JavaOptionsDialogParent javaOptionsDialogParent
JDialog welcomeDialog
String toolName
JPanel backgroundPanel
JButton cancelButton
JButton javaOptionsHelpJButton
JLabel mbLabel
JLabel memoryLimitLabel
JTextField memoryTxt
JButton okButton
JPanel settingsPanel
UtilitiesUserPreferences utilitiesUserPreferences
String lastSelectedFolder
boolean dialogCanceled
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
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
Connection dbConnection
ArrayList<E> longKeys
ObjectsCache objectsCache
BufferedWriter debugSpeedWriter
BufferedWriter debugContentWriter
File debugFolder
boolean debugSpeed
boolean debugContent
boolean debugInteractions
JButton closeJButton
JScrollPane jScrollPane1
JEditorPane textJEditorPane
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
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
JPanel jPanel9
JRadioButton jRadioButton1
JScrollPane jScrollPane1
JScrollPane jScrollPane2
JScrollPane jScrollPane3
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
JTable peffAnnotationsJTable
JTable peffHeaderJTable
JPanel peptideAColorJPanel
JTextField peptideACompositionJTextField
JScrollPane peptideAJScrollPane
org.jdesktop.swingx.JXTable peptideAJXTable
JTextField peptideAMzJTextField
JPanel peptideBColorJPanel
JTextField peptideBCompositionJTextField
JScrollPane peptideBJScrollPane
org.jdesktop.swingx.JXTable peptideBJXTable
JTextField peptideBMzJTextField
JTextField peptideSequenceAJTextField
JTextField peptideSequenceBJTextField
JPanel peptidesJPanel
JTable peptidesJTable
JScrollPane peptidesScrollPane
JTextField positionJTextField
JCheckBox profileSpectrumJCheckBox
JScrollPane proteinCoverageJScrollPane
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
Integer target
HashMap<K,V> aaTargeted
HashMap<K,V> aaExcluded
Ion.IonType type
double theoreticMass
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
String reference
String name
int subType
String name
int subtype
String name
And filter
And filter
double mz
double mzTolerance
boolean isPpm
double intensityQuantile
MzFilter brotherFilter
ArrayList<E> mzArray
String spectrumKey
double mz
double mzTolerance
boolean isPpm
double intensity
double intensityTolerance
SpectrumFilter spectrumFilter
ArrayList<E> mzArray
JButton addButton
JButton cancelButton
JTextField intTxt
JLabel jLabel1
JLabel jLabel2
JLabel jLabel3
JLabel jLabel4
JScrollPane jScrollPane1
JSeparator jSeparator1
JTable mzTable
JTextField mzTolTxt
JButton okButtonButton
JComboBox<E> ppmCmb
JButton removeButton
SpectrumFilter spectrumFilter
ArrayList<E> mzArray
ArrayList<E> intArray
JButton addButton
JButton cancelButton
JTextField intTxt
JLabel jLabel1
JLabel jLabel2
JLabel jLabel3
JLabel jLabel4
JScrollPane jScrollPane1
JSeparator jSeparator1
JTable mzTable
JTextField mzTolTxt
JButton okButton
JComboBox<E> ppmCmb
JButton removeButton
SpectrumFilter spectrumFilter
JButton cancelButton
JTextField intTxt
JLabel jLabel1
JLabel jLabel2
JLabel jLabel3
JLabel jLabel4
JSeparator jSeparator1
JTextField mzTolTxt
JTextField mzTxt
JButton okButton
JComboBox<E> ppmCmb
SpectrumFilter spectrumFilter
JButton cancelButton
JTextField intTolTxt
JTextField intTxt
JLabel jLabel1
JLabel jLabel2
JLabel jLabel3
JLabel jLabel4
JLabel jLabel5
JSeparator jSeparator1
JTextField mzTolTxt
JTextField mzTxt
JButton okButton
JComboBox<E> ppmCmb
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
int rank
Peptide peptide
int advocate
Charge identificationCharge
double eValue
String file
Boolean isDecoy
SearchParameters.PrecursorAccuracyType currentPrecursorAccuracyType
Double precursorTolerance
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
Double maxEValue
Integer hitListLength
Charge minimalChargeForMultipleChargedFragments
Integer minPeptideLength
Integer maxPeptideLength
Boolean removePrecursor
Boolean scalePrecursor
Boolean estimateCharge
Boolean correctPrecursorMass
Boolean discardLowQualitySpectra
String fragmentationModel
Boolean generateQuery
String theoreticPtm
boolean variable
int modifiedSite
boolean confident
boolean inferred
Peptide theoreticPeptide
String mainMatchKey
ArrayList<E> spectrumMatches
Boolean isDecoy
String spectrumKey
HashMap<K,V> assumptions
PeptideAssumption bestAssumption
HashMap<K,V> firstHits
ArrayList<E> advocates
Integer spectrumNumber
HashMap<K,V> index
uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile bufferedRandomAccessFile
String fileName
HashMap<K,V> indexMap
ArrayList<E> spectrumTitles
String fileName
Double maxRT
Double minRT
Double maxMz
Double maxIntensity
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
String scanNumber
double scanStartTime
Quantification.QuantificationMethod methodUsed
ArrayList<E> proteinQuantification
ArrayList<E> peptideQuantification
HashMap<K,V> modifiedPeptidesQuantification
HashMap<K,V> psmIDentificationToQuantification
QuantificationDB quantificationDB
String dbName
String proteinTableName
String proteinParametersTableSuffix
String peptideTableName
String peptideParametersTableSuffix
String psmTableSuffix
String psmParametersTableSuffix
ArrayList<E> psmTables
ArrayList<E> psmParametersTables
ArrayList<E> peptideParametersTables
ArrayList<E> proteinParametersTables
ObjectsDB objectsDB
String spectrumKey
String spectrumMatchKey
HashMap<K,V> reporterMatches
HashMap<K,V> deisotopedIntensities
double referenceIntensity
HashMap<K,V> sampleAssignement
ReporterMethod reporterMethod
org.apache.log4j.Logger logger
String element
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
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 tabelModel
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
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
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
HashMap<K,V> fileMap
boolean canceled
JButton cancelButton
JList<E> fileList
JScrollPane jScrollPane1
JButton okButton
JLabel txtLabel
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
HashMap<K,V> fragmentIonRectangles
String[] iSequenceComponents
ArrayList<E> profiles
Font iBaseFont
double iMaxBarHeight
int iBarWidth
int iHorizontalSpace
int iXStart
int iYStart
boolean isModifiedSequence
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
PtmDialogParent ptmDialogParent
PTMFactory ptmFactory
PTM currentPtm
ArrayList<E> neutralLosses
ArrayList<E> reporterIons
PtmToPrideMap ptmToPrideMap
CvTerm cvTerm
boolean editable
AminoAcidPattern pattern
JButton addNeutralLoss
JButton addReporterIon
JPanel backgroundPanel
JButton cancelButton
JPanel detailsPanel
JButton helpJButton
JLabel jLabel1
JPanel jPanel1
JLabel massLabel
JTextField massTxt
JLabel nameLabel
JTextField nameTxt
JPanel neutralLossesAndReporterIonsPanel
JScrollPane neutralLossesJScrollPane
JTable neutralLossesTable
JButton okButton
JButton olsJButton
JLabel patternLabel
JTextField psiModMappingJTextField
JPanel psiModMappingPanel
JButton removeNeutralLoss
JButton removerReporterIon
JScrollPane reporterIonsJScrollPane
JTable reporterIonsTable
JTextField residuesTxt
JComboBox<E> typeCmb
double minXAxisValue
double maxXAxisValue
TableCellRenderer delegate
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
boolean useMassDeltaCombinations
double deltaMassWindow
String iXAxisLabel
String iYAxisLabel
Color iFilenameColor
ArrayList<E> iDataPointAndLineColor
ArrayList<E> iAreaUnderCurveColor
Integer iPointSize
String iFilename
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
double iXAxisMin
double iXAxisMax
double iYAxisMin
double iYAxisMax
double iAnnotationYAxisThreshold
ArrayList<E> iYAxisData
double iPrecursorMZ
String iPrecursorCharge
ArrayList<E> iXAxisDataInPixels
ArrayList<E> iYAxisDataInPixels
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
int iDrawStyle
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> currentFragmentIons
boolean includeSinglyCharge
boolean includeDoublyCharge
boolean includeMoreThanTwoCharges
ArrayList<E> currentlyUsedIonMatches
org.jfree.chart.ChartPanel chartPanel
ArrayList<E> annotations
ArrayList<E> currentFragmentIons
boolean includeSinglyCharge
boolean includeDoublyCharge
boolean includeMoreThanTwoCharges
ArrayList<E> currentlyUsedIonMatches
org.jfree.chart.ChartPanel chartPanel
boolean useRelativeError
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
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
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
JPanel backgroundPanel
JCheckBox closeDialogWhenImportCompletesCheckBox
JButton closeJButton
JLayeredPane layeredPane
JButton nextJButton
JButton okButton
JPanel processProgressPanel
JProgressBar progressBar
JTextArea reportArea
JScrollPane reportAreaScrollPane
JLabel saveReportLabel
JProgressBar secondaryJProgressBar
JSplitPane secondaryProgressBarSplitPane
JCheckBox showTipOfTheDayCheckBox
JProgressBar tempJProgressBar
JEditorPane tipOfTheDayEditorPane
JPanel tipOfTheDayJPanel
JLayeredPane tipOfTheDayLayeredPane
JScrollPane tipOfTheDayScrollPane
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
int currentPrecursorCharge
boolean showForwardIonDeNovoTags
boolean showRewindIonDeNovoTags
int deNovoCharge
int minPepLength
int maxPepLength
double mascotMaxEvalue
double omssaMaxEvalue
double xtandemMaxEvalue
double maxMassDeviation
boolean isPpm
boolean unknownPtm
HashMap<K,V> modificationNames
ArrayList<E> fixedModifications
ArrayList<E> variableModifications
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
boolean aScoreCalculation
boolean aScoreNeutralLosses
double flr
Float spectrumAnnotatedPeakWidth
Float spectrumBackgroundPeakWidth
Color spectrumAnnotatedPeakColor
Color spectrumBackgroundPeakColor
Color sparklineColorValidated
Color sparklineColorNonValidated
Color sparklineColorNotFound
Color sparklineColorPossible
Color peptideSelected
int memoryPreference
String searchGuiPath
String peptideShakerPath
String reporterPath
String relimsPath
String localPrideFolder
ImportSettingsDialogParent importSettingsDialogParent
boolean editable
IdFilter idFilter
JPanel backgroundPanel
JButton cancelButton
JPanel filterPanel
JButton helpJButton
JLabel mascotEValueLabel
JTextField mascotEvalueTxt
JTextField nAAmaxTxt
JTextField nAAminTxt
JButton okButton
JLabel omssaEValueLabel
JTextField omssaEvalueTxt
JLabel peptideLengthLabel
JLabel peptideLengthRangeLabel
JTextField precDevTxt
JLabel precursorAccuracyLabel
JCheckBox ptmsCheck
JComboBox<E> unitCmb
JLabel xtandemEValueLabel
JTextField xtandemEvalueTxt
ProcessingPreferences processingPreferences
PTMScoringPreferences ptmScoringPreferences
JLabel aScoreLabel
JComboBox<E> ascoreCmb
JPanel backgroundPanel
JLabel estimateAScoreLabel
JTextField flrTxt
JPanel fractionsPanel
JComboBox<E> neutralLossesCmb
JLabel neutralLossesLabel
JButton okButton
JLabel peptideFdrLabel
JTextField peptideFdrTxt
JLabel percentLabel
JLabel percentLabel1
JLabel percentLabel2
JLabel percentLabel3
JLabel percentLabel4
JPanel processingParamsPanel
JTextField proteinConfidenceMwTxt
JLabel proteinFdrLabel
JTextField proteinFdrTxt
JLabel proteinMwLabel
JLabel psmFdrLabel
JTextField psmFdrTxt
JPanel ptmScoringPanel
String iID
String iForeignID
String iAccession
Header.DatabaseType databaseType
String iForeignAccession
String iDescription
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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