JavaMemoryDialogParent javaMemoryDialogParent
JDialog welcomeDialog
String toolName
JPanel backgroundPanel
JButton cancelButton
JSeparator jSeparator1
JButton javaOptionsHelpJButton
JLabel mbLabel
JLabel memoryLimitLabel
JTextField memoryTxt
JButton okButton
JavaMemoryDialogParent javaMemoryDialogParent
JFrame frameParent
String toolName
JDialog welcomeDialog
JPanel backgroundsPanel
JLabel bitLabel
JPanel bitPanel
JLabel bitRecommendationLabel
JLabel editMemoryJLabel
JLabel javaHelpJLabel
JLabel javaHomeLabel
JPanel javaHomePanel
JLabel memoryLabel
JPanel memoryPanel
JLabel memoryRecommendationLabel
JButton okButton
JLabel versionLabel
JPanel versionPanel
JLabel versionRecommendationLabel
UtilitiesUserPreferences utilitiesUserPreferences
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
UtilitiesUserPreferences utilitiesUserPreferences
String lastSelectedFolder
JPanel backgroundPanel
JButton browseButton
JButton cancelButton
JLabel jLabel2
JButton okButton
JButton relimsButton
JLabel relimsDownloadLinkLabel
JPanel relimsDownloadPanel
JLabel relimsInfoLabel
JTextField relimsInstallationJTextField
JPanel relimsInstallationPanel
JLabel relimsJarFileHelpLabel
UtilitiesUserPreferences utilitiesUserPreferences
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
UtilitiesUserPreferences utilitiesUserPreferences
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
org.apache.log4j.Logger logger
Color iEvenRowColor
Color iUnevenRowColor
org.apache.log4j.Logger logger
Exception iNested
String dbName
String path
Connection dbConnection
ArrayList<E> longKeys
ArrayList<E> longTableNames
HashMap<K,V> longKeysMap
ObjectsCache objectsCache
BufferedWriter debugSpeedWriter
BufferedWriter debugContentWriter
File debugFolder
boolean busy
String tableQueueUpdating
ArrayList<E> tableQueue
HashMap<K,V> contentQueue
ArrayList<E> contentTableQueue
boolean debugSpeed
boolean debugContent
boolean debugInteractions
boolean useSQLite
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
double averageMass
double monoisotopicMass
ArrayList<E> indistinguishableAACache
Double indistinguishableAACacheMass
Integer target
int length
HashMap<K,V> aaTargeted
HashMap<K,V> aaExcluded
HashMap<K,V> targetModifications
String sequence
StringBuilder sequenceStringBuilder
AminoAcidPattern aminoAcidPattern
HashMap<K,V> modifications
HashMap<K,V> isotopeMap
HashMap<K,V> representativeComposition
String name
String letter
int id
String name
ArrayList<E> aminoAcidBefore
ArrayList<E> aminoAcidAfter
ArrayList<E> restrictionBefore
ArrayList<E> restrictionAfter
Boolean isSemiSpecific
Ion.IonType type
double theoreticMass
String name
String description
HashMap<K,V> mutations
HashMap<K,V> mutationsReverse
MutationMatrix singleBaseSubstitution
MutationMatrix transitionsSingleBaseSubstitution
MutationMatrix transversalSingleBaseSubstitution
MutationMatrix synonymousMutation
MutationMatrix[] defaultMutationMatrices
String accession
boolean decoy
String sequence
Header.DatabaseType databaseType
int type
ArrayList<E> residuesArray
String name
String shortName
double mass
ArrayList<E> neutralLosses
ArrayList<E> reporterIons
AminoAcidPattern pattern
HashMap<K,V> ptmMap
ArrayList<E> defaultMods
ArrayList<E> userMods
HashMap<K,V> userColors
HashMap<K,V> shortNames
HashMap<K,V> defaultOmssaIndexes
boolean defaultModsSorted
boolean usersModsSorted
String reference
String name
int subType
String name
ArrayList<E> neutralLosses
int number
int subNumber
int subType
double massGap
HashMap<K,V> indexes
HashSet<E> decoyAccessions
String fileName
String name
Long lastModified
boolean isDefaultReversed
int nTarget
Header.DatabaseType databaseType
String version
boolean concatenatedTargetDecoy
String decoyTag
ArrayList<E> species
ArrayList<E> proteinIdentification
ArrayList<E> peptideIdentification
HashMap<K,V> spectrumIdentificationMap
ArrayList<E> spectrumIdentification
HashMap<K,V> proteinMap
int methodUsed
String serializationDirectory
HashMap<K,V> urParameters
ArrayList<E> longKeys
Boolean isDB
IdentificationDB identificationDB
String reference
ArrayList<E> orderedSpectrumFileNames
String dbName
String proteinTableName
String proteinParametersTableSuffix
String peptideTableName
String peptideParametersTableSuffix
String psmTableSuffix
String psmParametersTableSuffix
String parametersSuffix
ArrayList<E> psmTables
ArrayList<E> psmParametersTables
ArrayList<E> peptideParametersTables
ArrayList<E> proteinParametersTables
ArrayList<E> matchParametersTables
ObjectsDB objectsDB
HashMap<K,V> bBoundaries
HashMap<K,V> yBoundaries
Peptide peptide
int advocate
Charge identificationCharge
int rank
double eValue
String file
SearchParameters.MassAccuracyType precursorAccuracyType
SearchParameters.MassAccuracyType fragmentAccuracyType
Double precursorTolerance
Double precursorToleranceDalton
Double fragmentIonMZTolerance
ModificationProfile utilitiesModificationProfile
Enzyme enzyme
Integer nMissedCleavages
File fastaFile
File parametersFile
HashMap<K,V> fractionMolecularWeights
HashMap<K,V> fractionMolecularWeightRanges
Integer forwardIon
Integer rewindIon
Charge minChargeSearched
Charge maxChargeSearched
HashMap<K,V> algorithmParameters
SearchParameters.PrecursorAccuracyType currentPrecursorAccuracyType
Double maxEValue
Integer hitListLength
Integer hitListLengthDeNovo
Charge minimalChargeForMultipleChargedFragments
Integer minPeptideLength
Integer maxPeptideLength
Boolean removePrecursor
Boolean scalePrecursor
Boolean estimateCharge
Boolean correctPrecursorMass
Boolean discardLowQualitySpectra
String fragmentationModel
Boolean generateQuery
Map<K,V> pepNovoPtmMap
int rank
int advocate
Charge identificationCharge
double score
String identificationFile
Tag tag
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> variablePtms
boolean generateDecoy
String instrumentID
Integer maxRank
boolean monoisotopic
boolean searchDecoyDatabase
int instrumentID
int fragmentationType
int protocol
Integer minPeptideLength
Integer maxPeptideLength
Integer numberOfSpectrumMarches
boolean additionalOutput
Integer lowerIsotopeErrorRange
Integer upperIsotopeErrorRange
Integer numberTolerableTermini
Integer numberOfPtmsPerPeptide
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
Double maxEValue
Integer hitListLength
Charge minimalChargeForMultipleChargedFragments
Integer minPeptideLength
Integer maxPeptideLength
Boolean removePrecursor
Boolean scalePrecursor
Boolean estimateCharge
String selectedOutput
Boolean memoryMappedSequenceLibraries
Integer numberOfItotopicPeaks
Double neutronThreshold
Double lowIntensityCutOff
Double highIntensityCutOff
Double intensityCutOffIncrement
Integer singleChargeWindow
Integer doubleChargeWindow
Integer nPeaksInSingleChargeWindow
Integer nPeaksInDoubleChargeWindow
Integer maxHitsPerSpectrumPerCharge
Integer nAnnotatedMostIntensePeaks
Integer minAnnotatedPeaks
Integer minPeaks
Boolean cleaveNtermMethionine
Integer maxMzLadders
Integer maxFragmentCharge
Double fractionOfPeaksForChargeEstimation
Boolean determineChargePlusOneAlgorithmically
Boolean searchPositiveIons
Integer minPrecPerSpectrum
Boolean searchForwardFragmentFirst
Boolean searchRewindFragments
Integer maxFragmentPerSeries
Boolean useCorrelationCorrectionScore
Double consecutiveIonProbability
Double iterativeSequenceEvalue
Double iterativeReplaceEvalue
Double iterativeSpectrumEvalue
ArrayList<E> noProlineRuleSeries
Integer hitListLength
Boolean estimateCharge
Boolean correctPrecursorMass
Boolean discardLowQualitySpectra
String fragmentationModel
Boolean generateQuery
Map<K,V> pepNovoPtmMap
Double maxEValue
Double dynamicRange
Integer nPeaks
Double minPrecursorMass
Double minFragmentMz
Integer 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
String theoreticPtm
boolean variable
int modifiedSite
boolean confident
boolean inferred
Peptide theoreticPeptide
String matchKey
String mainMatchKey
ArrayList<E> spectrumMatches
Boolean isDecoy
String spectrumKey
HashMap<K,V> assumptions
HashMap<K,V> assumptionsMap
HashMap<K,V> firstHits
HashMap<K,V> firstHitsMap
PeptideAssumption bestAssumption
TagAssumption bestTagAsssumption
ArrayList<E> advocates
Integer spectrumNumber
int depth
HashMap<K,V> accessions
HashMap<K,V> termini
HashMap<K,V> subtree
boolean listening
HashMap<K,V> index
uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile bufferedRandomAccessFile
String fileName
String tagsGenerator
String tagsGeneratorVersion
String copyRight
String license
String timeStart
String timeEnd
Double taggingTimeSeconds
Integer nProcessingNode
String inputFile
HashMap<K,V> tagsParameters
HashMap<K,V> spectrumLineContent
HashMap<K,V> tagLineContent
HashMap<K,V> spectrumIndexes
HashMap<K,V> tagIndexes
uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile bufferedRandomAccessFile
File tagFile
SpectrumFactory spectrumFactory
double cTermCorrection
double nTermCorrection
HashMap<K,V> tempSoftwareVersions
HashMap<K,V> softwareVersions
File mzIdentMLFile
String mzIdentMLFileName
uk.ac.ebi.jmzidml.xml.io.MzIdentMLUnmarshaller unmarshaller
ArrayList<E> fixedModifications
HashMap<K,V> index
uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile bufferedRandomAccessFile
String fileName
double cTermCorrection
double nTermCorrection
HashMap<K,V> indexMap
HashMap<K,V> spectrumNumberIndexMap
ArrayList<E> spectrumTitles
HashMap<K,V> duplicatedSpectrumTitles
String fileName
Long lastModified
Double maxRT
Double minRT
Double maxMz
Double maxIntensity
Integer maxCharge
Integer maxPeakCount
Boolean peakPicked
Integer spectrumCount
Precursor precursor
double rt
Double rtMin
Double rtMax
double mz
double intensity
ArrayList<E> possibleCharges
String spectrumTitle
String fileName
int level
HashMap<K,V> peakList
HashMap<K,V> intensityPeakMap
String scanNumber
double scanStartTime
double[][] jFreePeakList
double[] mzValuesAsArray
Boolean mzOrdered
double[] intensityValuesAsArray
double[][] mzAndIntensityAsArray
Double totalIntensity
Double maxIntensity
Double maxMz
Double minMz
Quantification.QuantificationMethod methodUsed
HashMap<K,V> sampleAssignement
ArrayList<E> controlSamples
HashMap<K,V> normalisationFactors
ReporterMethod reporterMethod
org.apache.log4j.Logger logger
String element
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
GOFactory goFactory
GeneFactory geneFactory
ArrayList<E> proteinAccessions
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
Image normalIcon
UtilitiesUserPreferences utilitiesUserPreferences
JPanel backgroundPanel
JButton cancelButton
JLabel confidentialLabel
JButton okButton
JButton openDialogHelpJButton
JPanel settingsPanel
JCheckBox toolStartCheck
JCheckBox updatesCheck
Frame dialogParent
String 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
String 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
String selectionFolder
String toolName
String googleCodeToolName
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
ExportGraphicsDialogParent exportGraphicsDialogParent
JFrame frame
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
GOFactory goFactory
GeneFactory geneFactory
ProgressDialogX progressDialog
JFrame frameParent
JDialog dialogParent
Image waitingImage
Image normalImage
GenePreferences genePreferences
JPanel backgroundPanel
JButton cancelButton
JComboBox<E> ensemblCategoryJComboBox
JLabel ensemblVersionLabel
JPanel jPanel1
JButton okButton
JComboBox<E> speciesJComboBox
JLabel unknownSpeciesLabel
JButton updateMappingsButton
org.apache.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
File dbFolder
JPanel backgroundPanel
JButton browseDatabaseFolderButton
JButton cancelButton
JButton clearDatabaseFolderButton
JTextField databasesFolderTxt
JPanel folderPanel
JButton okButton
SequenceFactory sequenceFactory
String lastSelectedFolder
boolean dbEditable
Image waitingImage
Image normalImange
Frame parentFrame
UtilitiesUserPreferences utilitiesUserPreferences
JSpinner accessionsSpinner
JButton advancedButton
JPanel backgroundPanel
JButton browseButton
JButton cancelButton
JLabel databaseHelpSettingsJLabel
JPanel databaseInformationPanel
JTextField dbNameTxt
JButton decoyButton
JTextField decoyFlagTxt
JLabel decoyTagLabel
JLabel fileLabel
JTextField fileTxt
JLabel lastModifiedLabel
JTextField lastModifiedTxt
JLabel nameLabel
JButton okButton
JPanel previewPanel
JLabel proteinLabel
JTextArea proteinTxt
JScrollPane proteinYxtScrollPane
JLabel sizeLabel
JTextField sizeTxt
JLabel targetDecoyTxt
JComboBox<E> typeCmb
JLabel typeLabel
JLabel versionLabel
JTextField versionTxt
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
PTMFactory ptmFactory
PtmDialogParent ptmDialogParent
PtmToPrideMap ptmToPrideMap
Color sparklineColor
String selectedRowHtmlTagFontColor
String notSelectedRowHtmlTagFontColor
ArrayList<E> defaultModsTableToolTips
ArrayList<E> userModsTableToolTips
ArrayList<E> searchPossibilities
int searchCurrentSelection
String searchWelcomeText
JButton addUserPTM
JTable defaultModificationsTable
JPanel defaultModsPanel
JScrollPane defaultModsScrollPane
JPopupMenu defaultPtmPopupMenu
JButton deleteUserPTM
JMenuItem editDefaultPtmJMenuItem
JButton editUserPTM
JMenuItem editUserPtmJMenuItem
JLabel findJLabel
JPanel modificationsEditorPanel
JButton modificationsHelpJButton
JSplitPane modificationsSplitPane
JButton okButton
JLabel searchIndexLabel
JTextField searchInputTxt
JButton searchNextButton
JButton searchPreviousButton
JTable userModificationsTable
JPanel userModsPanel
JScrollPane userModsScrollPane
JPopupMenu userPtmPopupMenu
boolean canceled
PTMFactory ptmFactory
ArrayList<E> ptmList
ArrayList<E> modificationTableToolTips
JPanel backgroundPanel
JButton cancelButton
JButton okButton
JPanel ptmSelectionPanel
JTable ptmTable
JScrollPane ptmTableScrollPane
PtmDialogParent ptmDialogParent
PTMFactory ptmFactory
PTM currentPtm
ArrayList<E> neutralLosses
ArrayList<E> reporterIons
PtmToPrideMap ptmToPrideMap
boolean editable
AminoAcidPattern pattern
ArrayList<E> reporterIonTableToolTips
ArrayList<E> neutralLossesTableToolTips
JButton addNeutralLoss
JButton addReporterIon
JPanel backgroundPanel
JButton cancelButton
JLabel cvExampleLabel
JPanel detailsPanel
JButton helpJButton
JLabel jLabel1
JPanel jPanel1
JLabel massLabel
JTextField massTxt
JLabel nameLabel
JLabel nameShortLabel
JTextField nameShortTxt
JTextField nameTxt
JPanel neutralLossesAndReporterIonsPanel
JScrollPane neutralLossesJScrollPane
JTable neutralLossesTable
JButton okButton
JLabel patternLabel
JTextField patternTxt
JButton removeNeutralLoss
JButton removerReporterIon
JScrollPane reporterIonsJScrollPane
JTable reporterIonsTable
JComboBox<E> typeCmb
JTextField unimodAccessionJTextField
JLabel unimodAccessionLabel
JLabel unimodLinkLabel
JPanel unimodMappingPanel
JTextField unimodNameJTextField
JLabel unimodNameLabel
double minXAxisValue
double maxXAxisValue
TableCellRenderer delegate
EnzymeFactory enzymeFactory
boolean selectionCanceled
JPanel backgroundPanel
JButton cancelButton
JLabel enzymeLabel
JComboBox<E> enzymesCmb
JPanel mappingPanel
JButton okButton
JLabel prideEnzymeNameLabel
JTextField prideEnzymeNameTextField
SequenceFactory sequenceFactory
EnzymeFactory enzymeFactory
String[] forwardIons
String[] rewindIons
PTMFactory ptmFactory
File parametersFile
SearchSettingsDialogParent searchSettingsDialogParent
SearchParameters searchParameters
ArrayList<E> modificationTableToolTips
JFrame parentFrame
Image normalIcon
Image waitingIcon
int keyPressedCounter
String currentPtmSearchString
int waitingTime
JButton addFixedModification
JButton addVariableModification
JPanel availableModsPanel
JPanel backgroundPanel
JButton cancelButton
JPanel dataBasePanelSettings
JLabel databaseSettingsLbl
JTextField databaseSettingsTxt
JButton editDatabaseSettings
JLabel enzymeLabel
JComboBox<E> enzymesCmb
JLabel fixedModificationsLabel
JScrollPane fixedModsJScrollPane
JTable fixedModsTable
JComboBox<E> fragmentIon1Cmb
JComboBox<E> fragmentIon2Cmb
JTextField fragmentIonAccuracyTxt
JLabel fragmentIonLbl
JLabel fragmentIonType1Lbl
JPanel jPanel8
JPanel jPanel9
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
JLabel variableModificationsLabel
JScrollPane variableModsJScrollPane
JTable variableModsTable
MsAmandaParameters msAmandaParameters
boolean cancelled
JPanel advancedSearchSettingsPanel
JLabel advancedSettingsWarningLabel
JPanel backgroundPanel
JButton closeButton
JComboBox<E> decoyDatabaseCmb
JLabel decoyDatabaseLabel
JComboBox<E> instrumentCmb
JLabel instrumentLabel
JLabel maxRankLabel
JTextField maxRankTxt
JComboBox<E> monoIsotopicCmb
JLabel monoIsotopicLabel
JButton okButton
JButton openDialogHelpJButton
MsgfParameters msgfParameters
boolean cancelled
JComboBox<E> additionalOutputCmb
JLabel additionalOutputLabel
JPanel advancedSearchSettingsPanel
JLabel advancedSettingsWarningLabel
JPanel backgroundPanel
JButton closeButton
JComboBox<E> decoyDatabaseCmb
JLabel decoyDatabaseLabel
JComboBox<E> fragmentationMethodCmb
JLabel fragmentationMethodLabel
JTextField highIsotopeErrorRangeTxt
JComboBox<E> instrumentCmb
JLabel instrumentLabel
JLabel isotopeErrorRangeDividerLabel
JLabel isotopeErrorRangeLabel
JTextField lowIsotopeErrorRangeTxt
JTextField maxPepLengthTxt
JLabel maxPtmsLabel
JTextField maxPtmsTxt
JTextField minPepLengthTxt
JLabel numberMatchesLabel
JTextField numberMatchesTxt
JLabel numberTerminiLabel
JButton okButton
JButton openDialogHelpJButton
JLabel peptideLengthDividerLabel
JLabel peptideLengthLabel
JComboBox<E> protocolCmb
JLabel protocolLabel
JComboBox<E> terminiCmb
MyriMatchParameters myriMatchParameters
boolean cancelled
JPanel advancedSearchSettingsPanel
JLabel advancedSettingsWarningLabel
JPanel backgroundPanel
JLabel classSizeMultiplierLabel
JTextField classSizeMultiplierTxt
JButton closeButton
JComboBox<E> computeXCorrCmb
JLabel computeXCorrlLabel
JComboBox<E> fragmentationMethodCmb
JLabel fragmentationMethodLabel
JTextField highIsotopeErrorRangeTxt
JLabel isotopeErrorRangeDividerLabel
JLabel isotopeErrorRangeLabel
JTextField lowIsotopeErrorRangeTxt
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
JLabel peptideLengthDividerLabel
JLabel peptideLengthLabel
JLabel precursorMassDividerLabel
JLabel precursorMassLabel
JComboBox<E> terminiCmb
JLabel ticCutoffPercentageLabel
JTextField ticCutoffPercentageTxt
JComboBox<E> useSmartPlusThreeModelCmb
JLabel useSmartPlusThreeModelLabel
OmssaParameters omssaParameters
boolean cancelled
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 nIsotopesLbl
JTextField nIsotopesTxt
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 semiEnzymaticParametersPanel
JComboBox<E> sequenceMappingCmb
JLabel sequenceMappingLbl
JLabel singlyChargedNPeaksLbl
JTextField singlyChargedNpeaksTxt
JLabel singlyChargedWindowWidthLbl
JTextField singlyChargedWindowWidthTxt
JPanel spectrumProcessingPanel
JTabbedPane tabbedPane
XtandemParameters xtandemParameters
ModificationProfile modificationProfile
double fragmentIonMassAccuracy
boolean cancelled
ArrayList<E> modificationTableToolTips
PTMFactory ptmFactory
JPanel advancedSearchSettingsPanel
JLabel advancedSettingsWarningLabel
JPanel backgroundPanel
JButton closeButton
JLabel dynamicRangeLbl
JTextField dynamicRangeTxt
JLabel eValueLbl
JTextField eValueTxt
JTextField maxEValueRefineTxt
JLabel maxEValueRefinmentLbl
JLabel minFragMzLbl
JTextField minFragmentMzTxt
JLabel minPeaksLbl
JTextField minPeaksTxt
JLabel minPrecMassLbl
JTextField minPrecMassTxt
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> outputSequencesCmb
JLabel outputSequencesLabel
JPanel outputSettingsPanel
JComboBox<E> outputSpectraCmb
JLabel outputSpectraLabel
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
JComboBox<E> unanticipatedCleavageCmb
JLabel unanticipatedCleavageLabel
JLabel usePotentialModsLabel
ArrayList<E> currentFragmentIonTypes
NeutralLossesMap neutralLosses
boolean singleCharge
boolean twoCharges
ArrayList<E> tooltips
Peptide currentPeptide
String peptideSequence
ArrayList<E> allAnnotations
ArrayList<E> allSpectra
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
int iHighLightIndex
int iHighLightDatasetIndex
boolean iClicked
int iClickedIndex
int iClickedDataSetIndex
Vector<E> iClickedList
Vector<E> iClickedListDatasetIndices
Vector<E> iStoredSequence
Vector<E> iStoredSequenceDatasetIndices
Vector<E> iAnnotations
int iMinDrag
GraphicsPanel.DrawingStyle iCurrentDrawStyle
int iDotRadius
int iMSLevel
boolean showAllPeaks
boolean yAxisZoomExcludesBackgroundPeaks
GraphicsPanel.GraphicsPanelType currentGraphicsPanelType
org.apache.log4j.Logger logger
Color aSpectrumPeakColor
Color aSpectrumProfileModeLineColor
ArrayList<E> peptideSequences
ArrayList<E> peptideCharges
HashMap<K,V> iElements
boolean useRelativeError
ArrayList<E> currentlyUsedIonMatches
org.jfree.chart.ChartPanel chartPanel
ArrayList<E> dataSeriesfragmentIonColors
HashMap<K,V> tooltipRectangles
String[] iSequenceComponents
ArrayList<E> iIonMatches
double[] bIons
double[] yIons
Font iBaseFont
double iMaxBarHeight
int iBarWidth
int iHorizontalSpace
int iXStart
boolean isModifiedSequence
boolean iHighlightModifications
ModificationProfile modificationProfile
int forwardIon
int rewindIon
Color forwardColor
Color rewindColor
int rowStartLoading
int rowEndLoading
boolean selfUpdating
boolean updateScheduled
com.compomics.util.gui.tablemodels.SelfUpdatingTableModel.LoadingRunnable lastLoadingRunnable
ArrayList<E> viewIndexes
int lastColumnSorted
boolean sortAscending
boolean unsorted
ProgressDialogX progressDialog
boolean isScrolling
org.apache.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
org.apache.log4j.Logger logger
JProgressBar iProgress
boolean doNothingOnClose
boolean unstoppable
boolean canceled
boolean finished
Image waitingIcon
Image normalIcon
Frame waitingHandlerParentFrame
JDialog waitingHandlerParentDialog
WaitingActionListener waitingActionListener
JProgressBar progressBar
JDialog dialog
Point naturalLocation
Timer shakeTimer
boolean runFinished
boolean runCanceled
ArrayList<E> tips
int currentTipIndex
String lastSelectedFolder
Image waitingIcon
Image normalIcon
Frame waitingHandlerParent
boolean shakeWhenFinished
String processName
String toolName
String toolVersion
WaitingActionListener waitingActionListener
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
double stdUp
double stdDown
double mean
NormalDistribution distributionUp
NormalDistribution distributionDown
boolean yAxisZoomExcludesBackgroundPeaks
boolean intensityIonTable
boolean showBars
boolean showAllPeaks
double intensityLimit
boolean automaticAnnotation
HashMap<K,V> selectedIons
NeutralLossesMap neutralLossesMap
boolean neutralLossesSequenceDependant
ArrayList<E> selectedCharges
double fragmentIonAccuracy
Peptide currentPeptide
SpectrumIdentificationAssumption spectrumIdentificationAssumption
int currentPrecursorCharge
boolean showForwardIonDeNovoTags
boolean showRewindIonDeNovoTags
int deNovoCharge
Boolean highResolutionAnnotation
String currentSpecies
String currentSpeciesType
HashMap<K,V> goDomainMap
HashMap<K,V> speciesMap
HashMap<K,V> allSpeciesMap
HashMap<K,V> ensemblVersionsMap
ArrayList<E> availableSpecies
HashMap<K,V> allSpecies
Vector<E> species
int minPepLength
int maxPepLength
double mascotMaxEvalue
double omssaMaxEvalue
double xtandemMaxEvalue
double msgfMaxEvalue
double msAmandaMaxEvalue
double maxMassDeviation
boolean isPpm
boolean unknownPtm
HashMap<K,V> modificationNames
ArrayList<E> fixedModifications
ArrayList<E> variableModifications
ArrayList<E> refinementVariableModifications
ArrayList<E> refinementFixedModifications
ArrayList<E> refinementModifications
HashMap<K,V> omssaIndexes
HashMap<K,V> colors
HashMap<K,V> backUp
boolean aScore
double proteinFDR
double peptideFDR
double psmFDR
Double proteinConfidenceMwPlots
HashMap<K,V> spectrumMatchingScores
boolean aScoreCalculation
boolean aScoreNeutralLosses
double flr
Boolean probabilitsticScoreCalculation
PtmScore selectedProbabilisticScore
boolean estimateFlr
double probabilisticScoreThreshold
Boolean probabilisticScoreNeutralLosses
Float spectrumAnnotatedPeakWidth
Float spectrumBackgroundPeakWidth
Color spectrumAnnotatedPeakColor
Color spectrumBackgroundPeakColor
Color sparklineColorValidated
Color sparklineColorNonValidated
Color sparklineColorNotFound
Color sparklineColorPossible
Color sparklineColorDoubtful
Color sparklineColorFalsePositive
Color peptideSelected
int memoryPreference
File proteinTreeFolder
HashMap<K,V> proteinTreeImportTime
String searchGuiPath
String peptideShakerPath
String reporterPath
String relimsPath
String localPrideFolder
File dbFolder
ArrayList<E> favoriteDBs
ArrayList<E> readTweets
ArrayList<E> displayedTips
Boolean autoUpdate
Boolean notifyStart
boolean editable
IdFilter userFilter
IdFilter originalFilter
JPanel backgroundPanel
JButton cancelButton
JPanel filterPanel
JButton helpJButton
JTextField nAAmaxTxt
JTextField nAAminTxt
JButton okButton
JLabel peptideLengthLabel
JLabel peptideLengthRangeLabel
JTextField precDevTxt
JLabel precursorAccuracyLabel
JCheckBox ptmsCheck
JComboBox<E> unitCmb
ProcessingPreferences processingPreferences
PTMScoringPreferences ptmScoringPreferences
JLabel aScoreLabel
JPanel backgroundPanel
JLabel estimateAScoreLabel
JPanel fractionsPanel
JButton helpJButton
JComboBox<E> neutralLossesCmb
JComboBox<E> neutralLossesCmb2
JLabel neutralLossesLabel
JLabel neutralLossesLabel1
JLabel neutralLossesLabel2
JLabel neutralLossesLabel3
JButton okButton
JLabel peptideFdrLabel
JTextField peptideFdrTxt
JLabel percentLabel
JLabel percentLabel2
JLabel percentLabel3
JLabel percentLabel4
JComboBox<E> probabilisticScoreCmb
JPanel processingParamsPanel
JTextField proteinConfidenceMwTxt
JLabel proteinFdrLabel
JTextField proteinFdrTxt
JLabel proteinMwLabel
JLabel psmFdrLabel
JTextField psmFdrTxt
JPanel ptmScoringPanel
JComboBox<E> scoreCmb
JComboBox<E> thresholdCmb
JTextField thresholdTxt
String iID
String iForeignID
String iAccession
Header.DatabaseType databaseType
String iForeignAccession
String iDescription
String iDescriptionShort
String iDescriptionProteinName
String iGeneName
String iProteinEvidence
String iTaxonomy
String iForeignDescription
String iRest
StringBuffer iAddenda
int iStart
int iEnd
org.apache.log4j.Logger logger
ModificationTemplate iTemplate
int iLocation
org.apache.log4j.Logger logger
TableModel model
org.apache.log4j.Logger logger
int[] indexes
Vector<E> sortingColumns
boolean ascending
int compares
MouseAdapter listMouseListener
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