JavaOptionsDialogParent javaOptionsDialogParent
javax.swing.JDialog welcomeDialog
java.lang.String toolName
javax.swing.JPanel backgroundPanel
javax.swing.JButton cancelButton
javax.swing.JButton javaOptionsHelpJButton
javax.swing.JLabel mbLabel
javax.swing.JLabel memoryLimitLabel
javax.swing.JTextField memoryTxt
javax.swing.JButton okButton
javax.swing.JPanel settingsPanel
UtilitiesUserPreferences utilitiesUserPreferences
java.lang.String lastSelectedFolder
javax.swing.JPanel backgroundPanel
javax.swing.JButton browseButton
javax.swing.JButton cancelButton
javax.swing.JLabel jLabel2
javax.swing.JButton okButton
javax.swing.JButton peptideShakerButton
javax.swing.JLabel peptideShakerDownloadLinkLabel
javax.swing.JPanel peptideShakerDownloadPanel
javax.swing.JLabel peptideShakerInfoLabel
javax.swing.JPanel peptideShakerInstallationPanel
javax.swing.JLabel peptideShakerJarFileHelpLabel
javax.swing.JTextField peptideShakernstallationJTextField
UtilitiesUserPreferences utilitiesUserPreferences
java.lang.String lastSelectedFolder
javax.swing.JPanel backgroundPanel
javax.swing.JButton browseButton
javax.swing.JButton cancelButton
javax.swing.JLabel jLabel2
javax.swing.JButton okButton
javax.swing.JButton relimsButton
javax.swing.JLabel relimsDownloadLinkLabel
javax.swing.JPanel relimsDownloadPanel
javax.swing.JLabel relimsInfoLabel
javax.swing.JTextField relimsInstallationJTextField
javax.swing.JPanel relimsInstallationPanel
javax.swing.JLabel relimsJarFileHelpLabel
UtilitiesUserPreferences utilitiesUserPreferences
java.lang.String lastSelectedFolder
javax.swing.JPanel backgroundPanel
javax.swing.JButton browseButton
javax.swing.JButton cancelButton
javax.swing.JLabel jLabel2
javax.swing.JButton okButton
javax.swing.JButton reporterButton
javax.swing.JLabel reporterDownloadLinkLabel
javax.swing.JPanel reporterDownloadPanel
javax.swing.JLabel reporterInfoLabel
javax.swing.JTextField reporterInstallationJTextField
javax.swing.JPanel reporterInstallationPanel
javax.swing.JLabel reporterJarFileHelpLabel
UtilitiesUserPreferences utilitiesUserPreferences
java.lang.String lastSelectedFolder
javax.swing.JPanel backgroundPanel
javax.swing.JButton browseButton
javax.swing.JButton cancelButton
javax.swing.JLabel jLabel2
javax.swing.JButton okButton
javax.swing.JButton searchGuiButton
javax.swing.JLabel searchGuiDownloadLinkLabel
javax.swing.JPanel searchGuiDownloadPanel
javax.swing.JLabel searchGuiInfoLabel
javax.swing.JTextField searchGuiInstallationJTextField
javax.swing.JPanel searchGuiInstallationPanel
javax.swing.JLabel searchGuiJarFileHelpLabel
org.apache.log4j.Logger logger
java.awt.Color iEvenRowColor
java.awt.Color iUnevenRowColor
org.apache.log4j.Logger logger
int iColCount
int iRowCount
java.lang.String[] iColNames
java.lang.Object[][] iData
java.lang.String dbName
java.sql.Connection dbConnection
java.util.ArrayList<E> longKeys
ObjectsCache objectsCache
java.io.BufferedWriter debugSpeedWriter
java.io.BufferedWriter debugContentWriter
java.io.File debugFolder
boolean debugSpeed
boolean debugContent
boolean debugInteractions
java.util.HashMap<K,V> peffAnnotationsColorMap
java.util.HashMap<K,V> peffAnnotationsTooltipMap
boolean peffFormat
java.util.TreeMap<K,V> keyValuePairs
java.io.File currentSequenceFile
java.io.BufferedReader currentPeffBufferedReader
java.lang.String currentSequence
java.lang.String currentSequenceLine
java.util.HashMap<K,V> linkedSpectrumPanels
java.util.HashMap<K,V> allAnnotations
SpectrumPanel spectrumAPanel
SpectrumPanel spectrumBPanel
int spectrumPanelMaxPadding
int chromatogramPanelMaxPadding
MascotEnzymeReader mascotEnzymeReader
java.lang.String cleanProteinSequence
java.util.HashMap<K,V> selectedAnnotationTypes
java.util.ArrayList<E> sequenceAnnotationColumnHeaderTooltips
java.awt.Color sparklineColor
javax.swing.JCheckBox H2OIonsJCheckBox
javax.swing.JCheckBox NH3IonsJCheckBox
javax.swing.JCheckBox aIonsJCheckBox
javax.swing.JCheckBox allPeaksJCheckBox
javax.swing.JCheckBox bIonsJCheckBox
javax.swing.JButton browseJButton
javax.swing.JCheckBox cIonsJCheckBox
javax.swing.JCheckBox chargeOneJCheckBox
javax.swing.JCheckBox chargeOverTwoJCheckBox
javax.swing.JSpinner chargePeptideAJSpinner
javax.swing.JSpinner chargePeptideBJSpinner
javax.swing.JCheckBox chargeTwoJCheckBox
javax.swing.JPanel chromatogramAJPanel
javax.swing.JPanel chromatogramJPanel
javax.swing.JLabel chromatogramPanelHelpJLabel
javax.swing.JLabel chromatogramPanelInfoJLabel
javax.swing.JComboBox<E> enzymesJComboBox
javax.swing.JButton exportJButton
javax.swing.JLabel inSilicoDigestionHelpJLabel
javax.swing.JEditorPane informationJEditorPane
javax.swing.JPanel informationJPanel
javax.swing.JScrollPane informationJScrollPane
javax.swing.JTextField inhibitorsJTextField
javax.swing.JPanel ionSelectionJPanel
javax.swing.JPanel isotopicDistributionAJPanel
javax.swing.JLabel isotopicDistributionCalculatorHelpJLabel
javax.swing.JLabel isotopicDistributionCalculatorInfoJLabel
javax.swing.JPanel isotopicDistributionJPanel
javax.swing.JLabel jLabel1
javax.swing.JLabel jLabel10
javax.swing.JLabel jLabel11
javax.swing.JLabel jLabel12
javax.swing.JLabel jLabel13
javax.swing.JLabel jLabel14
javax.swing.JLabel jLabel15
javax.swing.JLabel jLabel16
javax.swing.JLabel jLabel17
javax.swing.JLabel jLabel18
javax.swing.JLabel jLabel19
javax.swing.JLabel jLabel2
javax.swing.JLabel jLabel20
javax.swing.JLabel jLabel21
javax.swing.JLabel jLabel24
javax.swing.JLabel jLabel3
javax.swing.JLabel jLabel4
javax.swing.JLabel jLabel5
javax.swing.JLabel jLabel6
javax.swing.JLabel jLabel7
javax.swing.JLabel jLabel8
javax.swing.JLabel jLabel9
javax.swing.JPanel jPanel1
javax.swing.JPanel jPanel10
javax.swing.JPanel jPanel11
javax.swing.JPanel jPanel12
javax.swing.JPanel jPanel2
javax.swing.JPanel jPanel3
javax.swing.JPanel jPanel4
javax.swing.JPanel jPanel5
javax.swing.JPanel jPanel6
javax.swing.JPanel jPanel7
javax.swing.JPanel jPanel8
javax.swing.JPanel jPanel9
javax.swing.JRadioButton jRadioButton1
javax.swing.JScrollPane jScrollPane1
javax.swing.JScrollPane jScrollPane2
javax.swing.JScrollPane jScrollPane3
javax.swing.JSeparator jSeparator1
javax.swing.JSeparator jSeparator2
javax.swing.JSeparator jSeparator3
javax.swing.JSeparator jSeparator4
javax.swing.JSeparator jSeparator5
javax.swing.JSeparator jSeparator6
javax.swing.JSeparator jSeparator9
javax.swing.JTabbedPane jTabbedPane
javax.swing.JCheckBox linkedSpectraJCheckBox
javax.swing.JSpinner lowerMassJSpinner
javax.swing.JSpinner missedCleavagesJSpinner
javax.swing.JButton nextJButton
javax.swing.JCheckBox otherIonsJCheckBox
javax.swing.JTable peffAnnotationsJTable
javax.swing.JTable peffHeaderJTable
javax.swing.JPanel peptideAColorJPanel
javax.swing.JTextField peptideACompositionJTextField
javax.swing.JScrollPane peptideAJScrollPane
org.jdesktop.swingx.JXTable peptideAJXTable
javax.swing.JTextField peptideAMzJTextField
javax.swing.JPanel peptideBColorJPanel
javax.swing.JTextField peptideBCompositionJTextField
javax.swing.JScrollPane peptideBJScrollPane
org.jdesktop.swingx.JXTable peptideBJXTable
javax.swing.JTextField peptideBMzJTextField
javax.swing.JTextField peptideSequenceAJTextField
javax.swing.JTextField peptideSequenceBJTextField
javax.swing.JPanel peptidesJPanel
javax.swing.JTable peptidesJTable
javax.swing.JScrollPane peptidesScrollPane
javax.swing.JTextField positionJTextField
javax.swing.JCheckBox profileSpectrumJCheckBox
javax.swing.JScrollPane proteinCoverageJScrollPane
javax.swing.JLabel proteinDigestionJLabel
javax.swing.JPanel proteinDigestionJPanel
javax.swing.JTable proteinHeaderJTable
javax.swing.JEditorPane proteinSequenceCoverageJEditorPane
javax.swing.JPanel sequenceCoverageJPanel
javax.swing.JTextField sequenceFileJTextField
javax.swing.JTabbedPane sequenceJTabbedPane
javax.swing.JComboBox<E> silacLabelPeptideAJComboBox
javax.swing.JComboBox<E> silacLabelPeptideBJComboBox
javax.swing.JTextField siteJTextField
javax.swing.JPanel spectraJPanel
javax.swing.JPanel spectrumAJPanel
javax.swing.JPanel spectrumBJPanel
javax.swing.JPanel spectrumJPanel
javax.swing.JLabel spectrumPanelHelpJLabel
javax.swing.JLabel spectrumPanelInfoJLabel
javax.swing.JSpinner upperMassJSpinner
javax.swing.JCheckBox xIonsJCheckBox
javax.swing.JCheckBox yIonsJCheckBox
javax.swing.JCheckBox zIonsJCheckBox
Sample sample
java.util.HashMap<K,V> analysis
java.lang.String singleLetterCode
java.lang.String threeLetterCode
java.lang.String name
double averageMass
double monoisotopicMass
java.lang.Integer target
java.util.HashMap<K,V> aaTargeted
java.util.HashMap<K,V> aaExcluded
Ion.IonType type
double theoreticMass
java.lang.String accession
boolean decoy
java.lang.String sequence
Header.DatabaseType databaseType
int type
java.util.ArrayList<E> residuesArray
java.lang.String name
java.lang.String shortName
double mass
java.util.ArrayList<E> neutralLosses
java.util.ArrayList<E> reporterIons
AminoAcidPattern pattern
java.util.HashMap<K,V> ptmMap
java.util.ArrayList<E> defaultMods
java.util.ArrayList<E> userMods
java.util.HashMap<K,V> userColors
java.util.HashMap<K,V> shortNames
java.util.HashMap<K,V> defaultOmssaIndexes
And filter
And filter
double mz
double mzTolerance
boolean isPpm
double intensityQuantile
MzFilter brotherFilter
java.util.ArrayList<E> mzArray
java.lang.String spectrumKey
double mz
double mzTolerance
boolean isPpm
double intensity
double intensityTolerance
SpectrumFilter spectrumFilter
java.util.ArrayList<E> mzArray
javax.swing.JButton addButton
javax.swing.JButton cancelButton
javax.swing.JTextField intTxt
javax.swing.JLabel jLabel1
javax.swing.JLabel jLabel2
javax.swing.JLabel jLabel3
javax.swing.JLabel jLabel4
javax.swing.JScrollPane jScrollPane1
javax.swing.JSeparator jSeparator1
javax.swing.JTable mzTable
javax.swing.JTextField mzTolTxt
javax.swing.JButton okButtonButton
javax.swing.JComboBox<E> ppmCmb
javax.swing.JButton removeButton
SpectrumFilter spectrumFilter
java.util.ArrayList<E> mzArray
java.util.ArrayList<E> intArray
javax.swing.JButton addButton
javax.swing.JButton cancelButton
javax.swing.JTextField intTxt
javax.swing.JLabel jLabel1
javax.swing.JLabel jLabel2
javax.swing.JLabel jLabel3
javax.swing.JLabel jLabel4
javax.swing.JScrollPane jScrollPane1
javax.swing.JSeparator jSeparator1
javax.swing.JTable mzTable
javax.swing.JTextField mzTolTxt
javax.swing.JButton okButton
javax.swing.JComboBox<E> ppmCmb
javax.swing.JButton removeButton
SpectrumFilter spectrumFilter
javax.swing.JButton cancelButton
javax.swing.JTextField intTxt
javax.swing.JLabel jLabel1
javax.swing.JLabel jLabel2
javax.swing.JLabel jLabel3
javax.swing.JLabel jLabel4
javax.swing.JSeparator jSeparator1
javax.swing.JTextField mzTolTxt
javax.swing.JTextField mzTxt
javax.swing.JButton okButton
javax.swing.JComboBox<E> ppmCmb
SpectrumFilter spectrumFilter
javax.swing.JButton cancelButton
javax.swing.JTextField intTolTxt
javax.swing.JTextField intTxt
javax.swing.JLabel jLabel1
javax.swing.JLabel jLabel2
javax.swing.JLabel jLabel3
javax.swing.JLabel jLabel4
javax.swing.JLabel jLabel5
javax.swing.JSeparator jSeparator1
javax.swing.JTextField mzTolTxt
javax.swing.JTextField mzTxt
javax.swing.JButton okButton
javax.swing.JComboBox<E> ppmCmb
java.util.HashMap<K,V> indexes
java.lang.String fileName
boolean isDecoy
int nTarget
java.util.ArrayList<E> proteinIdentification
java.util.ArrayList<E> peptideIdentification
java.util.HashMap<K,V> spectrumIdentificationMap
java.util.ArrayList<E> spectrumIdentification
java.util.HashMap<K,V> proteinMap
int methodUsed
java.lang.String serializationDirectory
java.util.HashMap<K,V> urParameters
java.util.ArrayList<E> longKeys
java.lang.Boolean isDB
IdentificationDB identificationDB
java.lang.String reference
java.util.ArrayList<E> orderedSpectrumFileNames
java.lang.String dbName
java.lang.String proteinTableName
java.lang.String proteinParametersTableSuffix
java.lang.String peptideTableName
java.lang.String peptideParametersTableSuffix
java.lang.String psmTableSuffix
java.lang.String psmParametersTableSuffix
java.lang.String parametersSuffix
java.util.ArrayList<E> psmTables
java.util.ArrayList<E> psmParametersTables
java.util.ArrayList<E> peptideParametersTables
java.util.ArrayList<E> proteinParametersTables
java.util.ArrayList<E> matchParametersTables
ObjectsDB objectsDB
java.util.HashMap<K,V> bBoundaries
java.util.HashMap<K,V> yBoundaries
int rank
Peptide peptide
int advocate
Charge identificationCharge
double eValue
java.lang.String file
java.lang.Boolean isDecoy
SearchParameters.PrecursorAccuracyType currentPrecursorAccuracyType
java.lang.Double precursorTolerance
java.lang.Double fragmentIonMZTolerance
ModificationProfile utilitiesModificationProfile
Enzyme enzyme
java.lang.Integer nMissedCleavages
java.io.File fastaFile
java.io.File parametersFile
java.util.HashMap<K,V> fractionMolecularWeights
java.util.HashMap<K,V> fractionMolecularWeightRanges
java.lang.Integer forwardIon
java.lang.Integer rewindIon
Charge minChargeSearched
Charge maxChargeSearched
java.lang.Double maxEValue
java.lang.Integer hitListLength
Charge minimalChargeForMultipleChargedFragments
java.lang.Integer minPeptideLength
java.lang.Integer maxPeptideLength
java.lang.Boolean removePrecursor
java.lang.Boolean scalePrecursor
java.lang.Boolean estimateCharge
java.lang.String theoreticPtm
boolean variable
int modifiedSite
boolean confident
boolean inferred
Peptide theoreticPeptide
java.lang.String mainMatchKey
java.util.ArrayList<E> spectrumMatches
java.lang.Boolean isDecoy
java.util.ArrayList<E> theoreticProtein
java.lang.String mainMatch
java.util.ArrayList<E> peptideMatches
java.lang.String spectrumKey
java.util.HashMap<K,V> assumptions
PeptideAssumption bestAssumption
java.util.HashMap<K,V> firstHits
java.util.ArrayList<E> advocates
java.lang.Integer spectrumNumber
java.util.HashMap<K,V> index
uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile bufferedRandomAccessFile
java.lang.String fileName
java.util.HashMap<K,V> indexMap
java.util.ArrayList<E> spectrumTitles
java.lang.String fileName
java.lang.Double maxRT
java.lang.Double minRT
java.lang.Double maxMz
java.lang.Double maxIntensity
Precursor precursor
double rt
java.lang.Double rtMin
java.lang.Double rtMax
double mz
double intensity
java.util.ArrayList<E> possibleCharges
java.lang.String spectrumTitle
java.lang.String fileName
int level
java.util.HashMap<K,V> peakList
java.lang.String scanNumber
double scanStartTime
Quantification.QuantificationMethod methodUsed
java.util.ArrayList<E> proteinQuantification
java.util.ArrayList<E> peptideQuantification
java.util.HashMap<K,V> modifiedPeptidesQuantification
java.util.HashMap<K,V> psmIDentificationToQuantification
QuantificationDB quantificationDB
java.lang.String dbName
java.lang.String proteinTableName
java.lang.String proteinParametersTableSuffix
java.lang.String peptideTableName
java.lang.String peptideParametersTableSuffix
java.lang.String psmTableSuffix
java.lang.String psmParametersTableSuffix
java.util.ArrayList<E> psmTables
java.util.ArrayList<E> psmParametersTables
java.util.ArrayList<E> peptideParametersTables
java.util.ArrayList<E> proteinParametersTables
ObjectsDB objectsDB
java.lang.String spectrumKey
java.lang.String spectrumMatchKey
java.util.HashMap<K,V> reporterMatches
java.util.HashMap<K,V> deisotopedIntensities
double referenceIntensity
java.util.HashMap<K,V> sampleAssignement
ReporterMethod reporterMethod
AminoAcidPattern pattern
boolean editable
boolean cancel
java.util.ArrayList<E> patternDesignTableToolTips
java.lang.String exampleSequence
javax.swing.JMenuItem addJMenuItem
javax.swing.JPanel backgroundPanel
javax.swing.JButton cancelButton
javax.swing.JMenuItem deleteSelectedRowJMenuItem
javax.swing.JLabel exampleLabel
javax.swing.JSeparator jSeparator3
javax.swing.JSeparator jSeparator4
javax.swing.JMenuItem moveDownJMenuItem
javax.swing.JMenuItem moveUpJMenuItem
javax.swing.JButton okButton
javax.swing.JPanel patternDesignPanel
javax.swing.JScrollPane patternDesignScrollPane
javax.swing.JTable patternDesignTable
javax.swing.JEditorPane patternTestEditorPane
javax.swing.JScrollPane patternTestJScrollPane
javax.swing.JPopupMenu popupJMenu
javax.swing.JLabel rightClickHelpLabel
javax.swing.JPanel testPanel
java.lang.String[] samples
java.lang.String choice
javax.swing.JPanel backgroundPanel
javax.swing.JComboBox<E> comboBox
javax.swing.JLabel jLabel1
javax.swing.JLabel jLabel2
javax.swing.JButton okButton
javax.swing.JLabel titleLbl
VisibleTableColumnsDialogParent visibleTableColumnsDialogParent
javax.swing.JPanel backgroundPanel
javax.swing.JMenuItem deselectAllMenuItem
javax.swing.JButton okButton
javax.swing.JMenuItem selectAllMenuItem
javax.swing.JPopupMenu selectJPopupMenu
javax.swing.JTable selectedColumnsTable
javax.swing.JScrollPane selectedValuesTableScrollPane
ProgressDialogX progressDialog
javax.swing.table.TableModel tabelModel
org.jfree.chart.ChartPanel chartPanel
double bubbleSize
double bubbleScalingFactor
int numberOfBins
boolean userDefinedBinSize
java.awt.Frame dialogParent
boolean isPlotting
boolean mouseDragged
java.awt.Point dragStart
java.awt.Point dragEnd
java.util.HashMap<K,V> selectedDataPoints
boolean selectionActive
java.util.HashMap<K,V> dataPointToRowNumber
java.util.ArrayList<E> selectedModelRows
java.util.HashMap<K,V> cellRenderers
java.util.HashMap<K,V> maxColumnWidths
java.util.HashMap<K,V> minColumnWidths
java.util.ArrayList<E> tableToolTips
no.uib.jsparklines.renderers.util.GradientColorCoding.ColorGradient colorGradient
java.awt.Color histogramColor
java.lang.String lastSelectedFolder
java.awt.Image normalIcon
java.awt.Image waitingIcon
java.util.ArrayList<E> allTableColumns
java.util.HashMap<K,V> visibleColumns
boolean useGradientColorCoding
boolean showRegressionLine
javax.swing.JPanel backgroundPanel
javax.swing.JSpinner binSizeSpinner
javax.swing.JLabel binsLabel
javax.swing.JComboBox<E> bubbleSizeComboBox
javax.swing.JLabel bubbleSizeLabel
javax.swing.JLabel colorLabel
javax.swing.JComboBox<E> colorsComboBox
javax.swing.JPanel contextMenuPlotBackgroundPanel
javax.swing.JPanel contextMenuSelectedValuesTableBackgroundPanel
javax.swing.JRadioButton densityPlotRadioButton
javax.swing.ButtonGroup dragButtonGroup
javax.swing.JPanel dragSettingsPanel
javax.swing.JRadioButton dragToSelectRadioButton
javax.swing.JRadioButton dragToZoomRadioButton
javax.swing.JMenuItem exportPlotMenuItem
javax.swing.JMenuItem exportSelectedValuesMenuItem
javax.swing.JMenuItem hideColumnsMenuItem
javax.swing.JRadioButton histogramRadioButton
javax.swing.JPanel logAcisPanel
javax.swing.JButton plotHelpJButton
javax.swing.JLayeredPane plotLayeredPane
javax.swing.JButton plotOptionsJButton
javax.swing.JPanel plotPanel
javax.swing.JPopupMenu plotPopupMenu
javax.swing.ButtonGroup plotTypeButtonGroup
javax.swing.JPanel plotTypePanel
javax.swing.JCheckBoxMenuItem regressionLineCheckBoxMenuItem
javax.swing.JLayeredPane selectedValuesLayeredPane
javax.swing.JPanel selectedValuesPanel
javax.swing.JScrollPane selectedValuesScrollPane
javax.swing.JTable selectedValuesTable
javax.swing.JButton selectedValuesTableHelpJButton
javax.swing.JButton selectedValuesTableOptionsJButton
javax.swing.JPopupMenu selectedValuesTablePopupMenu
javax.swing.JCheckBox sizeLogCheckBox
javax.swing.JComboBox<E> xAxisComboBox
javax.swing.JLabel xAxisLabel
javax.swing.JCheckBox xAxisLogCheckBox
javax.swing.JPanel xAxisPanel
javax.swing.JPanel xyPlotPanel
javax.swing.JRadioButton xyPlotRadioButton
javax.swing.JComboBox<E> yAxisComboBox
javax.swing.JLabel yAxisLabel
javax.swing.JCheckBox yAxisLogCheckBox
java.lang.String selectionFolder
java.lang.String toolName
java.lang.String googleCodeToolName
java.lang.String toolVersion
java.io.File logFile
javax.swing.JPanel backgroundPanel
javax.swing.JButton clearJButton
javax.swing.JButton exitButton
javax.swing.JEditorPane infoJEditorPane
javax.swing.JPanel infoJPanel
javax.swing.JScrollPane infoJScrollPane
javax.swing.JPanel logJPanel
javax.swing.JScrollPane logJScrollPane
javax.swing.JTextArea logTxt
javax.swing.JButton saveJButton
java.awt.Frame frameParent
javax.swing.JDialog dialogParent
javax.swing.JPanel backgroundPanel
javax.swing.JButton closeJButton
javax.swing.JScrollPane jScrollPane1
javax.swing.JEditorPane textJEditorPane
org.jfree.chart.ChartPanel chartPanel
java.awt.Component graphicsPanel
ProgressDialogX progressDialog
ExportGraphicsDialogParent exportGraphicsDialogParent
javax.swing.JFrame frame
javax.swing.JPanel backgroundPanel
javax.swing.ButtonGroup buttonGroup
javax.swing.JButton cancelJButton
javax.swing.JButton exportJButton
javax.swing.JRadioButton pdfJRadioButton
javax.swing.JPanel plottingTypeJPanel
javax.swing.JRadioButton pngJRadioButton
javax.swing.JRadioButton svgJRadioButton
javax.swing.JRadioButton tiffJRadioButton
java.util.HashMap<K,V> fileMap
boolean canceled
javax.swing.JButton cancelButton
javax.swing.JList<E> fileList
javax.swing.JScrollPane jScrollPane1
javax.swing.JButton okButton
javax.swing.JLabel txtLabel
org.apache.log4j.Logger logger
javax.swing.JTextArea txtSequence
javax.swing.JLabel lblComp
javax.swing.JLabel lblMass
javax.swing.JButton calculateButton
AlternateRowColoursJTable table1
javax.swing.JPanel jpanContent
javax.swing.JPanel headerTable
javax.swing.JPanel spectrumPanel
javax.swing.JSpinner spinCharge
javax.swing.JLabel lblPeptide
AASequenceImpl iSequence
java.util.HashMap<K,V> iElements
double iCharge
java.util.HashMap<K,V> fragmentIonRectangles
java.lang.String[] iSequenceComponents
java.util.ArrayList<E> profiles
java.awt.Font iBaseFont
double iMaxBarHeight
int iBarWidth
int iHorizontalSpace
int iXStart
int iYStart
boolean isModifiedSequence
PTMFactory ptmFactory
PtmDialogParent ptmDialogParent
PtmToPrideMap ptmToPrideMap
java.awt.Color sparklineColor
java.lang.String selectedRowHtmlTagFontColor
java.lang.String notSelectedRowHtmlTagFontColor
java.util.ArrayList<E> defaultModsTableToolTips
java.util.ArrayList<E> userModsTableToolTips
java.util.ArrayList<E> searchPossibilities
int searchCurrentSelection
java.lang.String searchWelcomeText
javax.swing.JButton addUserPTM
javax.swing.JTable defaultModificationsTable
javax.swing.JPanel defaultModsPanel
javax.swing.JScrollPane defaultModsScrollPane
javax.swing.JPopupMenu defaultPtmPopupMenu
javax.swing.JButton deleteUserPTM
javax.swing.JMenuItem editDefaultPtmJMenuItem
javax.swing.JButton editUserPTM
javax.swing.JMenuItem editUserPtmJMenuItem
javax.swing.JLabel findJLabel
javax.swing.JPanel modificationsEditorPanel
javax.swing.JButton modificationsHelpJButton
javax.swing.JSplitPane modificationsSplitPane
javax.swing.JButton okButton
javax.swing.JLabel searchIndexLabel
javax.swing.JTextField searchInputTxt
javax.swing.JButton searchNextButton
javax.swing.JButton searchPreviousButton
javax.swing.JTable userModificationsTable
javax.swing.JPanel userModsPanel
javax.swing.JScrollPane userModsScrollPane
javax.swing.JPopupMenu userPtmPopupMenu
PtmDialogParent ptmDialogParent
PTMFactory ptmFactory
PTM currentPtm
java.util.ArrayList<E> neutralLosses
java.util.ArrayList<E> reporterIons
PtmToPrideMap ptmToPrideMap
CvTerm cvTerm
boolean editable
AminoAcidPattern pattern
javax.swing.JButton addNeutralLoss
javax.swing.JButton addReporterIon
javax.swing.JPanel backgroundPanel
javax.swing.JButton cancelButton
javax.swing.JPanel detailsPanel
javax.swing.JButton helpJButton
javax.swing.JLabel jLabel1
javax.swing.JPanel jPanel1
javax.swing.JLabel massLabel
javax.swing.JTextField massTxt
javax.swing.JLabel nameLabel
javax.swing.JTextField nameTxt
javax.swing.JPanel neutralLossesAndReporterIonsPanel
javax.swing.JScrollPane neutralLossesJScrollPane
javax.swing.JTable neutralLossesTable
javax.swing.JButton okButton
javax.swing.JButton olsJButton
javax.swing.JLabel patternLabel
javax.swing.JTextField psiModMappingJTextField
javax.swing.JPanel psiModMappingPanel
javax.swing.JButton removeNeutralLoss
javax.swing.JButton removerReporterIon
javax.swing.JScrollPane reporterIonsJScrollPane
javax.swing.JTable reporterIonsTable
javax.swing.JTextField residuesTxt
javax.swing.JComboBox<E> typeCmb
java.util.Vector<E> tooltips
int align
int MAX_TOOLTIP_WIDTH
java.util.ArrayList<E> currentFragmentIonTypes
NeutralLossesMap neutralLosses
boolean singleCharge
boolean twoCharges
java.util.ArrayList<E> tooltips
Peptide currentPeptide
java.lang.String peptideSequence
java.util.ArrayList<E> allAnnotations
java.util.ArrayList<E> allSpectra
float peakWidth
float backgroundPeakWidth
boolean subscriptAnnotationNumbers
java.awt.Color peakWaterMarkColor
boolean scientificXAxis
boolean scientificYAxis
java.lang.String scientificPattern
java.util.HashMap<K,V> referenceAreasXAxis
java.util.HashMap<K,V> referenceAreasYAxis
boolean miniature
boolean yDataIsPositive
float alphaLevel
boolean useMassDeltaCombinations
double deltaMassWindow
java.lang.String iXAxisLabel
java.lang.String iYAxisLabel
java.awt.Color iFilenameColor
java.util.ArrayList<E> iDataPointAndLineColor
java.util.ArrayList<E> iAreaUnderCurveColor
java.lang.Integer iPointSize
java.lang.String iFilename
java.util.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
java.util.ArrayList<E> iXAxisData
double iXAxisMin
double iXAxisMax
double iYAxisMin
double iYAxisMax
double iAnnotationYAxisThreshold
java.util.ArrayList<E> iYAxisData
double iPrecursorMZ
java.lang.String iPrecursorCharge
java.util.ArrayList<E> iXAxisDataInPixels
java.util.ArrayList<E> iYAxisDataInPixels
boolean iHighLight
int iHighLightIndex
int iHighLightDatasetIndex
boolean iClicked
int iClickedIndex
int iClickedDataSetIndex
java.util.Vector<E> iClickedList
java.util.Vector<E> iClickedListDatasetIndices
java.util.Vector<E> iStoredSequence
java.util.Vector<E> iStoredSequenceDatasetIndices
java.util.Vector<E> iAnnotations
int iMinDrag
int iDrawStyle
int iDotRadius
int iMSLevel
boolean showAllPeaks
boolean yAxisZoomExcludesBackgroundPeaks
GraphicsPanel.GraphicsPanelType currentGraphicsPanelType
org.apache.log4j.Logger logger
java.awt.Color aSpectrumPeakColor
java.awt.Color aSpectrumProfileModeLineColor
java.util.ArrayList<E> peptideSequences
java.util.ArrayList<E> peptideCharges
java.util.HashMap<K,V> iElements
boolean useRelativeError
java.util.ArrayList<E> currentFragmentIons
boolean includeSinglyCharge
boolean includeDoublyCharge
boolean includeMoreThanTwoCharges
java.util.ArrayList<E> currentlyUsedIonMatches
org.jfree.chart.ChartPanel chartPanel
java.util.ArrayList<E> annotations
java.util.ArrayList<E> currentFragmentIons
boolean includeSinglyCharge
boolean includeDoublyCharge
boolean includeMoreThanTwoCharges
java.util.ArrayList<E> currentlyUsedIonMatches
org.jfree.chart.ChartPanel chartPanel
boolean useRelativeError
java.util.HashMap<K,V> tooltipRectangles
java.lang.String[] iSequenceComponents
java.util.ArrayList<E> iIonMatches
double[] bIons
double[] yIons
java.awt.Font iBaseFont
double iMaxBarHeight
int iBarWidth
int iHorizontalSpace
int iXStart
boolean isModifiedSequence
boolean iHighlightModifications
ModificationProfile modificationProfile
int forwardIon
int rewindIon
java.awt.Color forwardColor
java.awt.Color rewindColor
org.apache.log4j.Logger logger
java.util.ArrayList<E> iConnections
javax.swing.JComboBox<E> cmbConfigurations
javax.swing.JTextField txtDriver
javax.swing.JTextField txtUrl
javax.swing.JTextField txtUser
javax.swing.JPasswordField txtPassword
javax.swing.JButton btnOK
javax.swing.JButton btnCancel
Connectable iTarget
java.lang.String iPropsFile
java.lang.String iLastInitiatedConfiguration
java.util.Calendar iSelectedCalendar
java.util.Calendar iShownCalendar
int iSelectedDayIndex
javax.swing.JLabel[] lblDayNames
javax.swing.JLabel[] lblDays
java.lang.Integer[] iDays
javax.swing.JLabel lblCurrentMonthYear
boolean doNothingOnClose
boolean unstoppable
boolean canceled
boolean finished
java.awt.Image waitingIcon
java.awt.Image normalIcon
java.awt.Frame waitingHandlerParentFrame
javax.swing.JDialog waitingHandlerParentDialog
javax.swing.JProgressBar progressBar
javax.swing.JDialog dialog
java.awt.Point naturalLocation
javax.swing.Timer shakeTimer
boolean runFinished
boolean runCanceled
java.util.ArrayList<E> tips
int currentTipIndex
java.lang.String lastSelectedFolder
java.awt.Image waitingIcon
java.awt.Image normalIcon
java.awt.Frame waitingHandlerParent
boolean shakeWhenFinished
java.lang.String processName
java.lang.String toolName
java.lang.String toolVersion
javax.swing.JPanel backgroundPanel
javax.swing.JCheckBox closeDialogWhenImportCompletesCheckBox
javax.swing.JButton closeJButton
javax.swing.JLayeredPane layeredPane
javax.swing.JButton nextJButton
javax.swing.JButton okButton
javax.swing.JPanel processProgressPanel
javax.swing.JProgressBar progressBar
javax.swing.JTextArea reportArea
javax.swing.JScrollPane reportAreaScrollPane
javax.swing.JLabel saveReportLabel
javax.swing.JProgressBar secondaryJProgressBar
javax.swing.JSplitPane secondaryProgressBarSplitPane
javax.swing.JCheckBox showTipOfTheDayCheckBox
javax.swing.JProgressBar tempJProgressBar
javax.swing.JEditorPane tipOfTheDayEditorPane
javax.swing.JPanel tipOfTheDayJPanel
javax.swing.JLayeredPane tipOfTheDayLayeredPane
javax.swing.JScrollPane tipOfTheDayScrollPane
boolean yAxisZoomExcludesBackgroundPeaks
boolean intensityIonTable
boolean showBars
boolean showAllPeaks
double intensityLimit
boolean automaticAnnotation
java.util.HashMap<K,V> selectedIons
NeutralLossesMap neutralLossesMap
boolean neutralLossesSequenceDependant
java.util.ArrayList<E> selectedCharges
double fragmentIonAccuracy
Peptide currentPeptide
int currentPrecursorCharge
boolean showForwardIonDeNovoTags
boolean showRewindIonDeNovoTags
int deNovoCharge
java.util.HashMap<K,V> modificationNames
java.util.ArrayList<E> fixedModifications
java.util.ArrayList<E> variableModifications
java.util.ArrayList<E> refinementModifications
java.util.HashMap<K,V> omssaIndexes
java.util.HashMap<K,V> colors
java.util.HashMap<K,V> backUp
java.lang.Float spectrumAnnotatedPeakWidth
java.lang.Float spectrumBackgroundPeakWidth
java.awt.Color spectrumAnnotatedPeakColor
java.awt.Color spectrumBackgroundPeakColor
java.awt.Color sparklineColorValidated
java.awt.Color sparklineColorNonValidated
java.awt.Color sparklineColorNotFound
java.awt.Color sparklineColorPossible
java.awt.Color peptideSelected
int memoryPreference
java.lang.String searchGuiPath
java.lang.String peptideShakerPath
java.lang.String reporterPath
java.lang.String relimsPath
java.lang.String localPrideFolder
java.lang.String iID
java.lang.String iForeignID
java.lang.String iAccession
Header.DatabaseType databaseType
java.lang.String iForeignAccession
java.lang.String iDescription
java.lang.String iGeneName
java.lang.String iProteinEvidence
java.lang.String iTaxonomy
java.lang.String iForeignDescription
java.lang.String iRest
java.lang.StringBuffer iAddenda
int iStart
int iEnd
org.apache.log4j.Logger logger
ModificationTemplate iTemplate
int iLocation
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