JavaHomeOrMemoryDialogParent javaHomeOrMemoryDialogParent
JDialog welcomeDialog
String toolName
JPanel backgroundPanel
JButton browseButton
JButton cancelButton
JSeparator jSeparator1
JButton javaHomeHelpJButton
JLabel javaHomeLabel
JTextField javaHomeTxt
JButton okButton
JavaHomeOrMemoryDialogParent javaHomeOrMemoryDialogParent
JDialog welcomeDialog
String toolName
JPanel backgroundPanel
JButton cancelButton
JSeparator jSeparator1
JButton javaOptionsHelpJButton
JLabel mbLabel
JLabel memoryLimitLabel
JTextField memoryTxt
JButton okButton
JavaHomeOrMemoryDialogParent javaHomeOrMemoryDialogParent
JFrame frameParent
String toolName
JDialog welcomeDialog
JPanel backgroundsPanel
JLabel bitLabel
JPanel bitPanel
JLabel bitRecommendationLabel
JLabel javaHelpJLabel
JLabel javaHomeLabel
JPanel javaHomePanel
JLabel memoryLabel
JPanel memoryPanel
JLabel memoryRecommendationLabel
JButton okButton
JLabel versionLabel
JPanel versionPanel
JLabel versionRecommendationLabel1
JLabel versionRecommendationLabel2
UtilitiesUserParameters utilitiesUserParameters
String lastSelectedFolder
boolean dialogCanceled
JFrame parentFrame
JDialog parentDialog
ProgressDialogX progressDialog
JPanel backgroundPanel
JButton browseButton
JButton cancelButton
JLabel jLabel2
JButton okButton
JButton peptideShakerButton
JLabel peptideShakerDownloadLinkLabel
JPanel peptideShakerDownloadPanel
JLabel peptideShakerInfoLabel
JPanel peptideShakerInstallationPanel
JLabel peptideShakerJarFileHelpLabel
JTextField peptideShakernstallationJTextField
UtilitiesUserParameters utilitiesUserParameters
String lastSelectedFolder
boolean dialogCanceled
JPanel backgroundPanel
JButton browseButton
JButton cancelButton
JLabel downloadLinkLabel
JPanel downloadPanel
JLabel folderHelpLabel
JButton iconButton
JLabel infoLabel
JTextField installationJTextField
JPanel installationPanel
JLabel jLabel2
JButton okButton
UtilitiesUserParameters utilitiesUserParameters
String lastSelectedFolder
boolean dialogCanceled
JPanel backgroundPanel
JButton browseButton
JButton cancelButton
JLabel jLabel2
JButton okButton
JButton reporterButton
JLabel reporterDownloadLinkLabel
JPanel reporterDownloadPanel
JLabel reporterInfoLabel
JTextField reporterInstallationJTextField
JPanel reporterInstallationPanel
JLabel reporterJarFileHelpLabel
UtilitiesUserParameters utilitiesUserParameters
String lastSelectedFolder
boolean dialogCanceled
ProgressDialogX progressDialog
JFrame parentFrame
JDialog parentDialog
JPanel backgroundPanel
JButton browseButton
JButton cancelButton
JLabel jLabel2
JButton okButton
JButton searchGuiButton
JLabel searchGuiDownloadLinkLabel
JPanel searchGuiDownloadPanel
JLabel searchGuiInfoLabel
JTextField searchGuiInstallationJTextField
JPanel searchGuiInstallationPanel
JLabel searchGuiJarFileHelpLabel
boolean canceled
HashMap<K,V> originalKeyToPathMap
HashMap<K,V> keyToPathMap
ArrayList<E> keyList
HashMap<K,V> nameToKey
String toolName
ArrayList<E> pathsToolTips
ArrayList<E> pathTableToolTips
JButton cancelButton
JMenuItem editPathMenuItem
JLabel helpLabel
JPanel informationPanel
JScrollPane informationScrollPane
JTextArea informationTxt
JButton okButton
JPanel pathSettingsJPanel
JPopupMenu pathSettingsPopupMenu
JTable pathTable
JScrollPane pathTableScrollPane
JMenuItem setDefaultPath
JPanel tablePanel
org.apache.logging.log4j.Logger logger
Color iEvenRowColor
Color iUnevenRowColor
org.apache.logging.log4j.Logger logger
Exception iNested
byte[] blob
Object getBlob
JButton closeJButton
JScrollPane textEditorScrollPane
JEditorPane textJEditorPane
JPanel backgroundPanel
HashMap<K,V> peffAnnotationsColorMap
HashMap<K,V> peffAnnotationsTooltipMap
boolean peffFormat
TreeMap<K,V> keyValuePairs
File currentSequenceFile
BufferedReader currentPeffBufferedReader
String currentSequence
String currentSequenceLine
HashMap<K,V> linkedSpectrumPanels
HashMap<K,V> allAnnotations
SpectrumPanel spectrumAPanel
SpectrumPanel spectrumBPanel
int spectrumPanelMaxPadding
int chromatogramPanelMaxPadding
MascotEnzymeReader mascotEnzymeReader
String cleanProteinSequence
HashMap<K,V> selectedAnnotationTypes
ArrayList<E> sequenceAnnotationColumnHeaderTooltips
Color sparklineColor
JCheckBox H2OIonsJCheckBox
JCheckBox NH3IonsJCheckBox
JCheckBox aIonsJCheckBox
JCheckBox allPeaksJCheckBox
JCheckBox bIonsJCheckBox
JPanel backgroundPanel
JButton browseJButton
JCheckBox cIonsJCheckBox
JCheckBox chargeOneJCheckBox
JCheckBox chargeOverTwoJCheckBox
JSpinner chargePeptideAJSpinner
JSpinner chargePeptideBJSpinner
JCheckBox chargeTwoJCheckBox
JPanel chromatogramAJPanel
JPanel chromatogramJPanel
JLabel chromatogramPanelHelpJLabel
JLabel chromatogramPanelInfoJLabel
JComboBox<E> enzymesJComboBox
JButton exportJButton
JLabel inSilicoDigestionHelpJLabel
JEditorPane informationJEditorPane
JPanel informationJPanel
JScrollPane informationJScrollPane
JTextField inhibitorsJTextField
JPanel ionSelectionJPanel
JPanel isotopicDistributionAJPanel
JLabel isotopicDistributionCalculatorHelpJLabel
JLabel isotopicDistributionCalculatorInfoJLabel
JPanel isotopicDistributionJPanel
JLabel jLabel1
JLabel jLabel10
JLabel jLabel11
JLabel jLabel12
JLabel jLabel13
JLabel jLabel14
JLabel jLabel15
JLabel jLabel16
JLabel jLabel17
JLabel jLabel18
JLabel jLabel19
JLabel jLabel2
JLabel jLabel20
JLabel jLabel21
JLabel jLabel24
JLabel jLabel3
JLabel jLabel4
JLabel jLabel5
JLabel jLabel6
JLabel jLabel7
JLabel jLabel8
JLabel jLabel9
JPanel jPanel1
JPanel jPanel10
JPanel jPanel11
JPanel jPanel12
JPanel jPanel2
JPanel jPanel3
JPanel jPanel4
JPanel jPanel5
JPanel jPanel6
JPanel jPanel7
JPanel jPanel8
JRadioButton jRadioButton1
JSeparator jSeparator1
JSeparator jSeparator2
JSeparator jSeparator3
JSeparator jSeparator4
JSeparator jSeparator5
JSeparator jSeparator6
JSeparator jSeparator9
JTabbedPane jTabbedPane
JCheckBox linkedSpectraJCheckBox
JSpinner lowerMassJSpinner
JSpinner missedCleavagesJSpinner
JButton nextJButton
JCheckBox otherIonsJCheckBox
JPanel peffAnnotationPanel
JTable peffAnnotationsJTable
JScrollPane peffAnnotationsScrollPane
JTable peffHeaderJTable
JScrollPane peffHeaderScrollPane
JPanel peptideAColorJPanel
JTextField peptideACompositionJTextField
JScrollPane peptideAJScrollPane
JTable peptideAJTable
JTextField peptideAMzJTextField
JPanel peptideBColorJPanel
JTextField peptideBCompositionJTextField
JScrollPane peptideBJScrollPane
JTable peptideBJTable
JTextField peptideBMzJTextField
JTextField peptideSequenceAJTextField
JTextField peptideSequenceBJTextField
JPanel peptidesJPanel
JTable peptidesJTable
JScrollPane peptidesScrollPane
JTextField positionJTextField
JCheckBox profileSpectrumJCheckBox
JScrollPane proteinCoverageJScrollPane
JScrollPane proteinDetailsScrollPane
JLabel proteinDigestionJLabel
JPanel proteinDigestionJPanel
JTable proteinHeaderJTable
JEditorPane proteinSequenceCoverageJEditorPane
JPanel sequenceCoverageJPanel
JTextField sequenceFileJTextField
JTabbedPane sequenceJTabbedPane
JComboBox<E> silacLabelPeptideAJComboBox
JComboBox<E> silacLabelPeptideBJComboBox
JTextField siteJTextField
JPanel spectraJPanel
JPanel spectrumAJPanel
JPanel spectrumBJPanel
JPanel spectrumJPanel
JLabel spectrumPanelHelpJLabel
JLabel spectrumPanelInfoJLabel
JSpinner upperMassJSpinner
JCheckBox xIonsJCheckBox
JCheckBox yIonsJCheckBox
JCheckBox zIonsJCheckBox
String singleLetterCode
String threeLetterCode
String name
AtomChain monoisotopicAtomChain
char[] subAminoAcidsWithoutCombination
char[] subAminoAcidsWithCombination
char[] aminoAcidCombinations
String[] standardGeneticCode
HashSet<E> aaAtTarget
int length
HashMap<K,V> residueTargeted
String sequence
StringBuilder sequenceStringBuilder
ModificationMatch[] variableModifications
double monoisotopicMass
HashMap<K,V> isotopeMap
HashMap<K,V> representativeComposition
String name
String letter
String name
double theoreticMass
HashMap<K,V> ensemblVersionsMap
HashMap<K,V> geneNameToEnsemblIdMap
HashMap<K,V> geneNameToChromosomeMap
HashMap<K,V> proteinToGoMap
HashMap<K,V> goAccessionToProteinMap
HashMap<K,V> goNamesMap
String neutralLossesAsString
Ion.IonType type
Double theoreticMass
double theoreticMass1
AtomChain atomChain
AtomChain composition
String name
boolean fixed
CvTerm psiCvTerm
char[] aminoAcids
String name
int subType
int subType
char aa
NeutralLoss[] neutralLosses
int number
int subType
CvTerm cvTerm
CvTerm psiCvTerm
NeutralLoss[] neutralLosses
CvTerm cvTerm
CvTerm psiCvTerm
AminoAcid aminoAcidTarget
int subType
NeutralLoss[] neutralLosses
int number
int subNumber
int subType
double massGap
CvTerm cvTerm
CvTerm psiCvTerm
ModificationType modificationType
String name
String shortName
Double mass
ArrayList<E> neutralLosses
ArrayList<E> reporterIons
AminoAcidPattern pattern
AtomChain atomChainAdded
AtomChain atomChainRemoved
CvTerm unimodCvTerm
CvTerm psiModCvTerm
String ambiguityKey
ModificationCategory category
String sequence
long key
boolean keySet
long matchingKey
double mass
TreeMap<K,V> proteinMapping
ModificationMatch[] variableModifications
HashMap<K,V> variantMatches
String name
String description
HashMap<K,V> substitutions
HashMap<K,V> reverseMap
int index
String name
Advocate.AdvocateType type
Color color
IdentificationKeys identificationKeys
String dbDirectory
ObjectsDB objectsDB
HashSet<E> proteinIdentification
HashSet<E> peptideIdentification
HashMap<K,V> spectrumIdentification
HashMap<K,V> proteinMap
ArrayList<E> fractions
int index
int rank
int advocate
int identificationCharge
double score
String identificationFile
double rawScore
ArrayList<E> aminoAcidScores
double value
String sequence
int smallObjectsInCache
int largeObjectsInCache
HashMap<K,V> largeObjectsCache
HashMap<K,V> smallObjectsCache
long[] proteinListAfterHiding
long[] proteinList
long[] validatedProteinList
long[] peptideList
long[] psmList
boolean filtered
int maxSpectrumCount
int nValidatedPsms
long currentProteinKey
long currentPeptideKey
boolean readOnly
String name
String description
String condition
String reportPassed
String reportFailed
boolean active
HashSet<E> manualValidation
HashSet<E> exceptions
HashMap<K,V> comparatorsMap
HashMap<K,V> valuesMap
MatchFilter.FilterType filterType
int minPepLength
int maxPepLength
double maxMassDeviation
boolean isPpm
boolean unknownModification
Integer minMissedCleavages
Integer maxMissedCleavages
Integer minIsotopes
Integer maxIsotopes
AssumptionFilter assumptionFilter
double peakMz
double peakIntensity
Ion ion
int charge
String modification
int modifiedSite
boolean confident
boolean inferred
Peptide peptide
long key
long[] spectrumMatchesKeys
String[] accessions
String leadingAccession
long[] peptideMatchesKeys
long matchKey
boolean decoy
ProteinMatch p
long key
String spectrumFile
String spectrumtitle
HashMap<K,V> peptideAssumptionsMap
PeptideAssumption bestPeptideAssumption
HashMap<K,V> tagAssumptionsMap
TagAssumption bestTagAssumption
double maxPrecursorErrorDa
double maxPrecursorErrorPpm
double maxTagPrecursorErrorDa
double maxTagPrecursorErrorPpm
int[] foundCharges
Integer maxNPeptides
Integer maxNPsms
Double maxSpectrumCounting
Double maxMW
long[] proteinKeys
Integer maxProteinAccessionLength
int nValidatedProteins
Integer nConfidentProteins
TreeSet<E> foundModifications
HashMap<K,V> fractionPsmMatches
HashMap<K,V> totalPeptidesPerFractions
HashMap<K,V> observedFractionalMassesAll
Integer maxValidatedPeptidesPerFraction
Integer maxValidatedSpectraPerFraction
Double maxProteinAveragePrecursorIntensity
Double maxProteinSummedPrecursorIntensity
NonSymmetricalNormalDistribution peptideLengthDistribution
Double totalSpectrumCounting
Double totalSpectrumCountingMass
long[] validatedTargetProteinKeys
HashMap<K,V> deltaScoresAtAA
HashMap<K,V> probabilisticScoresAtAA
String ptmName
HashMap<K,V> ptmLocationAtAA
HashMap<K,V> modificationMap
HashMap<K,V> mainModificationSites
HashMap<K,V> confidentModificationsByModName
HashMap<K,V> ambiguousModificationsByRepresentativeSite
HashMap<K,V> ambiguousModificationsByModName
double algorithmDeltaPEP
double deltaPEP
double score
double probability
MatchValidationLevel matchValidationLevel
boolean manualValidation
boolean hidden
boolean starred
int proteinInferenceGroupClass
HashMap<K,V> fractionPEP
HashMap<K,V> fractionScore
HashMap<K,V> validatedPeptidesPerFraction
HashMap<K,V> validatedSpectraPerFraction
HashMap<K,V> precursorIntensityPerFraction
HashMap<K,V> precursorIntensityAveragePerFraction
HashMap<K,V> precursorIntensitySummedPerFraction
HashMap<K,V> qcFilters
HashMap<K,V> intermediateScores
int maxPTMsPerPeptide
boolean onlyTrypticPeptides
int indexParts
int indexChunkSize
ArrayList<E> suffixArraysPrimary
ArrayList<E> occurrenceTablesPrimary
ArrayList<E> occurrenceTablesReversed
ArrayList<E> lessTablesPrimary
ArrayList<E> lessTablesReversed
ArrayList<E> indexStringLengths
int samplingShift
int samplingMask
int sampling
ArrayList<E> boundaries
ArrayList<E> accessions
HashSet<E> decoyAccessions
HashMap<K,V> accessionMetaData
double[] aaMasses
int[] aaMassIndexes
int numMasses
String[] modifictationLabels
HashMap<K,V> modificationLabelsToId
boolean[] modificationFlags
boolean withVariableModifications
int[] BSubstitutions
int[] JSubstitutions
int[] ZSubstitutions
ArrayList<E> fmodc
ArrayList<E> fmodcMass
ArrayList<E>[] fmodcaa
ArrayList<E>[] fmodcaaMass
ArrayList<E> fmodn
ArrayList<E> fmodnMass
ArrayList<E>[] fmodnaa
ArrayList<E>[] fmodnaaMass
ArrayList<E> fmodcp
ArrayList<E> fmodcpMass
ArrayList<E>[] fmodcpaa
ArrayList<E>[] fmodcpaaMass
ArrayList<E> fmodnp
ArrayList<E> fmodnpMass
ArrayList<E>[] fmodnpaa
ArrayList<E>[] fmodnpaaMass
ArrayList<E> vmodc
ArrayList<E> vmodcMass
ArrayList<E>[] vmodcaa
ArrayList<E>[] vmodcaaMass
ArrayList<E> vmodn
ArrayList<E> vmodnMass
ArrayList<E>[] vmodnaa
ArrayList<E>[] vmodnaaMass
ArrayList<E> vmodcp
ArrayList<E> vmodcpMass
ArrayList<E>[] vmodcpaa
ArrayList<E>[] vmodcpaaMass
ArrayList<E> vmodnp
ArrayList<E> vmodnpMass
ArrayList<E>[] vmodnpaa
ArrayList<E>[] vmodnpaaMass
boolean hasCTermDirectionModification
boolean hasNTermDirectionModification
boolean hasModificationatTerminus
boolean hasFixedModification_CatTerminus
boolean hasFixedModification_NatTerminus
double negativeModificationMass
ArrayList<E> variantBitsPrimary
ArrayList<E> variantBitsReversed
ArrayList<E> variantsPrimary
ArrayList<E> variantsReversed
HashMap<K,V> SNPs
PeptideVariantsParameters.VariantType variantMatchingType
int maxNumberVariants
int maxNumberInsertions
int maxNumberDeletions
int maxNumberSubstitutions
boolean[][] substitutionMatrix
double lookupMultiplier
SearchParameters.MassAccuracyType massAccuracyType
double massTolerance
long[] lookupMasses
int maxXPerTag
long[][] Xlookup
ArrayList<E> modificationPatterns
HashMap<K,V> modificationPatternNames
int longestModificationpattern
int[][][] allPermutations
ArrayList<E> massIndexMaps
HashMap<K,V>[] cache
double mass
int[] indexes
int left
int right
int character
MatrixContent previousContent
double mass
String peptideSequence
String peptideSequenceSearch
int length
int numX
ModificationMatch modification
ArrayList<E> modifications
int modificationPos
int numVariants
int[] numSpecificVariants
char variant
String allVariants
int ambiguousChar
int tagComponent
ArrayList<E> allXcomponents
double XMassDiff
HashMap<K,V> allXMassDiffs
int numPTMs
int length
long[] bitfield
int[] sums
byte[] sumsSecondLevel
int position
char sourceAA
char targetAA
Rank rank
long[] alphabetDirections
int firstChar
int lastChar
int lenText
boolean continueLeftRangeQuery
boolean continueRightRangeQuery
WaveletTree leftChild
WaveletTree rightChild
int leftRightMask
int[] less
boolean yAxisZoomExcludesBackgroundPeaks
boolean showAllPeaks
AnnotationParameters.IntensityThresholdType intensityThresholdType
double intensityLimit
boolean automaticAnnotation
HashMap<K,V> selectedIonsMap
ArrayList<E> neutralLossesList
boolean neutralLossesAuto
boolean reporterIons
boolean relatedIons
double fragmentIonAccuracy
boolean fragmentIonPpm
boolean showForwardIonDeNovoTags
boolean showRewindIonDeNovoTags
int deNovoCharge
SpectrumAnnotator.TiesResolution tiesResolution
HashMap<K,V> forwardBoundaries
HashMap<K,V> rewindBoundaries
ArrayList<E> accountedNeutralLosses
Peptide peptide
Tag tag
boolean targetDecoy
String decoyFlag
boolean decoySuffix
String targetDecoyFileNameTag
String iID
String iForeignID
String iAccession
ProteinDatabase databaseType
String iForeignAccession
String iDescription
String iDescriptionShort
String iDescriptionProteinName
String iGeneName
Integer iProteinEvidence
String iTaxonomy
String iOrganismIdentifier
String iForeignDescription
String iRest
String iRawHeader
StringBuffer iAddenda
int iStart
int iEnd
File mzIdentMLFile
SearchParameters searchParameters
String species
WaitingHandler waitingHandler
String parametersReport
File identificationFile
double cTermCorrection
double nTermCorrection
File identificationFile
HashMap<K,V> indexMap
HashMap<K,V> spectrumNumberIndexMap
ArrayList<E> spectrumTitles
HashMap<K,V> duplicatedSpectrumTitles
HashMap<K,V> precursorMzMap
String fileName
Long lastModified
Double maxRT
Double minRT
Double maxMz
Double maxIntensity
Integer maxCharge
Integer maxPeakCount
Boolean peakPicked
Integer spectrumCount
Boolean precursorChargesMissing
double mz
double intensity
double rt
double mz
double intensity
int[] possibleCharges
Precursor precursor
double[] mz
double[] intensity
boolean canceled
JLabel advancedSettingsWarningLabel
JPanel backgourdPanel
JButton cancelButton
JPanel installationPanel
JButton okButton
JButton openDialogHelpJButton
JComboBox<E> outputFormatCmb
JLabel outputPepXmlLabel
JComboBox<E> peakPickingCmb
JLabel peakPickingLabel
Quantification.QuantificationMethod methodUsed
HashMap<K,V> sampleAssignement
HashMap<K,V> sampleIndexes
ArrayList<E> controlSamples
ReporterMethod reporterMethod
NormalizationFactors normalizationFactors
double rankScore
double mH
String fullName
String abbreviation
MetricsPrefix metricsPrefix
Object object
org.apache.logging.log4j.Logger logger
String element
org.apache.logging.log4j.Logger logger
JLabel daLbl
JLabel massLbl
JTextField massTxt
JLabel sequenceLbl
JTextField sequenceTxt
AminoAcidPattern pattern
boolean editable
boolean cancel
ArrayList<E> patternDesignTableToolTips
String exampleSequence
JMenuItem addJMenuItem
JPanel backgroundPanel
JButton cancelButton
JMenuItem deleteSelectedRowJMenuItem
JLabel exampleLabel
JSeparator jSeparator3
JSeparator jSeparator4
JMenuItem moveDownJMenuItem
JMenuItem moveUpJMenuItem
JButton okButton
JPanel patternDesignPanel
JScrollPane patternDesignScrollPane
JTable patternDesignTable
JEditorPane patternTestEditorPane
JScrollPane patternTestJScrollPane
JPopupMenu popupJMenu
JLabel rightClickHelpLabel
JPanel testPanel
boolean canceled
JPanel backgroundPanel
ButtonGroup buttonGroup
JButton cancelJButton
JRadioButton excelJRadioButton
JButton exportJButton
JPanel formatTypeJPanel
JRadioButton textJRadioButton
org.apache.logging.log4j.Logger logger
org.apache.logging.log4j.Logger logger
Image normalIcon
UtilitiesUserParameters utilitiesUserParameters
JPanel backgroundPanel
JButton cancelButton
JLabel confidentialLabel
JButton okButton
JButton openDialogHelpJButton
JPanel settingsPanel
JCheckBox updatesCheck
Frame dialogParent
LastSelectedFolder lastSelectedFolder
Image normalIcon
Image waitingIcon
VennDiagramPanel vennDiagramPanel
JPanel backgroundPanel
JPanel contextMenuPlotBackgroundPanel
JPanel dataPanel
JPanel datasetAColorJPanel
JScrollPane datasetAScrollPane
JTextArea datasetATextArea
JTextField datasetATextField
JPanel datasetBColorJPanel
JScrollPane datasetBScrollPane
JTextArea datasetBTextArea
JTextField datasetBTextField
JPanel datasetCColorJPanel
JScrollPane datasetCScrollPane
JTextArea datasetCTextArea
JTextField datasetCTextField
JPanel datasetDColorJPanel
JScrollPane datasetDScrollPane
JTextArea datasetDTextArea
JTextField datasetDTextField
JMenuItem exportPlotMenuItem
JMenu fontSizeMenu
JPopupMenu.Separator jSeparator1
JPopupMenu.Separator jSeparator2
JCheckBoxMenuItem legendCheckBoxMenuItem
JMenuItem legendFontSizeMenuItem
JMenuItem legendLocationMenuItem
JButton plotHelpJButton
JLayeredPane plotLayeredPane
JButton plotOptionsJButton
JPopupMenu plotPopupMenu
JMenuItem valueFontSizeMenuItem
JPanel xyPlotPanel
VennDiagramDialog vennDiagramDialog
double legendShiftSize
JPanel backgroundPanel
JLabel datasetALabel
JLabel datasetBLabel
JLabel datasetCLabel
JLabel datasetDLabel
JButton downDatasetAButton
JButton downDatasetBButton
JButton downDatasetCButton
JButton downDatasetDButton
JButton leftDatasetAButton
JButton leftDatasetBButton
JButton leftDatasetCButton
JButton leftDatasetDButton
JPanel legendLocationPanel
JButton okButton
JButton rightDatasetAButton
JButton rightDatasetBButton
JButton rightDatasetCButton
JButton rightDatasetDButton
JLabel shiftSizeLabel
JSpinner shiftSizeSpinner
JButton upDatasetAButton
JButton upDatasetBButton
JButton upDatasetCButton
JButton upDatasetDButton
HashMap<K,V> tooltipToDatasetMap
VennDiagramPanel.VennDiagramType currentVennDiagramType
HashMap<K,V> vennDiagramResults
HashMap<K,V> groupNames
org.jfree.chart.ChartPanel chartPanel
int fontSizeValues
int fontSizeLegend
boolean showLegend
no.uib.jsparklines.data.XYDataPoint legendDatasetAThreeWay
no.uib.jsparklines.data.XYDataPoint legendDatasetBThreeWay
no.uib.jsparklines.data.XYDataPoint legendDatasetCThreeWay
no.uib.jsparklines.data.XYDataPoint legendDatasetAFourWay
no.uib.jsparklines.data.XYDataPoint legendDatasetBFourWay
no.uib.jsparklines.data.XYDataPoint legendDatasetCFourWay
no.uib.jsparklines.data.XYDataPoint legendDatasetDFourWay
Color datasetAColor
Color datasetBColor
Color datasetCColor
Color datasetDColor
JPanel plotPanel
VisibleTableColumnsDialogParent visibleTableColumnsDialogParent
JPanel backgroundPanel
JMenuItem deselectAllMenuItem
JButton okButton
JMenuItem selectAllMenuItem
JPopupMenu selectJPopupMenu
JTable selectedColumnsTable
JScrollPane selectedValuesTableScrollPane
XYPlottingDialog xyPlottingDialog
JPanel backgroundPanel
JButton cancelButton
JLabel filterTypesLabel
JScrollPane filtersScrollPane
JTable filtersTable
JButton okButton
ProgressDialogX progressDialog
TableModel tableModel
org.jfree.chart.ChartPanel chartPanel
double bubbleSize
double bubbleScalingFactor
int numberOfBins
boolean userDefinedBinSize
Frame dialogParent
boolean isPlotting
boolean mouseDragged
Point dragStart
Point dragEnd
HashMap<K,V> selectedDataPoints
boolean selectionActive
HashMap<K,V> dataPointToRowNumber
ArrayList<E> selectedModelRows
HashMap<K,V> cellRenderers
HashMap<K,V> maxColumnWidths
HashMap<K,V> minColumnWidths
ArrayList<E> tableToolTips
no.uib.jsparklines.renderers.util.GradientColorCoding.ColorGradient colorGradient
Color histogramColor
LastSelectedFolder lastSelectedFolder
Image normalIcon
Image waitingIcon
ArrayList<E> allTableColumns
HashMap<K,V> visibleColumns
boolean useGradientColorCoding
boolean showRegressionLine
HashMap<K,V> filters
Vector<E> colummnNames
ArrayList<E> rowsAfterDataFiltering
JPanel backgroundPanel
JSpinner binSizeSpinner
JLabel binsLabel
JComboBox<E> bubbleSizeComboBox
JLabel bubbleSizeLabel
JLabel colorLabel
JComboBox<E> colorsComboBox
JPanel contextMenuPlotBackgroundPanel
JPanel contextMenuSelectedValuesTableBackgroundPanel
JRadioButton densityPlotRadioButton
ButtonGroup dragButtonGroup
JPanel dragSettingsPanel
JRadioButton dragToSelectRadioButton
JRadioButton dragToZoomRadioButton
JButton editFiltersButton
JMenuItem exportPlotMenuItem
JMenuItem exportSelectedValuesMenuItem
JPanel filterPanel
JMenuItem hideColumnsMenuItem
JRadioButton histogramRadioButton
JPanel logAcisPanel
JButton plotHelpJButton
JLayeredPane plotLayeredPane
JButton plotOptionsJButton
JPanel plotPanel
JPopupMenu plotPopupMenu
ButtonGroup plotTypeButtonGroup
JPanel plotTypePanel
JCheckBoxMenuItem regressionLineCheckBoxMenuItem
JLayeredPane selectedValuesLayeredPane
JPanel selectedValuesPanel
JScrollPane selectedValuesScrollPane
JTable selectedValuesTable
JButton selectedValuesTableHelpJButton
JButton selectedValuesTableOptionsJButton
JPopupMenu selectedValuesTablePopupMenu
JCheckBox sizeLogCheckBox
JComboBox<E> xAxisComboBox
JLabel xAxisLabel
JCheckBox xAxisLogCheckBox
JPanel xAxisPanel
JPanel xyPlotPanel
JRadioButton xyPlotRadioButton
JComboBox<E> yAxisComboBox
JLabel yAxisLabel
JCheckBox yAxisLogCheckBox
AtomChain atomChainAdded
AtomChain atomChainRemoved
boolean canceled
int atomPanelIndex
boolean settingUpGUI
boolean addOnly
JLabel MassLbl
JPanel backgroundPanel
JButton cancelButton
JLabel compositionLbl
JPanel compositionPanel
JTextField compositionTxt
JPanel editPanel
JPanel elementsPanel
JScrollPane elementsScrollPane
JButton helpJButton
JTextField massTxt
JButton okButton
HashMap<K,V> isotopesMap
AtomChainDialog atomChainDialog
int panelIndex
JLabel addLabel
JComboBox<E> atomCmb
JComboBox<E> isotopeCmb
JSpinner occurenceSpinner
JLabel removeLabel
EnzymeFactory enzymeFactory
ArrayList<E> defaultEnzymesTableToolTips
ArrayList<E> userEnzymesTableToolTips
String selectedRowHtmlTagFontColor
String notSelectedRowHtmlTagFontColor
JButton addUserEnzyme
JButton deleteEnzymeButton
JPanel enzymesEditorPanel
JButton enzymesHelpJButton
JPanel enzymesPanel
JScrollPane enzymesScrollPane
JTable enzymesTable
JLabel exportEnzymesLabel
JLabel importEnzymesLabel
JButton okButton
JLabel resetEnzymesLabel
EnzymeFactory enzymeFactory
EnzymesDialog enzymesDialog
boolean canceled
JPanel backgroundPanel
JLabel butNotAfterLabel
JTextField butNotAfterTxt
JLabel butNotBeforeLabel
JTextField butNotBeforeTxt
JButton cancelButton
JPanel cleavageRulesPanel
JLabel cleavesAfterLabel
JTextField cleavesAfterTxt
JLabel cleavesBeforeLabel
JTextField cleavesBeforeTxt
JButton helpJButton
JLabel nameLabel
JTextField nameTxt
JButton okButton
JPanel psMsMappingPanel
JTextField psiMsAccessionJTextField
JLabel psiMsAccessionLabel
JLabel psiMsLinkLabel
LastSelectedFolder lastSelectedFolder
String toolName
String gitHubProjectName
String toolVersion
String googleGroup
String googleGroupName
File logFile
JPanel backgroundPanel
JButton clearJButton
JButton exitButton
JEditorPane infoJEditorPane
JPanel infoJPanel
JScrollPane infoJScrollPane
JPanel logJPanel
JScrollPane logJScrollPane
JTextArea logTxt
JButton saveJButton
Frame frameParent
JDialog dialogParent
JPanel backgroundPanel
JButton closeJButton
JScrollPane jScrollPane1
JEditorPane textJEditorPane
JPanel backgroundPanel
JEditorPane notesEditorPane
JScrollPane notesScrollPane
JButton okButton
NotificationDialogParent notificationDialogParent
String notificationType
JLabel notificationLabel
JPanel notificationPanel
org.jfree.chart.ChartPanel chartPanel
Component graphicsPanel
ProgressDialogX progressDialog
JFrame frame
Image normalIcon
Image waitingIcon
LastSelectedFolder lastSelectedFolder
JPanel backgroundPanel
ButtonGroup buttonGroup
JButton cancelJButton
JButton exportJButton
JRadioButton pdfJRadioButton
JPanel plottingTypeJPanel
JRadioButton pngJRadioButton
JRadioButton svgJRadioButton
JRadioButton tiffJRadioButton
ExportFactory exportFactory
String oldName
boolean editable
HashMap<K,V> selection
String sectionName
ArrayList<E> featuresList
JCheckBox advancedFeaturesCheck
JPanel backgroundPanel
JButton cancelButton
JLabel columnDelimiterLabel
JRadioButton commaRadioButton
JCheckBox decoysCheck
ButtonGroup delimiterButtonGroup
JScrollPane featuresScrollPane
JTable featuresTable
JCheckBox headerCheckBox
JCheckBox lineNumberCheckBox
JTextField mainTitleTxt
JCheckBox maintTitleCheckBox
JLabel matchesLbl
JTextField nameTxt
JLabel numberOfSeparationLinesLabel
JButton okButton
JLabel reportTitleLabel
JPanel reporterSettingsPanel
JPanel reporterTypePanel
JLabel rowDelimiterLabel
JPanel sectionContentPanel
JCheckBox sectionTitleCheckBox
JPanel sectionsPanel
JScrollPane sectionsScrollPane
JTable sectionsTable
JRadioButton semicolonRadioButton
JSpinner separationLinesSpinner
JRadioButton spaceRadioButton
JLabel structureLabel
JCheckBox subFeaturesCheck
JRadioButton tabRadioButton
JCheckBox validatedCheck
ArrayList<E> files
boolean canceled
JPanel backgroundPanel
JButton okButton
JEditorPane selectedFilesEditorPane
JScrollPane selectedFilesScrollPane
HashMap<K,V> fileMap
boolean canceled
JButton cancelButton
JList<E> fileList
JScrollPane fileListScrollPane
JLabel helpLabel
JButton okButton
boolean canceled
MatchFilter matchFilter
ArrayList<E> itemsNames
ArrayList<E> allModifications
JMenuItem addItemMenuItem
JButton cancelButton
JLabel descriptionLbl
JScrollPane descriptionScrollPane
JTextArea descriptionTxt
JPanel exceptionsPanel
JScrollPane exceptionsScrollPane
JTextArea exceptionsTxt
JPanel filterItemsPanel
JTable filterItemsTable
JScrollPane filterItemsTableScrollPane
JPanel filterPanel
JPanel filterSettingsPanel
JSplitPane filterSplitPane
JLabel helpLbl
JPopupMenu itemPopupMenu
JSplitPane manualSelectionSplitPane
JPanel manualValidationPanel
JScrollPane manualValidationScrollPane
JTextArea manualValidationTxt
JLabel nameLbl
JTextField nameTxt
JButton okButton
JPanel propertiesPanel
JMenuItem removeItemMenuItem
HashMap<K,V> proteinStarFilters
HashMap<K,V> proteinHideFilters
HashMap<K,V> peptideStarFilters
HashMap<K,V> peptideHideFilters
HashMap<K,V> psmStarFilters
HashMap<K,V> psmHideFilters
GeneMaps geneMaps
ProteinDetailsProvider proteinDetailsProvider
String[] proteinAccessions
ArrayList<E> proteinAccessionColumn
ArrayList<E> goTermDescriptions
String selectedRowHtmlTagFontColor
String notSelectedRowHtmlTagFontColor
JPanel backgroundPanel
JLabel chromosomeLabel
JTextField chromosomeNameTxt
JPanel detailsPanel
JLabel ensemlbIdLabel
JTextField geneIdTxt
JLabel geneNameLabel
JTextField geneNameTxt
JLabel goAnnotationLabel
JTable goTable
JScrollPane goTableScrollPane
JButton okButton
Frame parentFrame
boolean canceled
ProteinGeneDetailsProvider geneFactory
SpeciesFactory speciesFactory
ProgressDialogX progressDialog
JDialog dialogParent
Image waitingImage
Image normalImage
HashMap<K,V> speciesToTaxonMap
ArrayList<E> selectedSpeciesList
JPanel backgroundPanel
JButton cancelButton
JLabel chickenLabel
JLabel comma1Label
JLabel comma2Label
JLabel comma3Label
JLabel comma4Label
JComboBox<E> ensemblCategoryJComboBox
JLabel ensemblVersionLabel
JLabel humanLabel
JLabel mouseLabel
JButton okButton
JLabel popularSpeciesLabel
JLabel ratLabel
JComboBox<E> speciesJComboBox
JPanel speciesPanel
JLabel unknownSpeciesLabel
JButton updateMappingsButton
JLabel zebrafishLabel
org.apache.logging.log4j.Logger logger
JTextArea txtSequence
JLabel lblComp
JLabel lblMass
JButton calculateButton
AlternateRowColoursJTable table1
JPanel jpanContent
JPanel headerTable
JPanel spectrumPanel
JSpinner spinCharge
JLabel lblPeptide
AASequenceImpl iSequence
HashMap<K,V> iElements
double iCharge
ModificationFactory modificationFactory
Modification currentPtm
ArrayList<E> neutralLosses
ArrayList<E> reporterIons
boolean editable
AminoAcidPattern pattern
AtomChain atomChainAdded
AtomChain atomChainRemoved
ArrayList<E> reporterIonTableToolTips
ArrayList<E> neutralLossesTableToolTips
boolean canceled
JButton addNeutralLoss
JButton addReporterIon
JPanel backgroundPanel
JButton cancelButton
JComboBox<E> categoryCmb
JLabel categoryLabel
JLabel compositionLabel
JTextField compositionTxt
JSplitPane cvTermSplitPane
JButton helpJButton
JLabel massLabel
JTextField massTxt
JLabel nameLabel
JLabel nameShortLabel
JTextField nameShortTxt
JTextField nameTxt
JTabbedPane neutralLossesAndReportIonsTabbedPane
JScrollPane neutralLossesJScrollPane
JPanel neutralLossesPanel
JTable neutralLossesTable
JButton okButton
JLabel patternLabel
JTextField patternTxt
JPanel propertiesPanel
JTextField psiModAccessionJTextField
JLabel psiModAccessionLabel
JLabel psiModLabel
JLabel psiModLinkLabel
JTextField psiModNameJTextField
JLabel psiModNameLabel
JPanel psiModPanel
JButton removeNeutralLoss
JButton removerReporterIon
JPanel reporterIonsAndNeutralLossesPanel
JScrollPane reporterIonsJScrollPane
JPanel reporterIonsPanel
JTable reporterIonsTable
JComboBox<E> typeCmb
JLabel typeLabel
JTextField unimodAccessionJTextField
JLabel unimodAccessionLabel
JLabel unimodLabel
JLabel unimodLinkLabel
JPanel unimodMappingPanel
JTextField unimodNameJTextField
JLabel unimodNameLabel
JPanel unimodPanel
ModificationFactory modificationFactory
Color sparklineColor
String selectedRowHtmlTagFontColor
String notSelectedRowHtmlTagFontColor
ArrayList<E> defaultModsTableToolTips
ArrayList<E> userModsTableToolTips
ArrayList<E> searchPossibilities
int searchCurrentSelection
String searchWelcomeText
JButton addUserModification
JTable defaultModificationsTable
JPanel defaultModsPanel
JPopupMenu defaultModsPopupMenu
JScrollPane defaultModsScrollPane
JButton deleteUserModification
JButton editUserModification
JMenuItem editUserPtmJMenuItem
JLabel exportDefaultModsLabel
JLabel exportUserModsLabel
JLabel findJLabel
JPanel modificationsEditorPanel
JButton modificationsHelpJButton
JSplitPane modificationsSplitPane
JButton okButton
JLabel searchIndexLabel
JTextField searchInputTxt
JButton searchNextButton
JButton searchPreviousButton
JTable userModificationsTable
JPanel userModsPanel
JPopupMenu userModsPopupMenu
JScrollPane userModsScrollPane
JMenuItem viewDefaultModsJMenuItem
AnnotationParameters annotationParameters
Identification identification
ModificationParameters modificationParameters
SequenceProvider sequenceProvider
SpectrumProvider spectrumProvider
SequenceMatchingParameters modificationSequenceMatchingParameters
ArrayList<E> tooltips
Modification modification
int nModifications
boolean areaChart
double maxAreaChartValue
ArrayList<E> modificationSites
PeptideMatch peptideMatch
UtilitiesUserParameters utilitiesUserParameters
JPanel backgroundPanel
JLabel doubtfulColorLabel
JPanel doubtfulColorPanel
JLabel falsePositiveColorLabel
JPanel falsePositiveColorPanel
JLabel mirroredPeakColorLabel3
JPanel mirroredPeakColorPanel2
JLabel notFoundColorLabel
JPanel notFoundColorPanel
JLabel notValidatedColorLabel
JPanel notValidatedColorPanel
JButton okButton
JLabel possibleColorLabel
JPanel possibleColorPanel
JPanel sparklineColorsPanel
JLabel validatedColorLabel
JPanel validatedColorPanel
Frame parentFrame
boolean canceled
Image normalIcon
Image waitingIcon
LastSelectedFolder lastSelectedFolder
boolean editable
AnnotationParameters annotationSettings
SearchParameters searchParameters
SequenceMatchingParameters sequenceMatchingPreferences
PeptideVariantsParameters peptideVariantsPreferences
GeneParameters genePreferences
PsmScoringParameters psmScoringPreferences
PeptideAssumptionFilter peptideAssumptionFilter
ModificationLocalizationParameters ptmScoringPreferences
ProteinInferenceParameters proteinInferencePreferences
IdMatchValidationParameters idValidationPreferences
FastaParameters fastaPreferences
FractionParameters fractionSettings
boolean showAdvancedSettings
IdentificationParametersFactory identificationParametersFactory
JLabel advancedSettingsLabel
JPanel attributesPanel
JPanel backgroundPanel
JButton cancelButton
JButton databaseProcessingButton
JLabel exportLabel
JButton fractionsButton
JButton geneMappingButton
JLabel importLabel
JButton matchesFiltersButton
JLabel nameLabel
JTextField nameTxt
JButton peptideVariantsButton
JButton proteinInferenceButton
JButton psmScoringButton
JButton ptmLocalizationButton
JButton qualityControlButton
JButton saveButton
JScrollPane scrollPane
JButton sequenceMatchingButton
JPanel settingsOuterPanel
JPanel settingsPanel
JButton spectrumAnnotationButton
JButton spectrumMatchingButton
JButton validationButton
Frame parentFrame
boolean canceled
boolean editable
String originalDescription
JPanel attributesPanel
JPanel backgroundPanel
JButton cancelButton
JLabel decriptionLbl
JTextArea descriptionTxt
JScrollPane jScrollPane1
JLabel nameLbl
JTextField nameTxt
JButton okButton
IdentificationParametersFactory identificationParametersFactory
JPanel backgroundPanel
JLabel helpLbl
JButton okButton
JPopupMenu parametersPopupMenu
JMenuItem removeMenuItem
JTable settingsTable
JScrollPane settingsTableScrollPane
JPanel tablePanel
Frame parentFrame
boolean canceled
ArrayList<E> reporterIons
HashMap<K,V> neutralLossesMap
boolean editable
double maxFragmentIonAccuracy
JCheckBox aBox
JSpinner accuracySpinner
JLabel annotationLevelLabel
JLabel annotationLevelPercentLabel
JButton annotationPreferencesHelpJButton
JCheckBox bBox
JPanel backgroundPanel
JCheckBox cBox
JButton cancelButton
JLabel fragmentIonAccuracyLabel
JLabel fragmentIonAccuracyTypeLabel
JCheckBox highResolutionBox
JCheckBox immoniumBox
JSpinner intensitySpinner
JComboBox<E> intensityThresholdCmb
JPanel ionsPanel
JPanel neutralLossPanel
JScrollPane neutralLossScrollPane
JTable neutralLossesTable
JButton okButton
JPanel peakMatchingPanel
JCheckBox precursorBox
JCheckBox relatedBox
JCheckBox reporterBox
JCheckBox xBox
JCheckBox yBox
JCheckBox zBox
Frame parentFrame
boolean canceled
GeneParameters genePreferences
FastaSummary fastaSummary
SpeciesFactory speciesFactory
HashMap<K,V> speciesMap
JPanel backgroundPanel
JButton cancelButton
JButton helpJButton
JPanel mappingPanel
JButton okButton
JComboBox<E> speciesCmb
JLabel speciesLabel
Frame parentFrame
boolean canceled
boolean editable
JPanel backgrounPanel
JButton cancelButton
JPanel fractionsPanel
JButton helpJButton
JButton okButton
JLabel proteinMwLabel
JSpinner proteinMwSpinner
Frame parentFrame
boolean canceled
boolean editable
GeneParameters genePreferences
JComboBox<E> autoUpdateCmb
JLabel autoUpdateLabel
JPanel backgroundPanel
JButton cancelButton
JButton helpJButton
JPanel mappingPanel
JButton okButton
JComboBox<E> useMappingCmb
JLabel useMappingLabel
boolean canceled
boolean editable
JPanel backgroundPanel
JButton cancelButton
JPanel filterPanel
JButton helpJButton
JLabel isotopesLbl
JLabel isotopesRangeLabel
JTextField maxIsotopesTxt
JTextField maxMissedCleavagesTxt
JTextField minIsotopesTxt
JTextField minMissedCleavagesTxt
JLabel missedCleavagesLabel
JLabel missedCleavagesRangeLabel
JTextField nAAmaxTxt
JTextField nAAminTxt
JButton okButton
JLabel peptideLengthLabel
JLabel peptideLengthRangeLabel
JTextField precDevTxt
JLabel precursorAccuracyLabel
JCheckBox ptmsCheck
JComboBox<E> unitCmb
Frame parentFrame
boolean canceled
boolean editable
JComboBox<E> alignOnConfidentCmb
JLabel alignOnConfidentLbl
JPanel backgroundPanel
JButton cancelButton
JButton helpJButton
JSeparator jSeparator1
JComboBox<E> neutralLossesCmb
JLabel neutralLossesLabel
JButton okButton
JPanel ptmScoringPanel
JComboBox<E> scoreCmb
JLabel scoreTypeLabel
JPanel siteAlignmentPanel
JLabel thresholdLabel
JTextField thresholdTxt
Frame parentFrame
boolean canceled
boolean editable
JPanel aaSubstitutionsTableJPanel
JPanel backgrounPanel
JButton cancelButton
JLabel deletionsLbl
JLabel deletionsLbl1
JLabel deletionsLbl2
JLabel deletionsLbl3
JSpinner deletionsSpinner
JButton helpJButton
JSpinner insertionsSpinner
JPanel maxVariantsJPanel
JButton okButton
JComboBox<E> specificVariantsComboBox
JLabel specificVariantsLbl
JSpinner subsitutionsSpinner
JComboBox<E> substitutionMatrixComboBox
JTable substitutionMatrixTable
JScrollPane substitutionMatrixTableJScrollPane
JSpinner swapSpinner
JLabel totalVariantsLbl
JSpinner totalVariantsSpinner
Frame parentFrame
Image normalIcon
Image waitingIcon
boolean canceled
boolean editable
JPanel backgroundPanel
JButton cancelButton
JLabel confidenceLbl
JTextField confidenceTxt
JButton helpJButton
JLabel modificationsLbl
JComboBox<E> modificatoinsCmb
JButton okButton
JPanel proteinGroupPanel
JComboBox<E> simplifyConfidenceCmb
JLabel simplifyConfidenceLbl
JLabel simplifyConfidenceLbl1
JComboBox<E> simplifyEnzymaticityCmb
JLabel simplifyEnzymaticityLbl
JComboBox<E> simplifyEvidenceCmb
JLabel simplifyEvidenceLbl
JComboBox<E> simplifyGroupsCmb
JLabel simplifyGroupsLbl
JComboBox<E> simplifyVariantsCmb
JLabel simplifyVariantsLbl
Frame parentFrame
boolean canceled
boolean editable
HashMap<K,V> spectrumMatchingScores
HashSet<E> defaultScores
ArrayList<E> psmScoresTableToolTips
ArrayList<E> advocateNames
ArrayList<E> scoresNames
JMenuItem addJMenuItem
JPanel backgroundPanel
JButton cancelButton
JButton helpJButton
JButton okButton
JScrollPane psmScoresJScrollPane
JTable psmScoresJTable
JPopupMenu psmScoresPopupMenu
JMenuItem removeJMenuItem
JPanel scoresSelectionJPanel
Frame parentFrame
boolean canceled
boolean editable
JButton annotationPreferencesHelpJButton
JPanel backgroundPanel
JButton cancelButton
JComboBox<E> matchingCmb
JLabel matchingMethodLbl
JLabel maxPtmsPerTagLbl
JTextField maxPtmsPerTagTextField
JLabel minAaScoreLbl
JSpinner minAaScoreSpinner
JLabel minTagLengthLbl
JTextField minTagLengthTextField
JButton okButton
JPanel sequenceMatchingPanel
JComboBox<E> tagMatchingCmb
JLabel tagMatchingLbl
JLabel xLbl
JSpinner xSpinner
Frame parentFrame
boolean canceled
boolean editable
JPanel backgroundPanel
JButton cancelButton
JButton helpJButton
JButton okButton
JLabel peptideFdrLabel
JTextField peptideFdrTxt
JPanel processingParamsPanel
JLabel proteinFdrLabel
JTextField proteinFdrTxt
JLabel psmFdrLabel
JTextField psmFdrTxt
Frame parentFrame
ArrayList<E> psmFilters
ArrayList<E> peptideFilters
ArrayList<E> proteinFilters
boolean canceled
boolean userInput
boolean editable
ArrayList<E> allModifications
JMenuItem addPeptideFilterMenuItem
JMenuItem addProteinFilterMenuItem
JMenuItem addPsmFilterMenuItem
JButton cancelButton
JCheckBox confidenceCheck
JCheckBox dbCheck
JMenuItem editPeptideFilterMenuItem
JMenuItem editProteinFilterMenuItem
JMenuItem editPsmFilterMenuItem
JPanel generalSettingsPanel
JButton helpJButton
JLabel helpLbl
JLabel markDoubtfulLabel
JCheckBox nTargetCheck
JButton okButton
JPanel peptideFiltersPanel
JPopupMenu peptidePopupMenu
JScrollPane peptideScrollPane
JTable peptideTable
JPanel proteinFiltersPanel
JPopupMenu proteinPopupMenu
JScrollPane proteinScrollPane
JTable proteinTable
JPanel psmFiltersPanel
JPopupMenu psmPopupMenu
JScrollPane psmScrollPane
JTable psmTable
JMenuItem removePeptideFilterMenuItem
JMenuItem removeProteinFilterMenuItem
JMenuItem removePsmFilterMenuItem
JPanel validationQCPreferencesDialogPanel
boolean cancelled
boolean editable
JLabel advancedSettingsWarningLabel
JComboBox<E> ammoniaLossCmb
JLabel ammoniaLossLabel
JPanel backgroundPanel
JButton closeButton
JComboBox<E> decoyModeCmb
JLabel decoyModeLabel
JComboBox<E> empiricalCorrectionCombo
JLabel empiricalCorrectionLabel
JComboBox<E> equalILCombo
JLabel equalILLabel
JComboBox<E> fragMethodCmb
JLabel fragMethodLabel
JComboBox<E> fragmentAllCmb
JLabel fragmentAllLabel
JComboBox<E> higherChargeCombo
JLabel higherChargeLabel
JLabel maxCombinationsLabel
JTextField maxCombinationsTxt
JTextField maxPepLengthNoEnzymeTxt
JLabel maxPeptideMassLabel
JTextField maxPeptideMassTxt
JLabel maxPtmsLabel
JTextField maxPtmsTxt
JTextField minPepLengthNoEnzymeTxt
JComboBox<E> neutralLossesCmb
JLabel neutralLossesLabel
JLabel numberMatchesLabel
JTextField numberMatchesTxt
JButton okButton
JButton openDialogHelpJButton
JLabel peptideLengthNoEnzymeDividerLabel
JLabel peptideLengthNoEnzymeLabel
JPanel settingsInnerPanel
JPanel settingsPanel
JScrollPane settingsScrollPane
JLabel topPeaksLabel
JTextField topPeaksTxt
JLabel topPeaksWindowLabel
JTextField topPeaksWindowTxt
JComboBox<E> waterLossCombo
JLabel waterLossLabel
boolean cancelled
boolean editable
JLabel advancedSettingsWarningLabel
JPanel backgroundPanel
JLabel batchSizeLabel
JTextField batchSizeTxt
JLabel clearMzRangeDividerLabel
JLabel clearMzRangeLabel
JTextField clearMzRangeLowerTxt
JTextField clearMzRangeUpperTxt
JButton closeButton
JComboBox<E> correlationScoreTypeCmb
JLabel correlationScoreTypeLabel
JComboBox<E> enzymeTypeCmb
JLabel enzymeTypeLabel
JLabel fragmentBinOffsetLabel
JTextField fragmentBinOffsetTxt
JPanel fragmentIonsPanel
JComboBox<E> isotopeCorrectionCmb
JLabel isotopeCorrectionLabel
JLabel maxFragmentChargeLabel
JTextField maxFragmentChargeTxt
JTextField maxPepLengthTxt
JTextField maxPrecursorMassTxt
JLabel maxPtmsLabel
JTextField maxPtmsTxt
JLabel minPeakIntensityLbl
JTextField minPeakIntensityTxt
JLabel minPeaksLbl
JTextField minPeaksTxt
JTextField minPepLengthTxt
JTextField minPrecursorMassTxt
JLabel numberMatchesLabel
JTextField numberMatchesTxt
JButton okButton
JButton openDialogHelpJButton
JComboBox<E> outputFormatCmb
JPanel outputPanel
JLabel outputPepXmlLabel
JLabel peptideLengthDividerLabel
JLabel peptideLengthLabel
JLabel precursorMassDividerLabel
JLabel precursorMassLabel
JLabel printExpecScoreLabel
JComboBox<E> printExpectScoreCmb
JComboBox<E> removeMethionineCmb
JLabel removeMethionineLabel
JComboBox<E> removePrecursorPeakCombo
JLabel removePrecursorPeakLabel
JLabel removePrecursorPeakToleranceLbl
JTextField removePrecursorPeakToleranceTxt
JComboBox<E> requireVariablePtmCmb
JLabel requireVariablePtmLabel
JPanel searchSettingsPanel
JPanel spectrumProcessingPanel
JTabbedPane tabbedPane
boolean canceled
boolean editable
JComboBox<E> adjustPrecursorMassCmb
JLabel adjustPrecursorMassLabel
JPanel backgroundPanel
JButton cancelButton
JLabel complementScoreWeightLabel
JTextField complementScoreWeightTextField
JLabel complementToleranceLabel
JTextField complementToleranceTextField
JLabel deisotopingModeLabel
JTextField deisptopingModeTextField
JPanel directTagPanel
JLabel duplicateSpectraLabel
JComboBox<E> duplicateSpectraPerChargeCmb
JLabel intensityScoreWeightLabel
JTextField intensityScoreWeightTextField
JLabel isotopeToleranceLabel
JTextField isotopeToleranceTextField
JLabel maxPeakCountLabel
JTextField maxPeakCountTextField
JLabel maxPrecursorAdjustmentLabel
JTextField maxPrecursorAdjustmentTextField
JLabel maxTagCountLabel
JSpinner maxTagCountSpinner
JLabel minPrecursorAdjustmentLabel
JTextField minPrecursorAdjustmentTextField
JLabel mzFidelityScoreWeightLabel
JTextField mzFidelityScoreWeightTextField
JLabel numVariableModsLabel
JTextField numVariableModsTextField
JLabel numberOfChargeStatesLabel
JTextField numberOfChargeStatesTextField
JLabel numberOfIntensityClassesLabel
JTextField numberOfIntensityClassesTextField
JButton okButton
JButton openDialogHelpJButton
JLabel outputSuffixLabel
JTextField outputSuffixTextField
JLabel precursorAdjustmentStepLabel
JTextField precursorAdjustmentStepTextField
JLabel tagLengthLabel
JTextField tagLengthTextField
JLabel ticCutoffLabel
JTextField ticCutoffTextField
JComboBox<E> useSpectrumChargeStateCmb
JLabel useSpectrumChargeStateLabel
boolean cancelled
boolean editable
JLabel advancedSettingsWarningLabel
JPanel backgroundPanel
JButton closeButton
JLabel deconvIntRatioLbl
JTextField deconvIntRatioTxt
JLabel deconvMassToleranceLbl
JTextField deconvMassToleranceTxt
JComboBox<E> deconvMassToleranceTypeCmb
JLabel deconvMassToleranceTypeLbl
JComboBox<E> decoyTypeCmb
JLabel decoyTypeLbl
JPanel deisotopingPanel
JComboBox<E> dissociationTypeCombo
JLabel dissociationTypeLbl
JComboBox<E> doPrecDeconvCmb
JLabel doPrecDeconvLbl
JComboBox<E> excludeOneHitWondersCmb
JLabel excludeOneHitWondersLbl
JComboBox<E> fragmentationTerminusCmb
JLabel fragmentationTerminusLbl
JScrollPane gPtmScrollPane
JTable gPtmTable
JPanel gptmPanel
JPanel inSilicoDigestionPanel
JComboBox<E> intitiatorMethBehaviorCombo
JLabel intitiatorMethBehaviorLabel
JSeparator jSeparator1
JComboBox<E> massDiffAcceptorTypeCmb
JLabel massDiffAcceptorTypeLbl
JLabel maxFragmentSizeLbl
JTextField maxFragmentSizeTxt
JLabel maxHetroVariantsLbl
JTextField maxHetroVariantsTxt
JLabel maxModIsoformsLbl
JTextField maxModIsoformsTxt
JLabel maxNumModPeptideLbl
JTextField maxNumModPeptideTxt
JTextField maxPepLengthTxt
JLabel minAllowedIntensityRatioToBasePeakLbl
JTextField minAllowedIntensityRatioToBasePeakTxt
JTextField minPepLengthTxt
JLabel minVariantDepthLabel
JTextField minVariantDepthTxt
JComboBox<E> modifiedPeptidesAreDifferentCmb
JLabel modifiedPeptidesAreDifferentLbl
JComboBox<E> normalizePeaksAcrossAllWindowsCmb
JLabel normalizePeaksAcrossAllWindowsLbl
JLabel numPeaksPerWindowLbl
JTextField numPeaksPerWindowTxt
JLabel numberOfPartitionsLbl
JTextField numberOfPartitionsTxt
JLabel numberOfWindowsLbl
JTextField numberOfWindowsTxt
JButton okButton
JButton openDialogHelpJButton
JPanel outputPanel
JPanel peakTrimmingPanel
JLabel peptideLengthDividerLabel
JLabel peptideLengthJLabel
JPanel proteinGroupingPanel
JLabel runGptmLbl
JComboBox<E> runGtpmCmb
JLabel scoreCutoffLabel
JTextField scoreCutoffTxt
JPanel searchPanel
JComboBox<E> searchTargetComboBox
JLabel searchTargetLabel
JComboBox<E> searchTypeCombo
JLabel searchTypeLabel
JTabbedPane tabbedPane
JComboBox<E> trimMs1Cmb
JLabel trimMs1Lbl
JComboBox<E> trimMsMsCmb
JLabel trimMsMsLbl
JComboBox<E> useDeltaScoreCmb
JLabel useDeltaScoreLbl
JComboBox<E> useProvidedPrecCmb
JLabel useProvidedPrecLabel
JLabel windowWidthThompsonLbl
JTextField windowWidthThompsonTxt
JComboBox<E> writeMzidCmb
JLabel writeMzidLbl
JComboBox<E> writePepXmlCmb
JLabel writePepXmlLbl
boolean cancelled
boolean editable
JPanel advancedSearchSettingsPanel
JLabel advancedSettingsWarningLabel
JPanel backgroundPanel
JButton closeButton
JComboBox<E> decoyDatabaseCmb
JLabel decoyDatabaseLabel
JComboBox<E> instrumentCmb
JLabel instrumentLabel
JComboBox<E> maxModPerPeptideCmb
JLabel maxModPerPeptideLabel
JComboBox<E> maxNeutralLossesPerPeptideCmb
JLabel maxNeutralLossesPerPeptideLabel
JTextField maxPeptideLengthTxt
JComboBox<E> maxPotentialModSitePerPeptideCmb
JLabel maxPotentialModSitePerPeptideLabel
JLabel maxProteinsLoadedLabel
JTextField maxProteinsLoadedTxt
JComboBox<E> maxPtmNeutalLossesPerPeptideCmb
JLabel maxPtmNeutalLossesPerPeptideLabel
JLabel maxRankLabel
JTextField maxRankTxt
JLabel maxSpectraLoadedLabel
JTextField maxSpectraLoadedTxt
JComboBox<E> maxVariableModPerPeptideCmb
JLabel maxVariableModPerPeptideLabel
JTextField minPeptideLengthTxt
JComboBox<E> monoIsotopicCmb
JLabel monoIsotopicLabel
JButton okButton
JButton openDialogHelpJButton
JComboBox<E> outputFormatCmb
JLabel outputFormatLabel
JLabel peptideLengthDividerLabel
JLabel peptideLengthLabel
JComboBox<E> performDeisotopingCmb
JLabel performDeisotopingLabel
JComboBox<E> rankTargetAndDecoySeparatelyCmb
JLabel rankTargetAndDecoySeparatelyLabel
boolean cancelled
boolean editable
JComboBox<E> additionalOutputCmb
JLabel additionalOutputLabel
JPanel advancedSearchSettingsPanel
JLabel advancedSettingsWarningLabel
JPanel backgroundPanel
JButton closeButton
JComboBox<E> decoyDatabaseCmb
JLabel decoyDatabaseLabel
JComboBox<E> fragmentationMethodCmb
JLabel fragmentationMethodLabel
JComboBox<E> instrumentCmb
JLabel instrumentLabel
JTextField maxPepLengthTxt
JLabel maxPtmsLabel
JTextField maxPtmsTxt
JTextField minPepLengthTxt
JLabel numberMatchesLabel
JTextField numberMatchesTxt
JLabel numberOfTasksLabel
JTextField numberOfTasksTxt
JLabel numberTerminiLabel
JButton okButton
JButton openDialogHelpJButton
JLabel peptideLengthDividerLabel
JLabel peptideLengthLabel
JComboBox<E> protocolCmb
JLabel protocolLabel
JComboBox<E> terminiCmb
boolean cancelled
boolean editable
JPanel advancedSearchSettingsPanel
JPanel advancedSettingsPanel
JLabel advancedSettingsWarningLabel
JPanel backgroundPanel
JLabel classSizeMultiplierLabel
JTextField classSizeMultiplierTxt
JButton closeButton
JComboBox<E> computeXCorrCmb
JLabel computeXCorrlLabel
JComboBox<E> fragmentationMethodCmb
JLabel fragmentationMethodLabel
JLabel maxPeakCountLabel
JTextField maxPeakCountTxt
JTextField maxPepLengthTxt
JTextField maxPrecursorMassTxt
JLabel maxPtmsLabel
JTextField maxPtmsTxt
JTextField minPepLengthTxt
JTextField minPrecursorMassTxt
JLabel numIntensityClassesLabel
JTextField numIntensityClassesTxt
JLabel numbBatchesLabel
JTextField numbBatchesTxt
JLabel numberMatchesLabel
JTextField numberMatchesTxt
JLabel numberTerminiLabel
JButton okButton
JButton openDialogHelpJButton
JComboBox<E> outputFormatCmb
JLabel outputFormatLabel
JLabel peptideLengthDividerLabel
JLabel peptideLengthLabel
JLabel precursorMassDividerLabel
JLabel precursorMassLabel
JScrollPane scrollPane
JComboBox<E> terminiCmb
JLabel ticCutoffPercentageLabel
JTextField ticCutoffPercentageTxt
JComboBox<E> useSmartPlusThreeModelCmb
JLabel useSmartPlusThreeModelLabel
boolean canceled
boolean editable
JPanel backgroundPanel
JButton cancelButton
JComboBox<E> fragmentationMethodCmb
JLabel fragmentationMethodLabel
JComboBox<E> massAnalyzerCmb
JLabel massAnalyzerLabel
JPanel novorPanel
JButton okButton
JButton openDialogHelpJButton
boolean cancelled
boolean editable
JPanel advancedSearchSettingsPanel
JLabel advancedSettingsWarningLabel
JPanel backgroundPanel
JComboBox<E> cTermIonsCmb
JLabel cTermIonsLbl
JComboBox<E> chargeEstimationCombo
JLabel chargeReductionLabel
JComboBox<E> cleaveNterminalMethionineCmb
JLabel cleaveNterminalMethionineLbl
JButton closeButton
JLabel consecutiveIonProbabilityLbl
JTextField consecutiveIonProbabilityTxt
JComboBox<E> correlationCorrectionScoreCmb
JLabel correlationCorrectionScoreLbl
JPanel databaseProcessingPanel
JLabel doublyChargedNPeaksLbl
JTextField doublyChargedNpeaksTxt
JLabel doublyChargedWindowWidthLbl
JTextField doublyChargedWindowWidthTxt
JLabel eValueLbl
JComboBox<E> eliminatePrecursorCombo
JComboBox<E> forwardIonsFirstCmb
JLabel forwardIonsFirstLbl
JLabel fractionChargeLbl
JTextField fractionChargeTxt
JLabel highIntensityLbl
JTextField highIntensityTxt
JLabel hitListLbl
JTextField hitlistTxt
JLabel intensityIncrementLbl
JTextField intensityIncrementTxt
JLabel iterativeReplaceEvalueLbl
JTextField iterativeReplaceEvalueTxt
JPanel iterativeSearchSettingsPanel
JLabel iterativeSequenceEvalueLbl
JTextField iterativeSequenceEvalueTxt
JLabel iterativeSpectraEvalueLbl
JTextField iterativeSpectraEvalueTxt
JSeparator jSeparator1
JLabel lowIntensityLbl
JTextField lowIntensityTxt
JTextField maxEvalueTxt
JLabel maxFragmentChargeLbl
JTextField maxFragmentChargeTxt
JLabel maxFragmentsPerSeriesLbl
JTextField maxFragmentsPerSeriesTxt
JLabel maxLaddersLbl
JTextField maxLaddersTxt
JTextField maxPepLengthTxt
JLabel minAnnotatedMostIntensePeaksLbl
JTextField minAnnotatedMostIntensePeaksTxt
JLabel minAnnotatedPeaksLbl
JTextField minAnnotatedPeaksTxt
JTextField minPepLengthTxt
JTextField minPrecChargeMultipleChargedFragmentsTxt
JLabel minPrecPerSpectrumLbl
JTextField minPrecPerSpectrumTxt
JLabel minPrecursorChargeConsideredMultiplyChargedFragmentsJLabel
JLabel nHitsPerSpectrumPerChargeLbl
JTextField nHitsPerSpectrumPerChargeTxt
JLabel nPeaksLbl
JTextField nPeaksTxt
JLabel neutronLbl
JTextField neutronTxt
JButton okButton
JComboBox<E> omssaOutputFormatComboBox
JLabel omssaOutputFormatLabel
JButton openDialogHelpJButton
JPanel outputParametersPanel
JLabel peptideLengthDividerLabel1
JLabel peptideLengthJLabel
JLabel plusOneChargeAutomaticLbl
JComboBox<E> plusOneChargeCmb
JLabel precursorChargeEstimationLabel
JLabel precursorMassScalingLabel
JComboBox<E> precursorScalingCombo
JComboBox<E> searchPositiveIonsCmb
JLabel searchPositiveIonsLbl
JPanel searchSettingsPanel
JScrollPane searchSettingsScrollPane
JPanel semiEnzymaticParametersPanel
JComboBox<E> sequenceMappingCmb
JLabel sequenceMappingLbl
JLabel singlyChargedNPeaksLbl
JTextField singlyChargedNpeaksTxt
JLabel singlyChargedWindowWidthLbl
JTextField singlyChargedWindowWidthTxt
JPanel spectrumProcessingPanel
JTabbedPane tabbedPane
boolean canceled
boolean editable
JPanel backgroundPanel
JButton cancelButton
JComboBox<E> correctPrecursorMassCmb
JLabel correctPrecursorMassLabel
JComboBox<E> estimateChargeCmb
JLabel estimateChargeLabel
JLabel hitListLengthLabel
JSpinner hitListLengthSpinner
JButton okButton
JButton openDialogHelpJButton
JPanel pepNovoPanel
boolean canceled
boolean editable
JComboBox<E> activationTypeCmb
JLabel activationTypeLabel
JPanel backgroundPanel
JButton cancelButton
JLabel maxPrecursorMassLabel
JTextField maxPrecursorMassTextField
JLabel minPrecursorMassLabel
JTextField minPrecursorMassTextField
JButton okButton
JButton openDialogHelpJButton
JPanel pNovoPanel
boolean cancelled
boolean editable
JLabel advancedSettingsWarningLabel
JPanel backgroundPanel
JComboBox<E> chargesCombo
JLabel chargesLabel
JButton closeButton
JComboBox<E> decoyFormatCombo
JLabel decoySeedLabel
JTextField decoySeedTxt
JLabel decoyformatLabel
JComboBox<E> enzymeTypeCmb
JLabel enzymeTypeLabel
JComboBox<E> exactPvalueCombo
JLabel exactPvalueLabel
JPanel indexPanel
JComboBox<E> keepTerminalAaCombo
JLabel keepTerminalAaLabel
JTextField maxPepLengthTxt
JTextField maxPrecursorMassTxt
JLabel maxPtmsLabel
JTextField maxPtmsTxt
JTextField maxSpectrumMzTxt
JLabel maxVariablePtmsPerTypeLabel
JTextField maxVariablePtmsPerTypeTxt
JLabel minPeaksLbl
JTextField minPeaksTxt
JTextField minPepLengthTxt
JTextField minPrecursorMassTxt
JTextField minSpectrumMzTxt
JComboBox<E> monoPrecursorCmb
JLabel monoPrecursorLabel
JLabel mzBinOffsetLabel
JTextField mzBinOffsetTxt
JLabel mzBinWidthLabel
JTextField mzBinWidthTxt
JLabel numberMatchesLabel
JTextField numberMatchesTxt
JButton okButton
JButton openDialogHelpJButton
JComboBox<E> outputFormatCombo
JLabel outputFormatLabel
JLabel peptideLengthDividerLabel
JLabel peptideLengthLabel
JComboBox<E> peptideListCmb
JLabel peptideListLabel
JLabel precursorMassDividerLabel
JLabel precursorMassLabel
JComboBox<E> removeMethionineCmb
JLabel removeMethionineLabel
JComboBox<E> removePrecursorPeakCombo
JLabel removePrecursorPeakLabel
JLabel removePrecursorPeakToleranceLbl
JTextField removePrecursorPeakToleranceTxt
JComboBox<E> removeTempFoldersCmb
JLabel removeTempFoldersLabel
JPanel searchPanel
JComboBox<E> spScoreCombo
JLabel spScoreLabel
JLabel spectrumMzDividerLabel
JLabel spectrumMzLabel
JTabbedPane tabbedPane
JComboBox<E> useFlankingCmb
JLabel useFlankingLabel
JComboBox<E> useNeutralLossCmb
JLabel useNeutralLossLabel
ModificationParameters modificationProfile
double fragmentIonMassAccuracyInDa
boolean cancelled
ArrayList<E> modificationTableToolTips
ModificationFactory modificationFactory
boolean modProfileChanged
boolean editable
JPanel advancedSearchSettingsPanel
JLabel advancedSettingsWarningLabel
JPanel backgroundPanel
JButton closeButton
JLabel dynamicRangeLbl
JTextField dynamicRangeTxt
JLabel eValueLbl
JTextField eValueTxt
JSeparator jSeparator1
JTextField maxEValueRefineTxt
JLabel maxEValueRefinmentLbl
JLabel minFragMzLbl
JTextField minFragmentMzTxt
JLabel minPeaksLbl
JTextField minPeaksTxt
JLabel minPrecMassLbl
JTextField minPrecMassTxt
JLabel modificationComplexityLbl
JTextField modificationComplexityTxt
JScrollPane modificationsJScrollPane
JTable modificationsTable
JLabel nPeaksLbl
JTextField nPeaksTxt
JComboBox<E> noiseSuppressionCmb
JLabel noiseSuppressionLabel
JButton okButton
JButton openDialogHelpJButton
JButton openModificationSettingsJButton
JComboBox<E> outputHistogramsCmb
JLabel outputHistogramsLabel
JComboBox<E> outputProteinsCmb
JLabel outputProteinsLabel
JComboBox<E> outputResultsCmb
JLabel outputResultsLabel
JComboBox<E> outputSequencesCmb
JLabel outputSequencesLabel
JPanel outputSettingsPanel
JComboBox<E> outputSpectraCmb
JLabel outputSpectraLabel
JComboBox<E> parentMonoisotopicMassIsotopeErrorCmb
JLabel parentMonoisotopicMassIsotopeErrorLabel
JLabel pointMutationLabel
JComboBox<E> pointMutationsCmb
JComboBox<E> potentialModificationsCmb
JComboBox<E> quickAcetylCmb
JLabel quickAcetylLabel
JComboBox<E> quickPyroCmb
JLabel quickPyroLabel
JComboBox<E> refinementCmb
JLabel refinementLabel
JPanel refinementModificationsJPanel
JLabel refinementModificationsLabel
JPanel refinementSettingsPanel
JComboBox<E> semiEnzymaticCmb
JLabel semiEnzymaticLabel
JLabel skylinePathValueLbl
JTextField skylineTxt
JComboBox<E> snapsCmb
JLabel snapsLabel
JPanel spectrumImportSettingsPanel
JComboBox<E> spectrumSynthesisCmb
JLabel spectrumSynthesisLabel
JComboBox<E> stpBiasCmb
JLabel stpBiasLabel
JTabbedPane tabbedPane
JComboBox<E> unanticipatedCleavageCmb
JLabel unanticipatedCleavageLabel
JLabel usePotentialModsLabel
EnzymeFactory enzymeFactory
boolean selectionCanceled
boolean editable
JPanel backgroundPanel
JButton cancelButton
JLabel enzymeLabel
JComboBox<E> enzymesCmb
JPanel mappingPanel
JButton okButton
JLabel prideEnzymeNameLabel
JTextField prideEnzymeNameTextField
EnzymeFactory enzymeFactory
String[] forwardIons
String[] rewindIons
ModificationFactory modificationFactory
SearchParameters searchParameters
ArrayList<E> modificationTableToolTips
Frame parentFrame
Image normalIcon
Image waitingIcon
int keyPressedCounter
String currentPtmSearchString
int waitingTime
boolean canceled
boolean editable
LastSelectedFolder lastSelectedFolder
Double refMass
UtilitiesUserParameters utilitiesUserParameters
JButton addFixedModification
JButton addVariableModification
JPanel availableModsPanel
JPanel backgroundPanel
JButton cancelButton
JComboBox<E> digestionCmb
JLabel digestionLabel
JLabel enzymeLabel
JComboBox<E> enzymesCmb
JLabel fixedModificationsLabel
JScrollPane fixedModsJScrollPane
JPanel fixedModsPanel
JTable fixedModsTable
JComboBox<E> fragmentIon1Cmb
JComboBox<E> fragmentIon2Cmb
JTextField fragmentIonAccuracyTxt
JLabel fragmentIonLbl
JLabel fragmentIonType1Lbl
JComboBox<E> fragmentIonUnit
JTextField isotopeMaxTxt
JTextField isotopeMinTxt
JLabel isotopeRangeLabel
JLabel isotopesLbl
JLabel maxMissedCleavagesLabel
JTextField maxMissedCleavagesTxt
JTextField maxPrecursorChargeTxt
JTextField minPrecursorChargeTxt
JSplitPane modificationTypesSplitPane
JScrollPane modificationsJScrollPane
JLayeredPane modificationsLayeredPane
JComboBox<E> modificationsListCombo
JPanel modificationsPanel
JTable modificationsTable
JButton okButton
JButton openDialogHelpJButton1
JButton openModificationSettingsJButton
JLabel precursorChargeLbl
JLabel precursorChargeRangeLabel
JTextField precursorIonAccuracyTxt
JLabel precursorIonLbl
JComboBox<E> precursorIonUnit
JPanel proteaseAndFragmentationPanel
JButton removeFixedModification
JButton removeVariableModification
JComboBox<E> specificityComboBox
JLabel specificityLabel
JLabel variableModificationsLabel
JScrollPane variableModsJScrollPane
JPanel variableModsPanel
JTable variableModsTable
LastSelectedFolder lastSelectedFolder
boolean dbEditable
Image waitingImage
Image normalImange
Frame parentFrame
UtilitiesUserParameters utilitiesUserParameters
String selectedFastaFile
FastaParameters fastaParameters
FastaSummary fastaSummary
ArrayList<E> accessionsSample
HashMap<K,V> proteinsSample
HashMap<K,V> headersSample
FastaIterator proteinIterator
boolean canceled
JSpinner accessionsSpinner
JPanel backgroundPanel
JButton browseButton
JButton cancelButton
JLabel databaseHelpSettingsJLabel
JPanel databaseInformationPanel
JTextField dbNameTxt
JButton decoyButton
JLabel editFastaParametersJLabel
JLabel fileLabel
JTextField fileTxt
JLabel lastModifiedLabel
JTextField lastModifiedTxt
JLabel nameLabel
JButton okButton
JPanel previewPanel
JLabel proteinLabel
JTextArea proteinTxt
JScrollPane proteinYxtScrollPane
JLabel sizeLabel
JTextField sizeTxt
JTextField speciesJTextField
JLabel speciesLabel
JLabel targetDecoyTxt
JTextField typeJTextField
JLabel typeLabel
JLabel versionLabel
JTextField versionTxt
boolean canceled
HashMap<K,V> filters
ArrayList<E> filterIndexes
String lastSelectedFolder
UtilitiesUserParameters utilitiesUserParameters
JMenu addFilterMenu
JPanel backgourdPanel
JButton browseButton
JButton cancelButton
JLabel filterHelpLabel
JLabel filtersLbl
JPopupMenu filtersPopupMenu
JTable filtersTable
JScrollPane filtersTableScrollPane
JLabel folderHelpLabel
JTextField installationJTextField
JPanel installationPanel
JPanel msconvertParameters
JButton okButton
JComboBox<E> outputFormatCmb
JLabel outputFormatLbl
JMenuItem removeFilterMenuItem
boolean canceled
boolean editable
JPanel backgroundPanel
JButton cancelButton
JSpinner nThreadsSpinner
JButton okButton
JLabel performanceLbl
JPanel performancePanel
JComboBox<E> processingTypeCmb
JLabel processingTypeLbl
JPanel processingTypePanel
Frame parentFrame
boolean canceled
boolean editable
JPanel backgroundPanel
JButton cancelButton
JTextField decoyFlagTxt
JLabel decoySuffixLabel
JLabel decoyTagLabel
JComboBox<E> decoyTypeComboBox
JLabel decoyTypeLabel
JTextField fastaSuffixTxt
JPanel fileProcessingPanel
JButton helpJButton
JButton okButton
JComboBox<E> targetDecoyComboBox
JLabel targetDecoyLabel
HashMap<K,V> fragmentIonRectangles
String[] iSequenceComponents
ArrayList<E> profiles
Font iBaseFont
double iMaxBarHeight
int iBarWidth
int iHorizontalSpace
int iXStart
int iYStart
boolean isModifiedSequence
String score1Name
String score2Name
int align
org.apache.logging.log4j.Logger logger
byte[] iData
double minXAxisValue
double maxXAxisValue
TableCellRenderer delegate
org.apache.logging.log4j.Logger logger
Vector<E> tooltips
int align
int MAX_TOOLTIP_WIDTH
Color backgroundColor
HashSet<E> currentFragmentIonTypes
NeutralLossesMap neutralLosses
boolean singleCharge
boolean twoCharges
ArrayList<E> tooltips
Peptide currentPeptide
String peptideSequence
ArrayList<E> allAnnotations
ArrayList<E> allSpectra
ModificationParameters modificationParameters
SequenceProvider sequenceProvider
SequenceMatchingParameters modificationSequenceMatchingParameters
float peakWidth
float backgroundPeakWidth
boolean subscriptAnnotationNumbers
Color peakWaterMarkColor
boolean scientificXAxis
boolean scientificYAxis
String scientificPattern
HashMap<K,V> referenceAreasXAxis
HashMap<K,V> referenceAreasYAxis
boolean miniature
boolean yDataIsPositive
float alphaLevel
int dataSetCounter
int dataSetCounterMirroredSpectra
int INTERACTIVE_STATUS
int ANNOTATED_STATUS
boolean useMassDeltaCombinations
double deltaMassWindow
String iXAxisLabel
String iYAxisLabel
Color iFilenameColor
ArrayList<E> iDataPointAndLineColor
ArrayList<E> iDataPointAndLineColorMirroredSpectra
ArrayList<E> iAreaUnderCurveColor
ArrayList<E> iAreaUnderCurveColorMirroredSpectra
Integer iPointSize
String iFilename
String iFilenameMirrorredSpectrum
ArrayList<E> iSpecPanelListeners
int iPointDetectionTolerance
int iStartXLoc
int iStartYLoc
int iEndXLoc
double xAxisZoomRangeLowerValue
double xAxisZoomRangeUpperValue
int iDragXLoc
double iXScaleUnit
double iYScaleUnit
int iXUnit
int iYUnit
int iXPadding
int iTopPadding
boolean iXAxisStartAtZero
boolean iDragged
int xTagCount
int yTagCount
int padding
int currentPadding
int maxPadding
boolean showFileName
boolean showPrecursorDetails
boolean showResolution
ArrayList<E> iXAxisData
ArrayList<E> iXAxisDataMirroredSpectrum
double iXAxisMin
double iXAxisMax
double iYAxisMin
double iYAxisMax
double iAnnotationYAxisThreshold
ArrayList<E> iYAxisData
ArrayList<E> iYAxisDataMirroredSpectrum
double iPrecursorMZ
double iPrecursorMZMirroredSpectrum
String iPrecursorCharge
String iPrecursorChargeMirorredSpectrum
ArrayList<E> iXAxisDataInPixels
ArrayList<E> iYAxisDataInPixels
ArrayList<E> iXAxisDataInPixelsMirroredSpectrum
ArrayList<E> iYAxisDataInPixelsMirroredSpectrum
boolean iHighLight
boolean iHighLightMirrored
int iHighLightIndex
int iHighLightIndexMirrored
int iHighLightDatasetIndex
int iHighLightDatasetIndexMirrored
boolean iClicked
boolean iClickedMirrored
int iClickedIndex
int iClickedIndexMirrored
int iClickedDataSetIndex
int iClickedDataSetIndexMirrored
Vector<E> iClickedList
Vector<E> iClickedListMirrored
Vector<E> iClickedListDatasetIndices
Vector<E> iClickedListDatasetIndicesMirrored
Vector<E> iStoredSequence
Vector<E> iStoredSequenceMirrored
Vector<E> iStoredSequenceDatasetIndices
Vector<E> iStoredSequenceDatasetIndicesMirrored
Vector<E> iAnnotations
Vector<E> iAnnotationsMirroredSpectra
int iMinDrag
GraphicsPanel.DrawingStyle iCurrentDrawStyle
int iDotRadius
int iMSLevel
boolean showAllPeaks
boolean yAxisZoomExcludesBackgroundPeaks
boolean annotateHighestPeak
GraphicsPanel.GraphicsPanelType currentGraphicsPanelType
org.jfree.chart.ChartPanel chartPanel
org.apache.logging.log4j.Logger logger
Color aSpectrumPeakColor
Color aSpectrumProfileModeLineColor
ArrayList<E> peptideSequences
ArrayList<E> peptideCharges
HashMap<K,V> iElements
boolean useRelativeError
IonMatch[] currentlyUsedIonMatches
org.jfree.chart.ChartPanel chartPanel
ArrayList<E> dataSeriesfragmentIonColors
IonMatch[] annotations
org.jfree.chart.ChartPanel chartPanel
HashMap<K,V> tooltipRectangles
String[] iSequenceComponents
IonMatch[] iIonMatches
double[] bIons
double[] yIons
Font iPeptideSequenceFont
double iMaxBarHeight
int iBarWidth
int iHorizontalSpace
int iXStart
boolean isModifiedSequence
boolean iHighlightModifications
ModificationParameters modificationProfile
int forwardIon
int rewindIon
Color forwardColor
Color rewindColor
Color fontColor
int rowStartLoading
int rowEndLoading
ExecutorService loadingPool
ExecutorService updatingPool
boolean selfUpdating
Semaphore updateMutex
com.compomics.util.gui.tablemodels.SelfUpdatingTableModel.LoadingRunnable lastLoadingRunnable
ArrayList<E> viewIndexes
int lastColumnSorted
boolean sortAscending
boolean unsorted
ProgressDialogX progressDialog
boolean isScrolling
org.apache.logging.log4j.Logger logger
ArrayList<E> iConnections
JComboBox<E> cmbConfigurations
JTextField txtDriver
JTextField txtUrl
JTextField txtUser
JPasswordField txtPassword
JButton btnOK
JButton btnCancel
Connectable iTarget
String iPropsFile
String iLastInitiatedConfiguration
ArrayList<E> items
boolean canceled
ArrayList<E> tableToolTips
JPanel backgroundPanel
JButton cancelButton
JLabel itemsLabel
JPanel itemsPanel
JTable itemsTable
JScrollPane itemsTableScrollPane
JButton okButton
ModificationFactory modificationsFactory
ArrayList<E> modificationsList
char[] aminoAcids
AaSubstitutionMatrix aaSubstitutionMatrix
boolean editable
org.apache.logging.log4j.Logger logger
JProgressBar iProgress
boolean doNothingOnClose
boolean unstoppable
boolean canceled
boolean finished
boolean displayProgress
Image waitingIcon
Image normalIcon
Frame waitingHandlerParentFrame
JDialog waitingHandlerParentDialog
WaitingActionListener waitingActionListener
SimpleSemaphore mutex
JProgressBar progressBar
JDialog dialog
Point naturalLocation
Timer shakeTimer
boolean runFinished
boolean runCanceled
boolean displayProgress
ArrayList<E> tips
int currentTipIndex
String lastSelectedFolder
Image waitingIcon
Image normalIcon
Frame waitingHandlerParent
boolean shakeWhenFinished
String processName
String toolName
String toolVersion
WaitingActionListener waitingActionListener
String lineBreak
SimpleSemaphore primaryMutex
SimpleSemaphore secondaryMutex
SimpleSemaphore textMutex
JPanel backgroundPanel
JCheckBox closeDialogWhenImportCompletesCheckBox
JButton closeJButton
JLayeredPane layeredPane
JButton nextJButton
JButton okButton
JPanel processProgressPanel
JProgressBar progressBar
JScrollPane reportScrollPane
JTextArea reportTextArea
JLabel saveReportLabel
JProgressBar secondaryJProgressBar
JSplitPane secondaryProgressBarSplitPane
JCheckBox showTipOfTheDayCheckBox
JProgressBar tempJProgressBar
JEditorPane tipOfTheDayEditorPane
JPanel tipOfTheDayJPanel
JLayeredPane tipOfTheDayLayeredPane
JScrollPane tipOfTheDayScrollPane
String name
boolean editable
String mainTitle
ArrayList<E> sectionList
HashMap<K,V> exportFeaturesMap
String separator
boolean indexes
boolean header
int separationLines
boolean includeSectionTitles
Boolean validatedOnly
Boolean includeDecoy
org.apache.logging.log4j.Logger logger
org.apache.logging.log4j.Logger logger
org.apache.logging.log4j.Logger logger
com.google.gson.Gson gson
com.google.gson.GsonBuilder builder
double stdUp
double stdDown
double mean
NormalDistribution distributionUp
NormalDistribution distributionDown
org.apache.commons.math.distribution.NormalDistributionImpl normalDistributionImpl
double mean
double std
float spectrumAnnotatedPeakWidth
float spectrumBackgroundPeakWidth
Color spectrumAnnotatedPeakColor
Color spectrumAnnotatedMirroredPeakColor
Color spectrumBackgroundPeakColor
Color sparklineColorValidated
Color sparklineColorNonValidated
Color sparklineColorNotFound
Color sparklineColorPossible
Color sparklineColorDoubtful
Color sparklineColorFalsePositive
Color peptideSelected
int memoryParameter
String javaHome
String proteoWizardPath
String searchGuiPath
String peptideShakerPath
String deNovoGuiPath
String reporterPath
String relimsPath
String localPrideFolder
String dbFolder
String spectrumFolder
String outputFolder
ArrayList<E> readTweets
ArrayList<E> displayedTips
boolean autoUpdate
LastSelectedFolder lastSelectedFolder
boolean sortPsmsOnRt
boolean checkPeakPicking
boolean checkDuplicateTitles
boolean checkMgfSize
double mgfMaxSize
int mgfNSpectra
double refMass
boolean gzip
OutputParameters outputOption
boolean outputData
boolean includeDateInOutputName
boolean renameXTandemFile
boolean checkSpectrumCharges
int minSpectrumChargeRange
int maxSpectrumChargeRange
String marshallableParameterType
String version
String name
String description
boolean defaultDescription
SearchParameters searchParameters
AnnotationParameters annotationParameters
SequenceMatchingParameters sequenceMatchingParameters
PeptideVariantsParameters peptideVariantsParameters
GeneParameters geneParameters
PsmScoringParameters psmScoringParameters
PeptideAssumptionFilter peptideAssumptionFilter
ModificationLocalizationParameters modificationLocalizationParameters
ProteinInferenceParameters proteinInferenceParameters
IdMatchValidationParameters idValidationParameters
FractionParameters fractionParameters
FastaParameters fastaParameters
Double proteinConfidenceMwPlots
HashMap<K,V> fractionMolecularWeightRanges
double defaultProteinFDR
double defaultPeptideFDR
double defaultPsmFDR
ValidationQcParameters validationQCPreferences
boolean probabilisticScoreCalculation
ModificationLocalizationScore selectedProbabilisticScore
double dScoreThreshold
double probabilisticScoreThreshold
boolean probabilisticScoreNeutralLosses
SequenceMatchingParameters sequenceMatchingParameters
boolean alignNonConfidentModifications
PeptideVariantsParameters.VariantType variantType
int nVariants
int nAaDeletions
int nAaInsertions
int nAaSubstitutions
int nAaSwap
AaSubstitutionMatrix aaSubstitutionMatrix
HashMap<K,V> fixedVariants
boolean modificationRefinement
boolean simplifyProteinGroups
boolean simplifyGroupsEvidence
boolean simplifyGroupsConfidence
boolean simplifyGroupsEnzymaticity
boolean simplifyGroupsVariants
double confidenceThreshold
HashMap<K,V> spectrumMatchingScores
HashSet<E> defaultScores
int minDecoysInBin
SequenceMatchingParameters.MatchingType sequenceMatchingType
double limitX
Boolean enzymaticTagsOnly
int maxPtmsPerTagPeptide
Integer minAminoAcidScore
Integer minTagLength
boolean dbSize
boolean firstDecoy
Double confidenceMargin
ArrayList<E> psmFilters
ArrayList<E> peptideFilters
ArrayList<E> proteinFilters
DigestionParameters.CleavageParameter cleavageParameter
ArrayList<E> enzymes
HashMap<K,V> nMissedCleavages
HashMap<K,V> specificity
ArrayList<E> fixedModifications
ArrayList<E> variableModifications
ArrayList<E> refinementVariableModifications
ArrayList<E> refinementFixedModifications
HashMap<K,V> colors
HashMap<K,V> backUp
String marshallableParameterType
String version
SearchParameters.MassAccuracyType precursorAccuracyType
SearchParameters.MassAccuracyType fragmentAccuracyType
double precursorTolerance
double fragmentIonMZTolerance
ModificationParameters modificationParameters
DigestionParameters digestionParameters
ArrayList<E> forwardIons
ArrayList<E> rewindIons
int minChargeSearched
int maxChargeSearched
int minIsotopicCorrection
int maxIsotopicCorrection
double refMass
HashMap<K,V> algorithmParameters
boolean flanking
Double maxPeptideMass
Integer maxCombinations
Integer topPeaks
Integer topPeaksWindow
Boolean includeWater
Boolean includeAmmonia
Boolean dependentLosses
Boolean fragmentAll
Boolean empiricalCorrection
Boolean higherCharge
FragmentationMethod fragmentationMethod
Integer maxNumberOfModifications
Integer minPeptideLengthNoEnzyme
Integer maxPeptideLengthNoEnzyme
Boolean equalIL
Integer numberOfCandidates
HashMap<K,V> ptmIndexes
AndromedaParameters.AndromedaDecoyMode decoyMode
Integer numberOfSpectrumMatches
Integer maxVariableMods
Boolean requireVariableMods
Integer minPeaks
Double minPeakIntensity
Integer removePrecursor
Double removePrecursorTolerance
Double lowerClearMzRange
Double upperClearMzRange
Integer enzymeType
Integer isotopeCorrection
Double minPrecursorMass
Double maxPrecursorMass
Integer maxFragmentCharge
Boolean removeMethionine
Integer batchSize
Boolean theoreticalFragmentIonsSumOnly
Double fragmentBinOffset
Boolean useSparseMatrix
CometParameters.CometOutputFormat selectedOutputFormat
Boolean printExpectScore
Integer minPeptideLength
Integer maxPeptideLength
double ticCutoffPercentage
int maxPeakCount
int numIntensityClasses
boolean adjustPrecursorMass
double minPrecursorAdjustment
double maxPrecursorAdjustment
double precursorAdjustmentStep
int numChargeStates
String outputSuffix
boolean useChargeStateFromMS
boolean duplicateSpectra
int deisotopingMode
double isotopeMzTolerance
double complementMzTolerance
int tagLength
int maxDynamicMods
int maxTagCount
double intensityScoreWeight
double mzFidelityScoreWeight
double complementScoreWeight
ArrayList<E> variableModifications
Integer minPeptideLength
Integer maxPeptideLength
MetaMorpheusParameters.MetaMorpheusSearchType searchType
Integer totalPartitions
MetaMorpheusParameters.MetaMorpheusDissociationType dissociationType
Integer maxModsForPeptide
MetaMorpheusParameters.MetaMorpheusInitiatorMethionineBehaviorType initiatorMethionineBehavior
Double scoreCutoff
boolean useDeltaScore
MetaMorpheusParameters.MetaMorpheusFragmentationTerminusType fragmentationTerminus
Double maxFragmentSize
MetaMorpheusParameters.MetaMorpheusMassDiffAcceptorType massDiffAcceptorType
Boolean writeMzId
Boolean writePepXml
Boolean useProvidedPrecursorInfo
Boolean doPrecursorDeconvolution
Double deconvolutionIntensityRatio
Double deconvolutionMassTolerance
MetaMorpheusParameters.MetaMorpheusToleranceType deconvolutionMassToleranceType
Boolean trimMs1Peaks
Boolean trimMsMsPeaks
Integer numberOfPeaksToKeepPerWindow
Double minAllowedIntensityRatioToBasePeak
Double windowWidthThomson
Integer numberOfWindows
Boolean normalizePeaksAcrossAllWindows
Boolean modPeptidesAreDifferent
Boolean noOneHitWonders
Boolean searchTarget
MetaMorpheusParameters.MetaMorpheusDecoyType decoyType
Integer maxModificationIsoforms
Integer minVariantDepth
Integer maxHeterozygousVariants
boolean runGptm
ArrayList<E> gPtmCategories
boolean generateDecoy
Boolean reportBothBestHitsForTD
String instrumentID
Integer maxRank
boolean monoisotopic
Boolean lowMemoryMode
Boolean performDeisotoping
Integer maxModifications
Integer maxVariableModifications
Integer maxModificationSites
Integer maxNeutralLosses
Integer maxNeutralLossesPerModification
Integer minPeptideLength
Integer maxPeptideLength
Integer maxLoadedProteins
Integer maxLoadedSpectra
String outputFormat
boolean searchDecoyDatabase
int instrumentID
int fragmentationType
int protocol
Integer minPeptideLength
Integer maxPeptideLength
Integer numberOfSpectrumMarches
boolean additionalOutput
Integer numberTolerableTermini
Integer numberOfModificationsPerPeptide
Integer numberOfTasks
Integer minPeptideLength
Integer maxPeptideLength
Integer numberOfSpectrumMatches
Double ticCutoffPercentage
Integer maxDynamicMods
Integer minTerminiCleavages
Double minPrecursorMass
Double maxPrecursorMass
Boolean useSmartPlusThreeModel
Boolean computeXCorr
Integer numIntensityClasses
Integer classSizeMultiplier
Integer numberOfBatches
Integer lowerIsotopeCorrection
Integer upperIsotopeCorrection
String fragmentationRule
Integer maxPeakCount
String outputFormat
double maxEValue
int hitListLength
int minimalChargeForMultipleChargedFragments
int minPeptideLength
int maxPeptideLength
boolean removePrecursor
boolean scalePrecursor
boolean estimateCharge
String selectedOutput
boolean memoryMappedSequenceLibraries
double neutronThreshold
double lowIntensityCutOff
double highIntensityCutOff
double intensityCutOffIncrement
int singleChargeWindow
int doubleChargeWindow
int nPeaksInSingleChargeWindow
int nPeaksIndoubleChargeWindow
int maxHitsPerSpectrumPerCharge
int nAnnotatedMostIntensePeaks
int minAnnotatedPeaks
int minPeaks
boolean cleaveNtermMethionine
int maxMzLadders
int maxFragmentCharge
double fractionOfPeaksForChargeEstimation
boolean determineChargePlusOneAlgorithmically
boolean searchPositiveIons
int minPrecPerSpectrum
boolean searchForwardFragmentFirst
boolean searchRewindFragments
int maxFragmentPerSeries
boolean useCorrelationCorrectionScore
double consecutiveIonProbability
double iterativeSequenceEvalue
double iterativeReplaceEvalue
double iterativeSpectrumEvalue
ArrayList<E> noProlineRuleSeries
HashMap<K,V> ptmIndexes
Integer hitListLength
Boolean estimateCharge
Boolean correctPrecursorMass
Boolean discardLowQualitySpectra
String fragmentationModel
Boolean generateQuery
Map<K,V> pepNovoPtmMap
int numberOfPeptides
int lowerPrecursorMass
int upperPrecursorMass
String acticationType
HashMap<K,V> pNovoPtmMap
HashMap<K,V> pNovoResidueMap
String fastIndexFolderName
Integer maxVariableModificationsPerPeptide
Integer maxVariableModificationsPerTypePerPeptide
Integer minPeptideLength
Integer maxPeptideLength
Double minPrecursorMass
Double maxPrecursorMass
String decoyFormat
String keepTerminalAminoAcids
Integer decoySeed
String outputFolderName
Boolean printPeptides
Integer verbosity
Boolean monoisotopicPrecursor
Boolean clipNtermMethionine
String digestionType
Boolean computeSpScore
Integer numberOfSpectrumMatches
Boolean computeExactPValues
Double minSpectrumMz
Double maxSpectrumMz
Integer minSpectrumPeaks
String spectrumCharges
Boolean removePrecursor
Double removePrecursorTolerance
Integer printProgressIndicatorSize
Boolean useFlankingPeaks
Boolean useNeutralLossPeaks
Double mzBinWidth
Double mzBinOffset
Boolean concatenateTargetDecoy
String storeSpectraFileName
Boolean textOutput
Boolean sqtOutput
Boolean pepXmlOutput
Boolean mzidOutput
Boolean pinOutput
Boolean removeTempFolders
double maxEValue
String outputResults
double dynamicRange
int nPeaks
double minPrecursorMass
double minFragmentMz
int minPeaksPerSpectrum
boolean proteinQuickAcetyl
boolean quickPyrolidone
boolean refine
boolean refineSemi
boolean refinePointMutations
boolean refineSpectrumSynthesis
boolean refineUnanticipatedCleavages
boolean refineSnaps
double maximumExpectationValueRefinement
boolean potentialModificationsForFullRefinment
String skylinePath
boolean outputProteins
boolean outputSequences
boolean outputSpectra
boolean outputHistograms
boolean stpBias
boolean useNoiseSuppression
double proteinPtmComplexity
boolean parentMonoisotopicMassIsotopeError
Double referenceMass
UnitOfMeasurement unit
Boolean normalize
SpectrumCountingMethod selectedMethod
Integer matchValidationLevel
org.apache.logging.log4j.Logger logger
TableModel model
org.apache.logging.log4j.Logger logger
int[] indexes
Vector<E> sortingColumns
boolean ascending
int compares
MouseAdapter listMouseListener
Copyright © 2021. All rights reserved.