would be removed when the remove_precursor_peak option is invoked.
        • requireVariableMods
          Boolean requireVariableMods
          Controls whether the peptides must contain at least one variable modification i.e. force all reported peptides to have a variable modification.
        • selectedOutputFormat
          CometParameters.CometOutputFormat selectedOutputFormat
          The selected output format.
        • theoreticalFragmentIonsSumOnly
          Boolean theoreticalFragmentIonsSumOnly
          The correlation score type. This parameter specifies how theoretical fragment ion peaks are represented.
        • upperClearMzRange
          Double upperClearMzRange
          Defines the upper m/z value to clear out in each MS/MS spectra.
        • useSparseMatrix
          Boolean useSparseMatrix
          Deprecated.
          from Comet release 2015.02 all searches use this internal data representation by default
          Controls whether or not internal sparse matrix data representation is used.
    • Class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters extends ExperimentObject implements Serializable

      serialVersionUID:
      -3107089648450731330L
      • Serialized Fields

        • adjustPrecursorMass
          boolean adjustPrecursorMass
          If true, the preprocessing step will correct the precursor mass by adjusting it through a specified range in steps of a specified length, finally choosing the optimal adjustment. The optimal adjustment is the one that maximizes the sum of products of all complementary peaks in the spectrum. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
        • complementMzTolerance
          double complementMzTolerance
          When adjusting the precursor mass, this parameter controls how much tolerance there is on each side of the calculated m/z when looking for a peaks complement. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
        • complementScoreWeight
          double complementScoreWeight
          This parameter controls how complement scores are combined to form a total score. Peaks that match to complementary ions within the spectrum are more trustworthy than other peaks. DirecTag assesses the number and concordance of complementary ions for each tag. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
        • deisotopingMode
          int deisotopingMode
          Deisotoping a spectrum (consolidating isotopic peak intensities into the monoisotopic peaks intensity) during preprocessing will significantly improve precursor adjustment, and it may be desirable to keep the deisotoped spectrum around for candidate scoring as well. Set to 0, no deisotoping will be used. Set to 1, deisotoping will be used for precursor adjustment only. Set to 2, deisotoping will be used for both precursor adjustment and for candidate scoring. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
        • duplicateSpectra
          boolean duplicateSpectra
          If DirecTag determines a spectrum to be multiply charged and this parameter is true, the spectrum will be copied and treated as if it was all possible charge states from +2 to +<NumChargeStates>. If this parameter is false, the spectrum will simply be treated as a +2. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
        • intensityScoreWeight
          double intensityScoreWeight
          This parameter controls how intensity scores are combined to form a total score. DirecTag scores tags on the basis of their peak intensities. Tags that contain intense peaks are more likely to be correct than those that contain average peaks. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
        • isotopeMzTolerance
          double isotopeMzTolerance
          When deisotoping a spectrum, an isotopic peak is one that is the mass of a neutron higher than another peak, tolerating variation based on the value of this parameter. Deisotoping actually traverses the spectrum at multiple charge states, starting from the highest (NumChargeStates) and ending at the lowest. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
        • maxDynamicMods
          int maxDynamicMods
          This parameter sets the maximum number of modified residues that may be in any candidate sequence. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
        • maxPeakCount
          int maxPeakCount
          Another way of increasing the effectiveness of the MVH scoring algorithm when used for tagging is to set an upper bound on the number of peaks in a spectrum before generating tags. This step tends to get rid of most noise peaks and makes tagging much more feasible because so many fewer false positives are generated. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
        • maxPrecursorAdjustment
          double maxPrecursorAdjustment
          When adjusting the precursor mass, this parameter sets the upper mass limit of adjustment allowable from the original precursor mass, measured in Daltons. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
        • maxTagCount
          int maxTagCount
          This parameter sets the maximum number of sequence tags to report for each spectrum. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
        • minPrecursorAdjustment
          double minPrecursorAdjustment
          When adjusting the precursor mass, this parameter sets the lower mass limit of adjustment allowable from the original precursor mass, measured in Daltons. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
        • mzFidelityScoreWeight
          double mzFidelityScoreWeight
          This parameter controls how mzFidelity scores are combined to form a total score. m/z fidelity for a tag can be characterized through SSE. DirecTag evaluates the consistency of fragment ion m/z values for each tag. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
        • numChargeStates
          int numChargeStates
          Controls the number of charge states that DirecTag will handle during all stages of the program. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
        • numIntensityClasses
          int numIntensityClasses
          Before scoring any candidates, experimental spectra have their peaks stratified into the number of intensity classes specified by this parameter. Spectra that are very dense in peaks will likely benefit from more intensity classes in order to best take advantage of the variation in peak intensities. Spectra that are very sparse will not see much benefit from using many intensity classes. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
        • outputSuffix
          String outputSuffix
          The output of a DirecTag job will be a TAGS file for each input file. The string specified by this parameter will be appended to each TAGS0.5 filename. It is useful for differentiating jobs within a single directory. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
        • precursorAdjustmentStep
          double precursorAdjustmentStep
          When adjusting the precursor mass, this parameter sets the size of the steps between adjustments, measured in Daltons. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
        • tagLength
          int tagLength
          A sequence tag is generated from the gaps between a number of peaks equal to this parameter plus one. Longer tag lengths are more specific, but harder to find because many consecutive ion fragments are rare. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
        • ticCutoffPercentage
          double ticCutoffPercentage
          In order to maximize the effectiveness of the MVH scoring algorithm, an important step in preprocessing the experimental spectra is filtering out noise peaks. Noise peaks are filtered out by sorting the original peaks in descending order of intensity, and then picking peaks from that list until the cumulative ion current of the picked peaks divided by the total ion current (TIC) is greater than or equal to this parameter. Lower percentages mean that less of the spectra total intensity will be allowed to pass through preprocessing. See the section on Advanced Usage for tips on how to use this parameter optimally. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
        • useChargeStateFromMS
          boolean useChargeStateFromMS
          If true, DirecTag will use the charge state from the input data if it is available. If false, or if charge state is not available from a particular spectrum, DirecTag will use its internal algorithm to determine charge state. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
        • variableModifications
          ArrayList<String> variableModifications
          The variable modifications in the order used.
    • Class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters extends ExperimentObject implements Serializable

      • Serialized Fields

        • deconvolutionIntensityRatio
          Double deconvolutionIntensityRatio
          Deconvolution intensity ratio.
        • deconvolutionMassTolerance
          Double deconvolutionMassTolerance
          Deconvolution mass tolerance.
        • deconvolutionMassToleranceType
          MetaMorpheusParameters.MetaMorpheusToleranceType deconvolutionMassToleranceType
          Deconvolution mass tolerance type: PPM or Absolute.
        • decoyType
          MetaMorpheusParameters.MetaMorpheusDecoyType decoyType
          Decoy type: None, Reverse or Slide.
        • dissociationType
          MetaMorpheusParameters.MetaMorpheusDissociationType dissociationType
          Dissociation type.
        • doPrecursorDeconvolution
          Boolean doPrecursorDeconvolution
          Do precursor deconvolution.
        • fragmentationTerminus
          MetaMorpheusParameters.MetaMorpheusFragmentationTerminusType fragmentationTerminus
          Fragmentation terminus type.
        • gPtmCategories
          ArrayList<ModificationCategory> gPtmCategories
          The modification categories to include in the G-PTM search.
        • initiatorMethionineBehavior
          MetaMorpheusParameters.MetaMorpheusInitiatorMethionineBehaviorType initiatorMethionineBehavior
          Initiator methionine behavior.
        • massDiffAcceptorType
          MetaMorpheusParameters.MetaMorpheusMassDiffAcceptorType massDiffAcceptorType
          Mass difference acceptor type.
        • maxFragmentSize
          Double maxFragmentSize
          Max fragment size.
        • maxHeterozygousVariants
          Integer maxHeterozygousVariants
          Max heterozygous variants.
        • maxModificationIsoforms
          Integer maxModificationIsoforms
          Max modification isoforms.
        • maxModsForPeptide
          Integer maxModsForPeptide
          Maximum number of modifications per peptide.
        • maxPeptideLength
          Integer maxPeptideLength
          Maximum peptide length.
        • minAllowedIntensityRatioToBasePeak
          Double minAllowedIntensityRatioToBasePeak
          Minimum allowed intensity ratio to base peak.
        • minPeptideLength
          Integer minPeptideLength
          Minimum peptide length.
        • minVariantDepth
          Integer minVariantDepth
          Min variant depth.
        • modPeptidesAreDifferent
          Boolean modPeptidesAreDifferent
          Modified peptides are different.
        • noOneHitWonders
          Boolean noOneHitWonders
          No one hit wonders.
        • normalizePeaksAcrossAllWindows
          Boolean normalizePeaksAcrossAllWindows
          Normalize peaks across all windows.
        • numberOfPeaksToKeepPerWindow
          Integer numberOfPeaksToKeepPerWindow
          Number of peaks to keep per window.
        • numberOfWindows
          Integer numberOfWindows
          Number of windows.
        • runGptm
          boolean runGptm
          If true, the G-PTM search is performed.
        • scoreCutoff
          Double scoreCutoff
          Score cut-off.
        • searchTarget
          Boolean searchTarget
          Search target.
        • searchType
          MetaMorpheusParameters.MetaMorpheusSearchType searchType
          Search type.
        • totalPartitions
          Integer totalPartitions
          Number of partitions when doing a modern or non-specific search.
        • trimMs1Peaks
          Boolean trimMs1Peaks
          Trim Ms1 peaks.
        • trimMsMsPeaks
          Boolean trimMsMsPeaks
          Trim MsMs peaks.
        • useDeltaScore
          boolean useDeltaScore
          Use delta score.
        • useProvidedPrecursorInfo
          Boolean useProvidedPrecursorInfo
          Use provided precursor info.
        • windowWidthThomson
          Double windowWidthThomson
          Window width in Thomson.
        • writeMzId
          Boolean writeMzId
          Write mzId output.
        • writePepXml
          Boolean writePepXml
          Write pepXml output.
    • Class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters extends ExperimentObject implements Serializable

      serialVersionUID:
      -8458620189315975268L
      • Serialized Fields

        • generateDecoy
          boolean generateDecoy
          Defines whether a decoy database shall be created and searched against. Decoy FASTS files are generated by reverting protein sequences, accessions are marked with the prefix “REV_”.
        • instrumentID
          String instrumentID
          The MS Amanda instrument ID.
        • lowMemoryMode
          Boolean lowMemoryMode
          Deprecated.
          since MS Amanda 2.0
          Defines whether the low memory mode is used.
        • maxLoadedProteins
          Integer maxLoadedProteins
          Maximum number of proteins loaded into memory (1000-500000).
        • maxLoadedSpectra
          Integer maxLoadedSpectra
          Maximum number of spectra loaded into memory (1000-500000).
        • maxModifications
          Integer maxModifications
          Maximum number of occurrences of a specific modification on a peptide (0-10).
        • maxModificationSites
          Integer maxModificationSites
          Maximum number of potential modification sites per modification per peptide (0-20).
        • maxNeutralLosses
          Integer maxNeutralLosses
          Maximum number of water and ammonia losses per peptide (0-5).
        • maxNeutralLossesPerModification
          Integer maxNeutralLossesPerModification
          Maximum number identical modification specific losses per peptide (0-5).
        • maxPeptideLength
          Integer maxPeptideLength
          Maximum peptide length.
        • maxRank
          Integer maxRank
          The maximum rank [1-999].
        • maxVariableModifications
          Integer maxVariableModifications
          Maximum number of variable modifications per peptide (0-10).
        • minPeptideLength
          Integer minPeptideLength
          Minimum peptide length.
        • monoisotopic
          boolean monoisotopic
          Defines whether monoisotopic mass values shall be used (in contrast to average mass values).
        • outputFormat
          String outputFormat
          The output format: csv or mzIdentML.
        • performDeisotoping
          Boolean performDeisotoping
          Defines whether deisotoping is to be performed.
        • reportBothBestHitsForTD
          Boolean reportBothBestHitsForTD
          False = combine ranks for target and decoy, true = own rankings for target and decoy.
    • Class com.compomics.util.parameters.identification.tool_specific.MsgfParameters extends ExperimentObject implements Serializable

      serialVersionUID:
      -2656523093031942973L
      • Serialized Fields

        • additionalOutput
          boolean additionalOutput
          Output additional features.
        • fragmentationType
          int fragmentationType
          The MS-GF+ fragmentation type ID: 0: As written in the spectrum or CID if no info, 1: CID, 2: ETD, 3: HCD, 4: UVPD.
        • instrumentID
          int instrumentID
          The MS-GF+ instrument ID: 0: Low-res LCQ/LTQ (Default), 1: Orbitrap/FTICR, 2: TOF, 3: Q-Exactive.
        • maxPeptideLength
          Integer maxPeptideLength
          The maximal peptide length.
        • minPeptideLength
          Integer minPeptideLength
          The minimum peptide length.
        • numberOfModificationsPerPeptide
          Integer numberOfModificationsPerPeptide
          The maximum number of modifications per peptide.
        • numberOfSpectrumMarches
          Integer numberOfSpectrumMarches
          The maximum number of spectrum matches.
        • numberOfTasks
          Integer numberOfTasks
          The number of tasks. Null if not set, meaning that it will be internally calculated based on the inputs. More tasks than threads will reduce the memory requirements of the search, but will be slower (how much depends on the inputs). If the spectrum file is particularly large, a larger number of tasks will decrease the possibility of out of memory errors. If the FASTA file being searched is larger than 10MB, more tasks will cause a noticeably longer search time.
        • numberTolerableTermini
          Integer numberTolerableTermini
          The number of tolerable termini. E.g. For trypsin, 0: non-tryptic, 1: semi-tryptic, 2: fully-tryptic peptides only.
        • protocol
          int protocol
          The MS-GF+ protocol ID: 0: Automatic, 1: Phosphorylation, 2: iTRAQ, 3: iTRAQPhospho, 4: TMT, 5: Standard.
        • searchDecoyDatabase
          boolean searchDecoyDatabase
          Indicates whether MS-GF+ is to create and search a decoy database or not.
    • Class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters extends ExperimentObject implements Serializable

      serialVersionUID:
      8755937399680481097L
      • Serialized Fields

        • classSizeMultiplier
          Integer classSizeMultiplier
          The multiplier controlling the size of each intensity class relative to the class above it.
        • computeXCorr
          Boolean computeXCorr
          If true, a Sequest-like cross correlation (xcorr) score will be calculated for the top ranking hits in each spectrum’s result set.
        • fragmentationRule
          String fragmentationRule
          The fragmentation rules. CID (b, y), ETD (c, z*) or manual (user-defined (a comma-separated list of [abcxyz] or z* (z+1), e.g. manual:b,y,z)
        • lowerIsotopeCorrection
          Integer lowerIsotopeCorrection
          Deprecated.
          now general search setting
          The lower isotope correction range.
        • maxDynamicMods
          Integer maxDynamicMods
          The maximum number of variable modifications.
        • maxPeakCount
          Integer maxPeakCount
          The max number of peaks to use.
        • maxPeptideLength
          Integer maxPeptideLength
          The maximal peptide length.
        • maxPrecursorMass
          Double maxPrecursorMass
          The maximum precursor mass considered.
        • minPeptideLength
          Integer minPeptideLength
          The minimum peptide length.
        • minPrecursorMass
          Double minPrecursorMass
          The minimum precursor mass considered.
        • minTerminiCleavages
          Integer minTerminiCleavages
          By default, when generating peptides from the protein database, a peptide must start and end at a valid cleavage site. Setting this parameter to 0 or 1 will reduce that requirement, so that neither terminus or only one terminus of the peptide must match one of the cleavage rules specified in the CleavageRules parameter. This parameter is useful to turn a tryptic digest into a semi-tryptic digest.
        • numberOfBatches
          Integer numberOfBatches
          The number of batches per node to strive for when using the MPI-based parallelization features.
        • numberOfSpectrumMatches
          Integer numberOfSpectrumMatches
          The maximum number of spectrum matches.
        • numIntensityClasses
          Integer numIntensityClasses
          The number of intensity classes.
        • outputFormat
          String outputFormat
          The output format.
        • ticCutoffPercentage
          Double ticCutoffPercentage
          The TicCutoffPercentage.
        • upperIsotopeCorrection
          Integer upperIsotopeCorrection
          Deprecated.
          now general search setting
          The upper isotope correction range.
        • useSmartPlusThreeModel
          Boolean useSmartPlusThreeModel
          If true, the UseSmartPlusThreeModel is used.
    • Class com.compomics.util.parameters.identification.tool_specific.NovorParameters extends ExperimentObject implements Serializable

      serialVersionUID:
      -1685402448885208852L
      • Serialized Fields

        • fragmentationMethod
          String fragmentationMethod
          The fragmentation method.
        • massAnalyzer
          String massAnalyzer
          The mass analyzer.
        • novorPtmMap
          HashMap<String,​String> novorPtmMap
          A map from the Novor PTM short name to the utilities PTM names. Novor PTM short name > utilities PTM name.
    • Class com.compomics.util.parameters.identification.tool_specific.OmssaParameters extends ExperimentObject implements Serializable

      serialVersionUID:
      -6704164074092668637L
      • Serialized Fields

        • cleaveNtermMethionine
          boolean cleaveNtermMethionine
          Cleave the N-term methionines.
        • consecutiveIonProbability
          double consecutiveIonProbability
          Probability of consecutive ions.
        • determineChargePlusOneAlgorithmically
          boolean determineChargePlusOneAlgorithmically
          Determine charge plus one algorithmically.
        • doubleChargeWindow
          int doubleChargeWindow
          Window width for doubly charged fragments.
        • estimateCharge
          boolean estimateCharge
          Indicates whether the precursor charge estimation option.
        • fractionOfPeaksForChargeEstimation
          double fractionOfPeaksForChargeEstimation
          Fraction of peaks below the precursor to estimate charge >1.
        • highIntensityCutOff
          double highIntensityCutOff
          High intensity cut-off as percentage of the most intense peak.
        • hitListLength
          int hitListLength
          The maximal hit list length.
        • intensityCutOffIncrement
          double intensityCutOffIncrement
          Intensity cut-off increment.
        • iterativeReplaceEvalue
          double iterativeReplaceEvalue
          E-value threshold to replace a hit in the iterative search (0 means replace if better).
        • iterativeSequenceEvalue
          double iterativeSequenceEvalue
          E-value threshold to include a sequence in the iterative search (0 means all).
        • iterativeSpectrumEvalue
          double iterativeSpectrumEvalue
          E-value threshold to include a spectrum in the iterative search (0 means all).
        • lowIntensityCutOff
          double lowIntensityCutOff
          Low intensity cut-off as percentage of the most intense peak.
        • maxEValue
          double maxEValue
          Maximal e-value cut-off.
        • maxFragmentCharge
          int maxFragmentCharge
          Maximum fragment charge.
        • maxFragmentPerSeries
          int maxFragmentPerSeries
          Maximal number of fragment per series.
        • maxHitsPerSpectrumPerCharge
          int maxHitsPerSpectrumPerCharge
          Maximum number of hits searched per spectrum and per charge.
        • maxMzLadders
          int maxMzLadders
          Maximum length of m/z ladders.
        • maxPeptideLength
          int maxPeptideLength
          The maximal peptide length (for semi and non tryptic searches).
        • memoryMappedSequenceLibraries
          boolean memoryMappedSequenceLibraries
          Map sequence in libraries in memory
        • minAnnotatedPeaks
          int minAnnotatedPeaks
          Minimal number of annotated peaks required per spectrum.
        • minimalChargeForMultipleChargedFragments
          int minimalChargeForMultipleChargedFragments
          The minimal charge to be considered for multiple fragment charges.
        • minPeaks
          int minPeaks
          Minimal number of peaks per spectrum.
        • minPeptideLength
          int minPeptideLength
          The minimum peptide length (for semi and non tryptic searches).
        • minPrecPerSpectrum
          int minPrecPerSpectrum
          Minimal precursor per spectrum.
        • nAnnotatedMostIntensePeaks
          int nAnnotatedMostIntensePeaks
          Number of annotated most intense peaks required per spectrum.
        • neutronThreshold
          double neutronThreshold
          Mass after which a the exact mass of a neutron should be considered.
        • noProlineRuleSeries
          ArrayList<Integer> noProlineRuleSeries
          ID numbers of ion series to apply no product ions at proline rule at. NOTE: not implemented for now.
        • nPeaksIndoubleChargeWindow
          int nPeaksIndoubleChargeWindow
          Number of peaks allowed in a doubly charged window.
        • nPeaksInSingleChargeWindow
          int nPeaksInSingleChargeWindow
          Number of peaks allowed in a singly charged window.
        • ptmIndexes
          HashMap<Integer,​String> ptmIndexes
          Map of the OMSSA indexes used for user modifications in this search.
        • removePrecursor
          boolean removePrecursor
          Indicates whether the precursor removal option is used.
        • scalePrecursor
          boolean scalePrecursor
          Indicates whether the precursor scaling option is used.
        • searchForwardFragmentFirst
          boolean searchForwardFragmentFirst
          Search forward ions (b1) first.
        • searchPositiveIons
          boolean searchPositiveIons
          Search positive ions (if false, negative ions).
        • searchRewindFragments
          boolean searchRewindFragments
          Search c-terminal ions.
        • selectedOutput
          String selectedOutput
          The selected output type (see omssaOutputTypes).
        • singleChargeWindow
          int singleChargeWindow
          Window width for singly charged fragments.
        • useCorrelationCorrectionScore
          boolean useCorrelationCorrectionScore
          Use correlation correction score.
    • Class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters extends ExperimentObject implements Serializable

      serialVersionUID:
      -8056507693211793829L
      • Serialized Fields

        • correctPrecursorMass
          Boolean correctPrecursorMass
          Indicates whether the precursor mass shall be corrected.
        • discardLowQualitySpectra
          Boolean discardLowQualitySpectra
          Indicates whether the low quality spectra shall be discarded.
        • estimateCharge
          Boolean estimateCharge
          Indicates whether the precursor charge estimation option.
        • fragmentationModel
          String fragmentationModel
          PepNovo fragmentation model.
        • generateQuery
          Boolean generateQuery
          Indicates whether a blast query shall be generated.
        • hitListLength
          Integer hitListLength
          The maximal hit list length for PepNovo+. Max is 20.
        • pepNovoPtmMap
          Map<String,​String> pepNovoPtmMap
          A map from the PepNovo PTM symbols to the utilities PTM names.
    • Class com.compomics.util.parameters.identification.tool_specific.PNovoParameters extends ExperimentObject implements Serializable

      serialVersionUID:
      7525455518683797145L
      • Serialized Fields

        • acticationType
          String acticationType
          The activation type (HCD, CID or ETD).
        • lowerPrecursorMass
          int lowerPrecursorMass
          The minimum precursor mass.
        • numberOfPeptides
          int numberOfPeptides
          The number of peptides reported.
        • pNovoPtmMap
          HashMap<Character,​String> pNovoPtmMap
          A map from the pNovo PTM character to the utilities PTM names. pNovo PTM character > utilities PTM name.
        • pNovoResidueMap
          HashMap<Character,​Character> pNovoResidueMap
          A map from the pNovo character to the original amino acids residue. pNovo PTM character > original amino acids residue.
        • upperPrecursorMass
          int upperPrecursorMass
          The maximum precursor mass.
    • Class com.compomics.util.parameters.identification.tool_specific.TideParameters extends ExperimentObject implements Serializable

      serialVersionUID:
      1049197890002802776L
      • Serialized Fields

        • clipNtermMethionine
          Boolean clipNtermMethionine
          If true, starting methionine peptides will be included both with and without the starting M.
        • computeExactPValues
          Boolean computeExactPValues
          If true, the exact p-values will be computed.
        • computeSpScore
          Boolean computeSpScore
          If true, the SP score will be computed.
        • concatenateTargetDecoy
          Boolean concatenateTargetDecoy
          If true, target and decoy search results are reported in a single file named "tide-search.txt," and only the top-scoring N matches (as specified via --top-match) are reported for each spectrum, irrespective of whether the matches involve target or decoy peptides.
        • decoyFormat
          String decoyFormat
          The decoy format.
        • decoySeed
          Integer decoySeed
          The seed of the random number generator with the given unsigned integer when generating the decoy decoys. When given the string "time," the seed is set with the system time.
        • digestionType
          String digestionType
          The enzyme digestion type: full-digest or partial-digest.
        • fastIndexFolderName
          String fastIndexFolderName
          The name of the FASTA index folder.
        • keepTerminalAminoAcids
          String keepTerminalAminoAcids
          Keep terminal amino acids when creating decoys.
        • maxPeptideLength
          Integer maxPeptideLength
          The maximal peptide length.
        • maxPrecursorMass
          Double maxPrecursorMass
          The maximum precursor mass considered.
        • maxSpectrumMz
          Double maxSpectrumMz
          The maximum spectrum m/z to search for. Null if no maximum.
        • maxVariableModificationsPerPeptide
          Integer maxVariableModificationsPerPeptide
          The maximum number of variable modifications allowed on a single peptide. The default is no limit (set to null).
        • maxVariableModificationsPerTypePerPeptide
          Integer maxVariableModificationsPerTypePerPeptide
          The maximum number of variable modifications of each type allowed on a single peptide.
        • minPeptideLength
          Integer minPeptideLength
          The minimum peptide length.
        • minPrecursorMass
          Double minPrecursorMass
          The minimum precursor mass considered.
        • minSpectrumMz
          Double minSpectrumMz
          The minimum spectrum m/z to search for.
        • minSpectrumPeaks
          Integer minSpectrumPeaks
          The minimum number of peaks in a spectrum for it to be searched.
        • monoisotopicPrecursor
          Boolean monoisotopicPrecursor
          If true, a monoisotopic precursor mass is used, false uses average.
        • mzBinOffset
          Double mzBinOffset
          In the discretization of the m/z axes of the observed and theoretical spectra, this parameter specifies the location of the left edge of the first bin, relative to mass = 0 (i.e., mz-bin-offset = 0.xx means the left edge of the first bin will be located at +0.xx Da). The parameter must lie in the range 0 ≤ mz-bin-offset ≤ 1.
        • mzBinWidth
          Double mzBinWidth
          Before calculation of the XCorr score, the m/z axes of the observed and theoretical spectra are discretized. This parameter specifies the size of each bin. The exact formula is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079 and for high resolution ms/ms 0.02 is recommended.
        • mzidOutput
          Boolean mzidOutput
          If true, mzid output is generated.
        • numberOfSpectrumMatches
          Integer numberOfSpectrumMatches
          The maximum number of spectrum matches per peptide.
        • outputFolderName
          String outputFolderName
          The name of the output folder (relative to the Tide working folder).
        • pepXmlOutput
          Boolean pepXmlOutput
          If true, pepxml output is generated.
        • pinOutput
          Boolean pinOutput
          If true, Percolator input file is generated.
        • printPeptides
          Boolean printPeptides
          If true, a list of all the peptides will be printed to the output folder.
        • printProgressIndicatorSize
          Integer printProgressIndicatorSize
          Show search progress by printing every n spectra searched. Set to 0 to show no search progress.
        • removePrecursor
          Boolean removePrecursor
          If true, the precursor peak will be removed. The range removed is specified by
        • removePrecursorTolerance
          Double removePrecursorTolerance
          The tolerance in (Th) used when removing the precursor using removePrecursor.
        • removeTempFolders
          Boolean removeTempFolders
          If true, the tide output and index folders are removed when the search has completed.
        • spectrumCharges
          String spectrumCharges
          The spectrum charges to search for: 1,2,3 or all. With 'all' every spectrum will be searched and spectra with multiple charge states will be searched once at each charge state. With 1, 2, or 3 only spectra with that charge will be searched.
        • sqtOutput
          Boolean sqtOutput
          If true, SQT output is generated.
        • storeSpectraFileName
          String storeSpectraFileName
          Specify the name of the file where the binarized fragmentation spectra will be stored. Subsequent runs of crux tide-search will execute more quickly if provided with the spectra in binary format. The filename is specified relative to the current working directory, not the Crux output directory (as specified by --output-dir).
        • textOutput
          Boolean textOutput
          If true, tab delimited text file output is generated.
        • useFlankingPeaks
          Boolean useFlankingPeaks
          If true, the search includes flanking peaks around singly charged b and y theoretical ions. Each flanking peak occurs in the adjacent m/z bin and has half the intensity of the primary peak.
        • useNeutralLossPeaks
          Boolean useNeutralLossPeaks
          Controls whether neutral loss ions are considered in the search. Two types of neutral losses are included and are applied only to singly charged b- and y-ions: loss of ammonia (NH3, 17.0086343 Da) and H2O (18.0091422). Each neutral loss peak has intensity 1/5 of the primary peak.
        • verbosity
          Integer verbosity
          The verbosity of the progress output: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info.
    • Class com.compomics.util.parameters.identification.tool_specific.XtandemParameters extends ExperimentObject implements Serializable

      serialVersionUID:
      -5898951075262732261L
      • Serialized Fields

        • dynamicRange
          double dynamicRange
          The dynamic range for spectrum filtering. When the highest peak is given the dynamic range value peaks smaller than one are ignored. e.g. for 100 peaks with an intensity <1% of the highest peak are ignored.
        • maxEValue
          double maxEValue
          Maximal e-value cut-off.
        • maximumExpectationValueRefinement
          double maximumExpectationValueRefinement
          The maximum expectation value for a hit to be considered during the refinement process.
        • minFragmentMz
          double minFragmentMz
          The minimum fragment mass.
        • minPeaksPerSpectrum
          int minPeaksPerSpectrum
          The minimum number of peaks per spectrum.
        • minPrecursorMass
          double minPrecursorMass
          The minimum precursor mass.
        • nPeaks
          int nPeaks
          The number of most intense peaks to consider.
        • outputHistograms
          boolean outputHistograms
          If true histograms will be exported to the result file.
        • outputProteins
          boolean outputProteins
          If true protein details will be exported to the to the result file.
        • outputResults
          String outputResults
          The output results filter: all, valid or stochastic.
        • outputSequences
          boolean outputSequences
          If true protein sequences will be added to the protein details to the result file.
        • outputSpectra
          boolean outputSpectra
          If true spectra will be exported to the result file.
        • parentMonoisotopicMassIsotopeError
          boolean parentMonoisotopicMassIsotopeError
          Sets whether the parent ion mass tolerance is expanded by opening up multiple tolerance windows centered on the first and second 13C isotope peaks for a peptide.
        • potentialModificationsForFullRefinment
          boolean potentialModificationsForFullRefinment
          Sets the modifications to be used during the refinement process.
        • proteinPtmComplexity
          double proteinPtmComplexity
          The value of the command "protein, ptm complexity" (C, a floating point number 0.0–12.0) sets the maximum number of variable modification alternatives that will be tested for a particular peptide. The number of alternatives is 2.0C. If this number is not specified, the default value C = 6.0 will be used.
        • proteinQuickAcetyl
          boolean proteinQuickAcetyl
          Indicates whether the protein quick acetylation option should be triggered.
        • quickPyrolidone
          boolean quickPyrolidone
          Indicates whether the quick pyrolidone option should be triggered.
        • refine
          boolean refine
          Triggers the refinement process.
        • refinePointMutations
          boolean refinePointMutations
          Sets whether point mutations should be search for during the refinement process.
        • refineSemi
          boolean refineSemi
          Sets whether semi enzymatic peptides should be search for during the refinement process.
        • refineSnaps
          boolean refineSnaps
          Indicates whether snAPs should be used during the refinement process.
        • refineSpectrumSynthesis
          boolean refineSpectrumSynthesis
          Sets whether the spectrum synthesis option should be used during the refinement process.
        • refineUnanticipatedCleavages
          boolean refineUnanticipatedCleavages
          Sets whether unexpected cleavages should be search for during the refinement process.
        • skylinePath
          String skylinePath
          The skyline path.
        • stpBias
          boolean stpBias
          Indicates whether the phospho stp bias option should be triggered.
        • useNoiseSuppression
          boolean useNoiseSuppression
          Triggers the noise suppression function. Note: ignored in X!Tandem VENGEANCE (2015.12.15) and newer.
  • Package com.compomics.util.parameters.quantification.spectrum_counting

  • Package com.compomics.util.pride

  • Package com.compomics.util.pride.prideobjects

  • Package com.compomics.util.sun