Serialized Form (PeptideShaker 3.0.12 API)

Package eu.isas.peptideshaker.gui

Class eu.isas.peptideshaker.gui.FractionDetailsDialog

class FractionDetailsDialog extends JDialog implements Serializable
- Serialized Fields
  - backgroundPanel
    
    JPanel backgroundPanel
  - cancelButton
    
    JButton cancelButton
  - disclaimerLabel
    
    JLabel disclaimerLabel
  - disclamierPanel
    
    JPanel disclamierPanel
  - fractionJScrollPane
    
    JScrollPane fractionJScrollPane
  - fractionsPanel
    
    JPanel fractionsPanel
  - fractionTable
    
    JTable fractionTable
  - helpLabel
    
    JLabel helpLabel
  - importFractionRangesButton
    
    JButton importFractionRangesButton
  - moveBottomButton
    
    JButton moveBottomButton
  - moveDownButton
    
    JButton moveDownButton
  - moveTopButton
    
    JButton moveTopButton
  - moveUpButton
    
    JButton moveUpButton
  - okButton
    
    JButton okButton
  - orderSettingsPanel
    
    JPanel orderSettingsPanel
  - peptideShakerGUI
    
    PeptideShakerGUI peptideShakerGUI
    
    The PeptideShakerGUI parent.
  - tableToolTips
    
    ArrayList<String> tableToolTips
    
    The table column header tooltips.
Class eu.isas.peptideshaker.gui.IdToSpectrumFileMappingDialog

class IdToSpectrumFileMappingDialog extends JDialog implements Serializable
- Serialized Fields
  - addButton
    
    JButton addButton
  - backgroundPanel
    
    JPanel backgroundPanel
  - browseButton
    
    JButton browseButton
  - cancelButton
    
    JButton cancelButton
  - fileList
    
    JList fileList
  - fileListScrollPane
    
    JScrollPane fileListScrollPane
  - fileTable
    
    JTable fileTable
  - fileTableScrollPane
    
    JScrollPane fileTableScrollPane
  - folderLabel
    
    JLabel folderLabel
  - folderTxt
    
    JTextField folderTxt
  - helpTextLabel
    
    JLabel helpTextLabel
  - idFiles
    
    ArrayList<File> idFiles
    
    The list of id files presenting a missing mgf file.
  - lastSelectedFolder
    
    File lastSelectedFolder
    
    The last selected folder.
  - missingFiles
    
    HashMap<File,String> missingFiles
    
    Map of the missing mgf files indexed by ID file.
  - newFiles
    
    HashMap<String,File> newFiles
    
    Map of the new mgf files indexed by the new ones.
  - okButton
    
    JButton okButton
  - removeButton
    
    JButton removeButton
  - waitingDialog
    
    com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog waitingDialog
    
    The waiting dialog.
Class eu.isas.peptideshaker.gui.ImageIconPanel

class ImageIconPanel extends JPanel implements Serializable
- Serialized Fields
  - imageIcon
    
    ImageIcon imageIcon
    
    The image icon to display.
Class eu.isas.peptideshaker.gui.JumpToPanel

class JumpToPanel extends JPanel implements Serializable
- Serialized Fields
  - currentSelection
    
    EnumMap<JumpToPanel.JumpType,Integer> currentSelection
    
    Currently selected item.
  - findJLabel
    
    JLabel findJLabel
  - indexLabel
    
    JLabel indexLabel
  - inputTxt
    
    JTextField inputTxt
  - lastInput
    
    EnumMap<JumpToPanel.JumpType,String> lastInput
    
    The text to display by default.
  - lastLabel
    
    EnumMap<JumpToPanel.JumpType,String> lastLabel
    
    The text to display by default.
  - newInput
    
    boolean newInput
    
    Counts the number of times the users has pressed a key on the keyboard in the search field.
  - nextButton
    
    JButton nextButton
  - peptideShakerGUI
    
    PeptideShakerGUI peptideShakerGUI
    
    Instance of the main GUI class.
  - possibilities
    
    EnumMap<JumpToPanel.JumpType,ArrayList<Object[]>> possibilities
    
    Items matching the criterion for each type. Keys are in an array: protein, peptide, PSM.
  - previousButton
    
    JButton previousButton
  - searchMutex
    
    com.compomics.util.threading.SimpleSemaphore searchMutex
    
    Semaphore for the synchronization of threads.
  - selectedJumpType
    
    JumpToPanel.JumpType selectedJumpType
    
    The type of data to jump to in that panel.
  - SPECTRUM_FILENAME_SPLITTER
    
    String SPECTRUM_FILENAME_SPLITTER
    
    Splitter between spectrum file and spectrum title.
  - spectrumfile
    
    String spectrumfile
    
    The spectrum file inspected when jumping to spectra.
  - welcomeText
    
    EnumMap<JumpToPanel.JumpType,String> welcomeText
    
    The text to display by default.

Class eu.isas.peptideshaker.gui.MatchValidationDialog

class MatchValidationDialog extends JDialog implements Serializable

Serialized Fields

backgroundPanel
```
JPanel backgroundPanel
```
bitLabel1
```
JLabel bitLabel1
```
bitRecommendationLabel1
```
JLabel bitRecommendationLabel1
```
bitRecommendationLabel3
```
JLabel bitRecommendationLabel3
```
bitRecommendationLabel4
```
JLabel bitRecommendationLabel4
```
cancelButton
```
JButton cancelButton
```
confidenceLbl
```
JLabel confidenceLbl
```
confidenceResolutionLbl
```
JLabel confidenceResolutionLbl
```
confidenceThresholdLbl
```
JLabel confidenceThresholdLbl
```
databaseSearchPanel
```
JPanel databaseSearchPanel
```
editLbl
```
JLabel editLbl
```
fastaFile
```
String fastaFile
```
The path to the FASTA file.

identificationParameters

com.compomics.util.parameters.identification.IdentificationParameters identificationParameters

the identification parameters used,

matchesBeforeFirstDecoyLbl
```
JLabel matchesBeforeFirstDecoyLbl
```
nTargetLbl
```
JLabel nTargetLbl
```
okButton
```
JButton okButton
```

psParameter

com.compomics.util.experiment.identification.peptide_shaker.PSParameter psParameter

The ps parameter of the match.

qualityFiltersPanel
```
JPanel qualityFiltersPanel
```
qualityFiltersTable
```
JTable qualityFiltersTable
```

qualityFiltersTableScrollPane

JScrollPane qualityFiltersTableScrollPane

recommendedNumberOfTargetHitsLbl
```
JLabel recommendedNumberOfTargetHitsLbl
```
recommendedResolutionLbl
```
JLabel recommendedResolutionLbl
```
targetDecoyGroupPanel
```
JPanel targetDecoyGroupPanel
```
targetDecoyLbl
```
JLabel targetDecoyLbl
```
targetDecoyPanel
```
JPanel targetDecoyPanel
```
type
```
MatchValidationDialog.MatchType type
```
The type of match selected.
validationChanged
```
boolean validationChanged
```
Indicates whether the validation status of the match changed.
validationLevelJComboBox
```
JComboBox validationLevelJComboBox
```
validationLevelPanel
```
JPanel validationLevelPanel
```
validationStatusLbl
```
JLabel validationStatusLbl
```
validationTableToolTips
```
ArrayList<String> validationTableToolTips
```
The filter table column header tooltips.
validationThresholdLbl
```
JLabel validationThresholdLbl
```
validationTypeLabel
```
JLabel validationTypeLabel
```

Class eu.isas.peptideshaker.gui.ModificationDialog

class ModificationDialog extends JDialog implements Serializable
- Serialized Fields
  - backgroundPanel
    
    JPanel backgroundPanel
  - cancel
    
    boolean cancel
    
    Boolean indicating whether the user pushed the cancel button.
  - cancelJButton
    
    JButton cancelJButton
  - jScrollPane2
    
    JScrollPane jScrollPane2
  - modificationList
    
    JList modificationList
  - modifications
    
    ArrayList<String> modifications
    
    The known modifications.
  - modificationsJScrollPane
    
    JScrollPane modificationsJScrollPane
  - okJButton
    
    JButton okJButton
  - textArea
    
    JTextArea textArea

Class eu.isas.peptideshaker.gui.ModificationSiteInferenceDialog

class ModificationSiteInferenceDialog extends JDialog implements Serializable

Serialized Fields

backgroundPanel
```
JPanel backgroundPanel
```
cancelButton
```
JButton cancelButton
```
mainSelection
```
boolean[] mainSelection
```
Main modification site selection.

modificationFactory

com.compomics.util.experiment.biology.modifications.ModificationFactory modificationFactory

The modification factory.

okButton
```
JButton okButton
```
openDialogHelpJButton
```
JButton openDialogHelpJButton
```

peptideMatch

com.compomics.util.experiment.identification.matches.PeptideMatch peptideMatch

The peptide match.

peptidePanel
```
JPanel peptidePanel
```

peptidePtmScore

com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores peptidePtmScore

The peptide modification scoring.

peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
The main GUI.

psms

ArrayList<com.compomics.util.experiment.identification.matches.SpectrumMatch> psms

list of PSMs for this peptide.

ptm

com.compomics.util.experiment.biology.modifications.Modification ptm

The modification investigated.

ptmConfidenceTooltipMap
```
HashMap<Integer,String> ptmConfidenceTooltipMap
```
Modification confidence tooltip map, key: modification confidence type, element: modification confidence as a string.
ptmSitePanel
```
JPanel ptmSitePanel
```
ptmSiteTable
```
JTable ptmSiteTable
```
ptmSiteTableScrollPane
```
JScrollPane ptmSiteTableScrollPane
```
ptmsTable
```
JTable ptmsTable
```
ptmsTableScrollPane
```
JScrollPane ptmsTableScrollPane
```
secondarySelection
```
boolean[] secondarySelection
```
Secondary modification site selection.
sequenceLabel
```
JLabel sequenceLabel
```

Class eu.isas.peptideshaker.gui.NewDialog

class NewDialog extends JDialog implements Serializable

Serialized Fields

aboutButton
```
JButton aboutButton
```
addSettingsButton
```
JButton addSettingsButton
```
browseDbButton
```
JButton browseDbButton
```
browseId
```
JButton browseId
```
browseSpectra
```
JButton browseSpectra
```
clearDbButton
```
JButton clearDbButton
```
clearId
```
JButton clearId
```
clearSpectra
```
JButton clearSpectra
```
databaseLabel
```
JLabel databaseLabel
```
displayPreferences
```
DisplayParameters displayPreferences
```
The display preferences.
editProcessingButton
```
JButton editProcessingButton
```
editSettingsButton
```
JButton editSettingsButton
```
fastaFile
```
File fastaFile
```
The FASTA files.
fastaFileTxt
```
JTextField fastaFileTxt
```

identificationParameters

com.compomics.util.parameters.identification.IdentificationParameters identificationParameters

The parameters to use when loading the files.

identificationParametersFactory

com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory identificationParametersFactory

The identification parameters factory.

identificationParametersLabel
```
JLabel identificationParametersLabel
```
idFiles
```
ArrayList<File> idFiles
```
The list of identification files.
idFilesLabel
```
JLabel idFilesLabel
```
idFilesTxt
```
JTextField idFilesTxt
```
inputFilesPanel
```
JPanel inputFilesPanel
```
loadButton
```
JButton loadButton
```

modificationFactory

com.compomics.util.experiment.biology.modifications.ModificationFactory modificationFactory

The modification factory.

modificationFiles
```
ArrayList<File> modificationFiles
```
The XML modification files found.

msFileHandler

com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler msFileHandler

The handler for mass spectrometry files.

peptideShaker
```
PeptideShaker peptideShaker
```
The peptide shaker class which will take care of the pre-processing.
peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
A reference to the main frame.
peptideShakerPublicationLabel
```
JLabel peptideShakerPublicationLabel
```
processingLbl
```
JLabel processingLbl
```

processingParameters

com.compomics.util.parameters.tools.ProcessingParameters processingParameters

The processing preferences.

processingParametersPanel
```
JPanel processingParametersPanel
```
processingTxt
```
JTextField processingTxt
```

progressDialog

com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog

The progress dialog.

projectDetails
```
ProjectDetails projectDetails
```
The project details.
projectDetailsPanel
```
JPanel projectDetailsPanel
```
projectNameIdTxt
```
JTextField projectNameIdTxt
```
projectReferenceLabel
```
JLabel projectReferenceLabel
```
projectSettingsButton
```
JButton projectSettingsButton
```
projectSettingsLabel
```
JLabel projectSettingsLabel
```
projectSettingsTxt
```
JTextField projectSettingsTxt
```
sampleDetailsPanel
```
JPanel sampleDetailsPanel
```
settingsComboBox
```
JComboBox settingsComboBox
```

spectrumCountingPreferences

com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences

The spectrum counting preferences.

spectrumFiles
```
ArrayList<File> spectrumFiles
```
The list of spectrum files.
spectrumFilesLabel
```
JLabel spectrumFilesLabel
```
spectrumFilesTxt
```
JTextField spectrumFilesTxt
```
typeCmb
```
JComboBox<String> typeCmb
```
welcomeDialog
```
WelcomeDialog welcomeDialog
```

Class eu.isas.peptideshaker.gui.PeptideShakerGUI

class PeptideShakerGUI extends JFrame implements Serializable

Serialized Fields

aboutJMenuItem
```
JMenuItem aboutJMenuItem
```
adaptCheckBoxMenuItem
```
JCheckBoxMenuItem adaptCheckBoxMenuItem
```
aIonCheckBoxMenuItem
```
JCheckBoxMenuItem aIonCheckBoxMenuItem
```
allCheckBoxMenuItem
```
JCheckBoxMenuItem allCheckBoxMenuItem
```
allTabsJTabbedPane
```
JTabbedPane allTabsJTabbedPane
```
annotationColorsJMenuItem
```
JMenuItem annotationColorsJMenuItem
```
annotationMenuBar
```
JMenuBar annotationMenuBar
```
annotationPanel
```
AnnotationPanel annotationPanel
```
The Annotation panel.
annotationPreferencesMenu
```
JMenuItem annotationPreferencesMenu
```
annotationsJPanel
```
JPanel annotationsJPanel
```
backgroundLayeredPane
```
JLayeredPane backgroundLayeredPane
```
backgroundPanel
```
JPanel backgroundPanel
```
barsCheckBoxMenuItem
```
JCheckBoxMenuItem barsCheckBoxMenuItem
```
bIonCheckBoxMenuItem
```
JCheckBoxMenuItem bIonCheckBoxMenuItem
```
bubblePlotJMenuItem
```
JMenuItem bubblePlotJMenuItem
```
bubbleScale
```
double bubbleScale
```
The scaling value for the bubbles.
bubbleScaleJMenuItem
```
JMenuItem bubbleScaleJMenuItem
```
chargeMenu
```
JMenu chargeMenu
```

chargeMenus

HashMap<Integer,JCheckBoxMenuItem> chargeMenus

The charge menus.

cIonCheckBoxMenuItem
```
JCheckBoxMenuItem cIonCheckBoxMenuItem
```
configurationFilesSettings
```
JMenuItem configurationFilesSettings
```
currentNotes
```
ArrayList<String> currentNotes
```
The list of current notes to the user.
currentTips
```
ArrayList<String> currentTips
```
The list of current tips to the user.
darkTheme
```
boolean darkTheme
```
Enable or disable the dark theme.

darkThemeCheckBoxMenuItem

JCheckBoxMenuItem darkThemeCheckBoxMenuItem

dataSaved
```
boolean dataSaved
```
If true, the latest changes have been saved.

defaultAnnotationCheckBoxMenuItem

JCheckBoxMenuItem defaultAnnotationCheckBoxMenuItem

deNovoChargeButtonGroup
```
ButtonGroup deNovoChargeButtonGroup
```

deNovoChargeOneJRadioButtonMenuItem

JRadioButtonMenuItem deNovoChargeOneJRadioButtonMenuItem

deNovoChargeTwoJRadioButtonMenuItem

JRadioButtonMenuItem deNovoChargeTwoJRadioButtonMenuItem

deNovoMenu
```
JMenu deNovoMenu
```
displayFeaturesGenerator
```
DisplayFeaturesGenerator displayFeaturesGenerator
```
The class used to provide graphical features.
editIdSettingsFilesMenuItem
```
JMenuItem editIdSettingsFilesMenuItem
```
editMenu
```
JMenu editMenu
```
EXAMPLE_DATASET_PATH
```
String EXAMPLE_DATASET_PATH
```
The path to the example dataset.

exceptionHandler

com.compomics.util.exceptions.exception_handlers.FrameExceptionHandler exceptionHandler

The exception handler

exitJMenuItem
```
JMenuItem exitJMenuItem
```
exportGraphicsMenu
```
JMenu exportGraphicsMenu
```

exportIntensityHistogramGraphicsJMenuItem

JMenuItem exportIntensityHistogramGraphicsJMenuItem

exportJMenu
```
JMenu exportJMenu
```

exportMassErrorPlotGraphicsJMenuItem

JMenuItem exportMassErrorPlotGraphicsJMenuItem

exportMzIdentMLMenuItem
```
JMenuItem exportMzIdentMLMenuItem
```
exportProjectMenuItem
```
JMenuItem exportProjectMenuItem
```

exportSequenceFragmentationGraphicsJMenuItem

JMenuItem exportSequenceFragmentationGraphicsJMenuItem

exportSpectrumAndPlotsGraphicsJMenuItem

JMenuItem exportSpectrumAndPlotsGraphicsJMenuItem

exportSpectrumGraphicsJMenuItem

JMenuItem exportSpectrumGraphicsJMenuItem

exportSpectrumGraphicsSeparator

JPopupMenu.Separator exportSpectrumGraphicsSeparator

exportSpectrumMenu
```
JMenu exportSpectrumMenu
```
exportSpectrumValuesJMenuItem
```
JMenuItem exportSpectrumValuesJMenuItem
```
fileJMenu
```
JMenu fileJMenu
```
findJMenuItem
```
JMenuItem findJMenuItem
```

fixedModsJCheckBoxMenuItem

JCheckBoxMenuItem fixedModsJCheckBoxMenuItem

followUpAnalysisMenuItem
```
JMenuItem followUpAnalysisMenuItem
```

forwardIonsDeNovoCheckBoxMenuItem

JCheckBoxMenuItem forwardIonsDeNovoCheckBoxMenuItem

fractionDetailsJMenuItem
```
JMenuItem fractionDetailsJMenuItem
```
gettingStartedMenuItem
```
JMenuItem gettingStartedMenuItem
```
goJPanel
```
JPanel goJPanel
```
goPanel
```
GOEAPanel goPanel
```
The GO Analysis panel.
helpJMenu
```
JMenu helpJMenu
```
helpJMenuItem
```
JMenuItem helpJMenuItem
```
helpMenu
```
JMenu helpMenu
```
helpMenuItem
```
JMenuItem helpMenuItem
```

highResAnnotationCheckBoxMenuItem

JCheckBoxMenuItem highResAnnotationCheckBoxMenuItem

identificationFeaturesMenuItem

JMenuItem identificationFeaturesMenuItem

immoniumIonsCheckMenu
```
JCheckBoxMenuItem immoniumIonsCheckMenu
```

intensityIonTableRadioButtonMenuItem

JRadioButtonMenuItem intensityIonTableRadioButtonMenuItem

ionsMenu
```
JMenu ionsMenu
```
ionTableButtonGroup
```
ButtonGroup ionTableButtonGroup
```
javaOptionsJMenuItem
```
JMenuItem javaOptionsJMenuItem
```
jSeparator1
```
JPopupMenu.Separator jSeparator1
```
jSeparator10
```
JPopupMenu.Separator jSeparator10
```
jSeparator11
```
JPopupMenu.Separator jSeparator11
```
jSeparator12
```
JPopupMenu.Separator jSeparator12
```
jSeparator13
```
JPopupMenu.Separator jSeparator13
```
jSeparator14
```
JPopupMenu.Separator jSeparator14
```
jSeparator15
```
JPopupMenu.Separator jSeparator15
```
jSeparator16
```
JPopupMenu.Separator jSeparator16
```
jSeparator17
```
JPopupMenu.Separator jSeparator17
```
jSeparator18
```
JPopupMenu.Separator jSeparator18
```
jSeparator19
```
JPopupMenu.Separator jSeparator19
```
jSeparator2
```
JPopupMenu.Separator jSeparator2
```
jSeparator20
```
JPopupMenu.Separator jSeparator20
```
jSeparator21
```
JPopupMenu.Separator jSeparator21
```
jSeparator3
```
JPopupMenu.Separator jSeparator3
```
jSeparator4
```
JPopupMenu.Separator jSeparator4
```
jSeparator5
```
JPopupMenu.Separator jSeparator5
```
jSeparator6
```
JPopupMenu.Separator jSeparator6
```
jSeparator7
```
JPopupMenu.Separator jSeparator7
```
jSeparator8
```
JPopupMenu.Separator jSeparator8
```
jSeparator9
```
JPopupMenu.Separator jSeparator9
```
jumpToPanel
```
JumpToPanel jumpToPanel
```
The Jump To panel.
lastSelectedFolder
```
com.compomics.util.io.file.LastSelectedFolder lastSelectedFolder
```
The last folder opened by the user. Defaults to user.home.
logReportMenu
```
JMenuItem logReportMenu
```
lossMenu
```
JMenu lossMenu
```

lossMenus

HashMap<com.compomics.util.experiment.biology.ions.NeutralLoss,JCheckBoxMenuItem> lossMenus

The neutral loss menus.

lossSplitter
```
JMenu lossSplitter
```
menuBar
```
JMenuBar menuBar
```
methodsSectionMenuItem
```
JMenuItem methodsSectionMenuItem
```

modificationFactory

com.compomics.util.experiment.biology.modifications.ModificationFactory modificationFactory

The modification factory.

modificationJPanel
```
JPanel modificationJPanel
```
modificationsPanel
```
ModificationsPanel modificationsPanel
```
The PTM panel.

mzIonTableRadioButtonMenuItem

JRadioButtonMenuItem mzIonTableRadioButtonMenuItem

newJMenuItem
```
JMenuItem newJMenuItem
```
newsButton
```
JButton newsButton
```
newTweets
```
ArrayList<String> newTweets
```
The list of new tweets.
notesButton
```
JButton notesButton
```
openExampleMenuItem
```
JMenuItem openExampleMenuItem
```
openingExistingProject
```
boolean openingExistingProject
```
True if an existing project is currently in the process of being opened.
openJMenuItem
```
JMenuItem openJMenuItem
```
openRecentJMenu
```
JMenu openRecentJMenu
```
otherMenu
```
JMenu otherMenu
```
overviewJPanel
```
JPanel overviewJPanel
```
overviewPanel
```
OverviewPanel overviewPanel
```
The overview panel.
overViewTabViewMenu
```
JMenu overViewTabViewMenu
```

peptidesAndPsmsJCheckBoxMenuItem

JCheckBoxMenuItem peptidesAndPsmsJCheckBoxMenuItem

precursorCheckMenu
```
JCheckBoxMenuItem precursorCheckMenu
```
preferencesMenuItem
```
JMenuItem preferencesMenuItem
```
privacyMenuItem
```
JMenuItem privacyMenuItem
```
processingMenuItem
```
JMenuItem processingMenuItem
```

processingParameters

com.compomics.util.parameters.tools.ProcessingParameters processingParameters

The processing preferences

progressDialog

com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog

A simple progress dialog.

projectExportMenu
```
JMenu projectExportMenu
```
projectPropertiesMenuItem
```
JMenuItem projectPropertiesMenuItem
```
projectSettingsMenuItem
```
JMenuItem projectSettingsMenuItem
```
proteinFractionsJPanel
```
JPanel proteinFractionsJPanel
```
proteinFractionsPanel
```
ProteinFractionsPanel proteinFractionsPanel
```
The protein fractions panel.

proteinsJCheckBoxMenuItem

JCheckBoxMenuItem proteinsJCheckBoxMenuItem

proteinStructureJPanel
```
JPanel proteinStructureJPanel
```
proteinStructurePanel
```
ProteinStructurePanel proteinStructurePanel
```
The protein structure panel.
psdbParent
```
PsdbParent psdbParent
```
The psdb parent used to manage the data.
psmSortOrderButtonGroup
```
ButtonGroup psmSortOrderButtonGroup
```
psmSortOrderMenu
```
JMenu psmSortOrderMenu
```

psmSortRtRadioButtonMenuItem

JRadioButtonMenuItem psmSortRtRadioButtonMenuItem

psmSortScoreRadioButtonMenuItem

JRadioButtonMenuItem psmSortScoreRadioButtonMenuItem

publishedTweets
```
ArrayList<String> publishedTweets
```
The list of already published tweets.
qcJPanel
```
JPanel qcJPanel
```
qcPanel
```
QCPanel qcPanel
```
The QC panel.
quantifyMenuItem
```
JMenuItem quantifyMenuItem
```
relatedIonsCheckMenu
```
JCheckBoxMenuItem relatedIonsCheckMenu
```
reporterIonsCheckMenu
```
JCheckBoxMenuItem reporterIonsCheckMenu
```
reporterPreferencesJMenuItem
```
JMenuItem reporterPreferencesJMenuItem
```
resetAnnotationMenu
```
JMenu resetAnnotationMenu
```
reshakeMenuItem
```
JMenuItem reshakeMenuItem
```

rewindIonsDeNovoCheckBoxMenuItem

JCheckBoxMenuItem rewindIonsDeNovoCheckBoxMenuItem

saveMenuItem
```
JMenuItem saveMenuItem
```
scoreAndConfidenceDecimalFormat
```
DecimalFormat scoreAndConfidenceDecimalFormat
```
The decimal format use for the score and confidence columns.

scoresJCheckBoxMenuItem

JCheckBoxMenuItem scoresJCheckBoxMenuItem

searchGuiPreferencesJMenuItem
```
JMenuItem searchGuiPreferencesJMenuItem
```
searchParametersMenu
```
JMenuItem searchParametersMenu
```
selectedPeptideKey
```
long selectedPeptideKey
```
The currently selected peptide key.
selectedProteinKey
```
long selectedProteinKey
```
The currently selected protein key.
selectedSpectrumFile
```
String selectedSpectrumFile
```
The currently selected spectrum file, null if none.
selectedSpectrumTitle
```
String selectedSpectrumTitle
```
The currently selected spectrum title, null if none.

sequenceCoverageJCheckBoxMenuItem

JCheckBoxMenuItem sequenceCoverageJCheckBoxMenuItem

settingsMenu
```
JMenu settingsMenu
```
sparklineColorsMenuItem
```
JMenuItem sparklineColorsMenuItem
```

sparklinesJCheckBoxMenuItem

JCheckBoxMenuItem sparklinesJCheckBoxMenuItem

speciesJMenuItem
```
JMenuItem speciesJMenuItem
```

spectrumIdentificationPanel

SpectrumIdentificationPanel spectrumIdentificationPanel

The spectrum panel.

spectrumJCheckBoxMenuItem

JCheckBoxMenuItem spectrumJCheckBoxMenuItem

spectrumJPanel
```
JPanel spectrumJPanel
```

spectrumSlidersCheckBoxMenuItem

JCheckBoxMenuItem spectrumSlidersCheckBoxMenuItem

splitterMenu2
```
JMenu splitterMenu2
```
splitterMenu3
```
JMenu splitterMenu3
```
splitterMenu4
```
JMenu splitterMenu4
```
splitterMenu5
```
JMenu splitterMenu5
```
splitterMenu6
```
JMenu splitterMenu6
```
splitterMenu7
```
JMenu splitterMenu7
```
splitterMenu8
```
JMenu splitterMenu8
```
splitterMenu9
```
JMenu splitterMenu9
```
starHideJMenuItem
```
JMenuItem starHideJMenuItem
```
starHider
```
StarHider starHider
```
Utility class to star or hide matches.
statsJPanel
```
JPanel statsJPanel
```
tipsButton
```
JButton tipsButton
```
toolsMenu
```
JMenu toolsMenu
```
updateNeeded
```
HashMap<Integer,Boolean> updateNeeded
```
Array containing the tab which must be updated as indexed by the static index. If true the whole panel will be reloaded, if false only the selection will be updated.

utilitiesUserParameters

com.compomics.util.parameters.UtilitiesUserParameters utilitiesUserParameters

The utilities user preferences.

validatedProteinsOnlyJCheckBoxMenuItem

JCheckBoxMenuItem validatedProteinsOnlyJCheckBoxMenuItem

validationPanel
```
ValidationPanel validationPanel
```
The statistics panel.
validationQcMenuItem
```
JMenuItem validationQcMenuItem
```
viewJMenu
```
JMenu viewJMenu
```
xIonCheckBoxMenuItem
```
JCheckBoxMenuItem xIonCheckBoxMenuItem
```
yIonCheckBoxMenuItem
```
JCheckBoxMenuItem yIonCheckBoxMenuItem
```
zIonCheckBoxMenuItem
```
JCheckBoxMenuItem zIonCheckBoxMenuItem
```

Class eu.isas.peptideshaker.gui.SaveDialog

class SaveDialog extends JDialog implements Serializable
- Serialized Fields
  - backgroundPanel
    
    JPanel backgroundPanel
  - exportJButton
    
    JButton exportJButton
  - exportPrideJButton
    
    JButton exportPrideJButton
  - exportPrideLabel
    
    JLabel exportPrideLabel
  - exportZipLabel
    
    JLabel exportZipLabel
  - peptideShakerGUI
    
    PeptideShakerGUI peptideShakerGUI
    
    The PeptideShaker parent frame.
  - saveJButton
    
    JButton saveJButton
  - saveLabel
    
    JLabel saveLabel

Class eu.isas.peptideshaker.gui.WelcomeDialog

class WelcomeDialog extends JDialog implements Serializable

Serialized Fields

aboutMenuItem
```
JMenuItem aboutMenuItem
```
backgroundPanel
```
JPanel backgroundPanel
```
bugReportMenuItem
```
JMenuItem bugReportMenuItem
```
compomicsButton
```
JButton compomicsButton
```
gettingStartedJButton1
```
JButton gettingStartedJButton1
```
gettingStartedMenuItem
```
JMenuItem gettingStartedMenuItem
```
helpMenu
```
JMenu helpMenu
```
isasButton
```
JButton isasButton
```
javaSettingsMenuItem
```
JMenuItem javaSettingsMenuItem
```
jSeparator1
```
JSeparator jSeparator1
```
jSeparator2
```
JPopupMenu.Separator jSeparator2
```
lowMemoryWarningLabel
```
JLabel lowMemoryWarningLabel
```
newJButton
```
JButton newJButton
```
openExampleDatasetJButton
```
JButton openExampleDatasetJButton
```
openJButton
```
JButton openJButton
```
pathSettingsMenu
```
JMenuItem pathSettingsMenu
```
peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
The PeptideShaker parent frame.
probeButton
```
JButton probeButton
```

progressDialog

com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog

The progress dialog.

quantifyJButton
```
JButton quantifyJButton
```
recentProjectsLabel
```
JLabel recentProjectsLabel
```
reshakeJButton
```
JButton reshakeJButton
```
searchGUISettingsMenuItem
```
JMenuItem searchGUISettingsMenuItem
```
searchJButton
```
JButton searchJButton
```
settingsLabel
```
JLabel settingsLabel
```
settingsMenu
```
JMenu settingsMenu
```
settingsPopupMenu
```
JPopupMenu settingsPopupMenu
```
toolsMenu
```
JMenu toolsMenu
```

Package eu.isas.peptideshaker.gui.export

Class eu.isas.peptideshaker.gui.export.FeaturesExportDialog

class FeaturesExportDialog extends JDialog implements Serializable

Serialized Fields

addReportLabel
```
JLabel addReportLabel
```
addReportMenuItem
```
JMenuItem addReportMenuItem
```
backgroundPanel
```
JPanel backgroundPanel
```
customReportsPanel
```
JPanel customReportsPanel
```
editReportMenuItem
```
JMenuItem editReportMenuItem
```
exitButton
```
JButton exitButton
```
exportFactory
```
PSExportFactory exportFactory
```
The export factory.
exportReportButton
```
JButton exportReportButton
```
exportSchemesNames
```
ArrayList<String> exportSchemesNames
```
List of the available export schemes.
featuresPanel
```
JPanel featuresPanel
```
helpJButton
```
JButton helpJButton
```
helpLabel
```
JLabel helpLabel
```
peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
PeptideShaker main GUI.
removeReportMenuItem
```
JMenuItem removeReportMenuItem
```
reportDocumentationMenuItem
```
JMenuItem reportDocumentationMenuItem
```
reportDocumentationPopupMenu
```
JPopupMenu reportDocumentationPopupMenu
```

reportPopUpMenuSeparator

JPopupMenu.Separator reportPopUpMenuSeparator

reportsTable
```
JTable reportsTable
```
reportsTableScrollPane
```
JScrollPane reportsTableScrollPane
```

Class eu.isas.peptideshaker.gui.export.FollowUpExportDialog

class FollowUpExportDialog extends JDialog implements Serializable

Serialized Fields

backgroundPanel
```
JPanel backgroundPanel
```

exportAllIdentifiedProteinAccessionsLabel

JLabel exportAllIdentifiedProteinAccessionsLabel

exportAllIdentifiedProteinsAsFastaLabel

JLabel exportAllIdentifiedProteinsAsFastaLabel

exportIdentifiedProteinAccessionNumbersAsCsvButton

JButton exportIdentifiedProteinAccessionNumbersAsCsvButton

exportIdentifiedProteinsAsFastaButton

JButton exportIdentifiedProteinsAsFastaButton

exportMgfButton
```
JButton exportMgfButton
```
exportProgenesisButton
```
JButton exportProgenesisButton
```
exportProteformsAsTxtButton
```
JButton exportProteformsAsTxtButton
```
exportSpectraLabel
```
JLabel exportSpectraLabel
```
exportToProgenesisLinkLabel
```
JLabel exportToProgenesisLinkLabel
```
graphDatabaseFormat
```
JComboBox graphDatabaseFormat
```
graphDatabasesLabel
```
JLabel graphDatabasesLabel
```
graphDatabasesPanel
```
JPanel graphDatabasesPanel
```
graphDatabasetButton
```
JButton graphDatabasetButton
```
includeValidatedPsmsLabel
```
JLabel includeValidatedPsmsLabel
```
inclusionListButton
```
JButton inclusionListButton
```
inclusionListFormat
```
JComboBox inclusionListFormat
```
inclusionListPanel
```
JPanel inclusionListPanel
```
peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
The main GUI.
progenesisPanel
```
JPanel progenesisPanel
```
proteinExportCmb1
```
JComboBox proteinExportCmb1
```
proteinExportCmb2
```
JComboBox proteinExportCmb2
```
proteinsPanel
```
JPanel proteinsPanel
```
proteoformsExportCmb
```
JComboBox proteoformsExportCmb
```
proteoformsLabel
```
JLabel proteoformsLabel
```
psmSelectionComboBox
```
JComboBox psmSelectionComboBox
```
recalibrateMgfButton
```
JButton recalibrateMgfButton
```
recalibrateSpectraLabel
```
JLabel recalibrateSpectraLabel
```
scrollPane
```
JScrollPane scrollPane
```
scrollPanel
```
JPanel scrollPanel
```
skylineExportButton
```
JButton skylineExportButton
```
skylineExportCmb
```
JComboBox skylineExportCmb
```
skylineExportLabel
```
JLabel skylineExportLabel
```
skylinePanel
```
JPanel skylinePanel
```
spectraPanel
```
JPanel spectraPanel
```
spectrumRecalibrationCmb
```
JComboBox spectrumRecalibrationCmb
```
spectrumValidationCmb
```
JComboBox spectrumValidationCmb
```
tppExportButton
```
JButton tppExportButton
```
tppExportCmb
```
JComboBox tppExportCmb
```
tppLabel
```
JLabel tppLabel
```
tppPanel
```
JPanel tppPanel
```
unipeptExportButton
```
JButton unipeptExportButton
```
unipeptiExportCmb
```
JComboBox unipeptiExportCmb
```
unipeptLabel
```
JLabel unipeptLabel
```
unipeptPanel
```
JPanel unipeptPanel
```

Class eu.isas.peptideshaker.gui.export.InclusionListExportDialog

class InclusionListExportDialog extends JDialog implements Serializable
- Serialized Fields
  - backgroundPanel
    
    JPanel backgroundPanel
  - cancelButton
    
    JButton cancelButton
  - degeneratedCheck
    
    JCheckBox degeneratedCheck
  - exportFormat
    
    InclusionListExport.ExportFormat exportFormat
    
    The export format.
  - followupPreferencesDialog
    
    FollowUpExportDialog followupPreferencesDialog
    
    References to the follow up export dialog.
  - jLabel1
    
    JLabel jLabel1
  - minRtWindowUnitLabel
    
    JLabel minRtWindowUnitLabel
  - miscleavedCheck
    
    JCheckBox miscleavedCheck
  - okButton
    
    JButton okButton
  - peptideFilterPanel
    
    JPanel peptideFilterPanel
  - proteinFilterPanel
    
    JPanel proteinFilterPanel
  - reactiveCheck
    
    JCheckBox reactiveCheck
  - relatedProteinsCheck
    
    JCheckBox relatedProteinsCheck
  - relatredAndUnrelatedCheck
    
    JCheckBox relatredAndUnrelatedCheck
  - rtFilterPanel
    
    JPanel rtFilterPanel
  - rtWindow
    
    JTextField rtWindow
  - unrelatedCheck
    
    JCheckBox unrelatedCheck

Class eu.isas.peptideshaker.gui.export.MethodsSectionDialog

class MethodsSectionDialog extends JDialog implements Serializable

Serialized Fields

algorithmsCheck
```
JCheckBox algorithmsCheck
```
backgroundPanel
```
JPanel backgroundPanel
```
cancelButton
```
JButton cancelButton
```
copyLbl
```
JLabel copyLbl
```
decoyCheck
```
JCheckBox decoyCheck
```
exportCoaLbl
```
JLabel exportCoaLbl
```
featuresPanel
```
JPanel featuresPanel
```
geneAnnotationCheck
```
JCheckBox geneAnnotationCheck
```
idParametersCheck
```
JCheckBox idParametersCheck
```
introductionPanel
```
JPanel introductionPanel
```
introductionTxt
```
JTextArea introductionTxt
```
jLabel1
```
JLabel jLabel1
```
jLabel2
```
JLabel jLabel2
```
jLabel3
```
JLabel jLabel3
```
jLabel4
```
JLabel jLabel4
```
jLabel5
```
JLabel jLabel5
```
jScrollPane1
```
JScrollPane jScrollPane1
```
okButton
```
JButton okButton
```
outputAreadScrollPane
```
JScrollPane outputAreadScrollPane
```
outputPanel
```
JPanel outputPanel
```
outputTextArea
```
JTextArea outputTextArea
```
peptideShakerCheck
```
JCheckBox peptideShakerCheck
```
peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
The main PeptideShaker frame.
proteinAbundanceIndexesCheck
```
JCheckBox proteinAbundanceIndexesCheck
```
proteinDbCkeck
```
JCheckBox proteinDbCkeck
```
ptmLocalizationCheck
```
JCheckBox ptmLocalizationCheck
```
pxCheck
```
JCheckBox pxCheck
```
searchGUICheck
```
JCheckBox searchGUICheck
```
validationCheck
```
JCheckBox validationCheck
```
waitingLabel
```
JLabel waitingLabel
```

Class eu.isas.peptideshaker.gui.export.MzIdentMLExportDialog

class MzIdentMLExportDialog extends JDialog implements Serializable

Serialized Fields

backgroundJPanel
```
JPanel backgroundJPanel
```
browseOutputFolderJButton
```
JButton browseOutputFolderJButton
```
contactAddressJTextField
```
JTextField contactAddressJTextField
```
contactAddressLabel
```
JLabel contactAddressLabel
```
contactEmailJTextField
```
JTextField contactEmailJTextField
```
contactEmailLabel
```
JLabel contactEmailLabel
```
contactFirstNameJTextField
```
JTextField contactFirstNameJTextField
```
contactFirstNameLabel
```
JLabel contactFirstNameLabel
```
contactLastNameJTextField
```
JTextField contactLastNameJTextField
```
contactLastNameLabel
```
JLabel contactLastNameLabel
```
contactPanel
```
JPanel contactPanel
```
contactUrlJTextField
```
JTextField contactUrlJTextField
```
contactUrlLabel
```
JLabel contactUrlLabel
```
convertJButton
```
JButton convertJButton
```
exportSdrf
```
boolean exportSdrf
```
Enables the export of an sdrf file next to the mzIdentML file.
helpLabel
```
JLabel helpLabel
```
includeSequencesCheckBox
```
JCheckBox includeSequencesCheckBox
```

mzIdentMLVersion

com.compomics.util.experiment.io.identification.MzIdentMLVersion mzIdentMLVersion

The version of mzIdentML to use.

openDialogHelpJButton
```
JButton openDialogHelpJButton
```

organizationAddressJTextField

JTextField organizationAddressJTextField

organizationAddressLabel
```
JLabel organizationAddressLabel
```
organizationEmailJTextField
```
JTextField organizationEmailJTextField
```
organizationEmailLabel
```
JLabel organizationEmailLabel
```
organizationNameJTextField
```
JTextField organizationNameJTextField
```
organizationNameLabel
```
JLabel organizationNameLabel
```
organizationPanel
```
JPanel organizationPanel
```
organizationUrlJTextField
```
JTextField organizationUrlJTextField
```
organizationUrlLabel
```
JLabel organizationUrlLabel
```
outputFolderJTextField
```
JTextField outputFolderJTextField
```
outputFolderLabel
```
JLabel outputFolderLabel
```
outputPanel
```
JPanel outputPanel
```
peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
The PeptideShakerGUI main class.
validateMzIdentML
```
boolean validateMzIdentML
```
If true, the created mzid file will be validated against the mzid 1.1 schema.

Class eu.isas.peptideshaker.gui.export.PtmSelectionDialog

class PtmSelectionDialog extends JDialog implements Serializable
- Serialized Fields
  - backgroundPanel
    
    JPanel backgroundPanel
  - cancelButton
    
    JButton cancelButton
  - canceled
    
    boolean canceled
    
    Boolean indicating whether the user canceled the input.
  - confidentCheck
    
    JCheckBox confidentCheck
  - modificationTable
    
    JTable modificationTable
  - modificationTableScrollPane
    
    JScrollPane modificationTableScrollPane
  - okButton
    
    JButton okButton
  - searchedModifications
    
    ArrayList<String> searchedModifications
    
    The modification profile used for the search.
  - selectedModifications
    
    ArrayList<String> selectedModifications
    
    The selected modifications.

Package eu.isas.peptideshaker.gui.filtering

Class eu.isas.peptideshaker.gui.filtering.FiltersDialog

class FiltersDialog extends JDialog implements Serializable

Serialized Fields

addHiddenPeptides
```
JButton addHiddenPeptides
```
addHiddenProtein
```
JButton addHiddenProtein
```
addHiddenPsm
```
JButton addHiddenPsm
```
addStarredPeptides
```
JButton addStarredPeptides
```
addStarredProtein
```
JButton addStarredProtein
```
addStarredPsm
```
JButton addStarredPsm
```
allModifications
```
ArrayList<String> allModifications
```
All the modifications that can be used for filtering.
backgroundPanel
```
JPanel backgroundPanel
```
cancelButton
```
JButton cancelButton
```
clearHiddenPeptides
```
JButton clearHiddenPeptides
```
clearHiddenProtein
```
JButton clearHiddenProtein
```
clearHiddenPsm
```
JButton clearHiddenPsm
```
clearStarredPeptides
```
JButton clearStarredPeptides
```
clearStarredProtein
```
JButton clearStarredProtein
```
clearStarredPsm
```
JButton clearStarredPsm
```
deleteHiddenPeptides
```
JButton deleteHiddenPeptides
```
deleteHiddenProtein
```
JButton deleteHiddenProtein
```
deleteHiddenPsm
```
JButton deleteHiddenPsm
```
deleteStarredPeptides
```
JButton deleteStarredPeptides
```
deleteStarredProtein
```
JButton deleteStarredProtein
```
deleteStarredPsm
```
JButton deleteStarredPsm
```
editHiddenPeptides
```
JButton editHiddenPeptides
```
editHiddenProtein
```
JButton editHiddenProtein
```
editHiddenPsm
```
JButton editHiddenPsm
```
editStarredPeptides
```
JButton editStarredPeptides
```
editStarredProtein
```
JButton editStarredProtein
```
editStarredPsm
```
JButton editStarredPsm
```
hiddenPeptidesPanel
```
JPanel hiddenPeptidesPanel
```
hiddenPeptidesScrollPane
```
JScrollPane hiddenPeptidesScrollPane
```
hiddenPeptidesTable
```
JTable hiddenPeptidesTable
```
hiddenProteinsPanel
```
JPanel hiddenProteinsPanel
```
hiddenProteinsScrollPane
```
JScrollPane hiddenProteinsScrollPane
```
hiddenProteinsTable
```
JTable hiddenProteinsTable
```
hiddenPsmsPanel
```
JPanel hiddenPsmsPanel
```
hiddenPsmsScrollPane
```
JScrollPane hiddenPsmsScrollPane
```
hiddenPsmTable
```
JTable hiddenPsmTable
```
okButton
```
JButton okButton
```
openDialogHelpJButton
```
JButton openDialogHelpJButton
```

peptideHideFilters

HashMap<String,com.compomics.util.experiment.identification.filtering.PeptideFilter> peptideHideFilters

The peptide hide filters.

peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
The main GUI.
peptidesSplitPane
```
JSplitPane peptidesSplitPane
```

peptideStarFilters

HashMap<String,com.compomics.util.experiment.identification.filtering.PeptideFilter> peptideStarFilters

The peptide star filters.

proteinHideFilters

HashMap<String,com.compomics.util.experiment.identification.filtering.ProteinFilter> proteinHideFilters

The protein hide filters.

proteinsSplitPane
```
JSplitPane proteinsSplitPane
```

proteinStarFilters

HashMap<String,com.compomics.util.experiment.identification.filtering.ProteinFilter> proteinStarFilters

The protein star filters.

psmHideFilters

HashMap<String,com.compomics.util.experiment.identification.filtering.PsmFilter> psmHideFilters

The PSM hide filters.

psmsSplitPane
```
JSplitPane psmsSplitPane
```

psmStarFilters

HashMap<String,com.compomics.util.experiment.identification.filtering.PsmFilter> psmStarFilters

The PSM star filters.

starredPeptidesPanel
```
JPanel starredPeptidesPanel
```
starredPeptidesScrollPane
```
JScrollPane starredPeptidesScrollPane
```
starredPeptidesTable
```
JTable starredPeptidesTable
```
starredProteinsPanel
```
JPanel starredProteinsPanel
```
starredProteinsScrollPane
```
JScrollPane starredProteinsScrollPane
```
starredProteinsTable
```
JTable starredProteinsTable
```
starredPsmsPanel
```
JPanel starredPsmsPanel
```
starredPsmsScrollPane
```
JScrollPane starredPsmsScrollPane
```
starredPsmTable
```
JTable starredPsmTable
```
tabbedPane
```
JTabbedPane tabbedPane
```

Package eu.isas.peptideshaker.gui.parameters
- Class eu.isas.peptideshaker.gui.parameters.DisplayPreferencesDialog
  
  class DisplayPreferencesDialog extends JDialog implements Serializable
  - Serialized Fields
    
    backgroundPanel
    
    JPanel backgroundPanel
    
    cancelButton
    
    JButton cancelButton
    
    canceled
    
    boolean canceled
    
    Boolean indicating whether the user canceled the editing.
    
    lowResolutionChartsComboBox
    
    JComboBox<String> lowResolutionChartsComboBox
    
    lowResolutionChartsLabel
    
    JLabel lowResolutionChartsLabel
    
    nAASpinner
    
    JSpinner nAASpinner
    
    okButton
    
    JButton okButton
    
    optionsPanel
    
    JPanel optionsPanel
    
    surroundingAminoAcidsLabel
    
    JLabel surroundingAminoAcidsLabel
- Class eu.isas.peptideshaker.gui.parameters.ProjectDetailsDialog
  
  class ProjectDetailsDialog extends JDialog implements Serializable
  - Serialized Fields
    
    backgroundPanel
    
    JPanel backgroundPanel
    
    closeButton
    
    JButton closeButton
    
    detailsPanel
    
    JPanel detailsPanel
    
    peptideShakerGUI
    
    PeptideShakerGUI peptideShakerGUI
    
    The PeptideShakerGUI.
    
    progressDialog
    
    com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog
    
    The progress dialog.
    
    projectDetailsJEditorPane
    
    JEditorPane projectDetailsJEditorPane
    
    projectDetailsJScrollPane
    
    JScrollPane projectDetailsJScrollPane
- Class eu.isas.peptideshaker.gui.parameters.ProjectParametersDialog
  
  class ProjectParametersDialog extends JDialog implements Serializable
  - Serialized Fields
    
    backgroundPanel
    
    JPanel backgroundPanel
    
    cancelButton
    
    JButton cancelButton
    
    canceled
    
    boolean canceled
    
    Boolean indicating whether the user canceled the edition of preferences.
    
    displayLbl
    
    JLabel displayLbl
    
    displayPreferences
    
    DisplayParameters displayPreferences
    
    The display preferences.
    
    editDisplayPreferencesButton
    
    JButton editDisplayPreferencesButton
    
    editSpectrumQuantificationButton
    
    JButton editSpectrumQuantificationButton
    
    helpJButton
    
    JButton helpJButton
    
    okButton
    
    JButton okButton
    
    parentFrame
    
    Frame parentFrame
    
    The parent frame.
    
    preferencesPanel
    
    JPanel preferencesPanel
    
    spectrumCountingPreferences
    
    com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences
    
    The spectrum counting preferences.
    
    spectrumQuantificationLbl
    
    JLabel spectrumQuantificationLbl
- Class eu.isas.peptideshaker.gui.parameters.SpectrumColorsDialog
  
  class SpectrumColorsDialog extends JDialog implements Serializable
  - Serialized Fields
    
    annotatedLabel
    
    JLabel annotatedLabel
    
    annotatedPeakColorPanel
    
    JPanel annotatedPeakColorPanel
    
    annotatedPeakWidthSpinner
    
    JSpinner annotatedPeakWidthSpinner
    
    annotatedWidthLabel
    
    JLabel annotatedWidthLabel
    
    annotationColorsPanel
    
    JPanel annotationColorsPanel
    
    backgroundLabel
    
    JLabel backgroundLabel
    
    backgroundPanel
    
    JPanel backgroundPanel
    
    backgroundPeakColorPanel
    
    JPanel backgroundPeakColorPanel
    
    backgroundPeakWidthSpinner
    
    JSpinner backgroundPeakWidthSpinner
    
    backgroundWidthLabel
    
    JLabel backgroundWidthLabel
    
    colorsScrollPane
    
    JScrollPane colorsScrollPane
    
    colorsTable
    
    JTable colorsTable
    
    helpJButton
    
    JButton helpJButton
    
    iontypes
    
    HashMap<com.compomics.util.experiment.biology.ions.Ion.IonType,HashSet<Integer>> iontypes
    
    The list of ion types.
    
    mirroredPeakColorLabel
    
    JLabel mirroredPeakColorLabel
    
    mirroredPeakColorPanel
    
    JPanel mirroredPeakColorPanel
    
    neutralLosses
    
    HashSet<String> neutralLosses
    
    The list of neutral losses.
    
    okButton
    
    JButton okButton
    
    peakColorsPanel
    
    JPanel peakColorsPanel
    
    peptideShakerGUI
    
    PeptideShakerGUI peptideShakerGUI
    
    A reference to PeptideShakerGUI.
- Class eu.isas.peptideshaker.gui.parameters.SpectrumCountingSettingsDialog
  
  class SpectrumCountingSettingsDialog extends JDialog implements Serializable
  - Serialized Fields
    
    backgroundPanel
    
    JPanel backgroundPanel
    
    cancelButton
    
    JButton cancelButton
    
    canceled
    
    boolean canceled
    
    Boolean indicating whether the user canceled the editing.
    
    helpJButton
    
    JButton helpJButton
    
    jLabel1
    
    JLabel jLabel1
    
    jLabel2
    
    JLabel jLabel2
    
    jSeparator1
    
    JSeparator jSeparator1
    
    methodCmb
    
    JComboBox methodCmb
    
    normalizationCmb
    
    JComboBox normalizationCmb
    
    normalizationPanel
    
    JPanel normalizationPanel
    
    okButton
    
    JButton okButton
    
    parentFrame
    
    Frame parentFrame
    
    The parent frame.
    
    quantificationOptionsPanel
    
    JPanel quantificationOptionsPanel
    
    referenceLbl
    
    JLabel referenceLbl
    
    referenceTxt
    
    JTextField referenceTxt
    
    unitCmb
    
    JComboBox unitCmb
    
    unitLbl
    
    JLabel unitLbl
    
    validationLevelCmb
    
    JComboBox validationLevelCmb
    
    validationLevelLbl
    
    JLabel validationLevelLbl
Package eu.isas.peptideshaker.gui.pride
- Class eu.isas.peptideshaker.gui.pride.DatabaseHelpDialog
  
  class DatabaseHelpDialog extends JDialog implements Serializable
  - Serialized Fields
    
    backgroundPanel
    
    JPanel backgroundPanel
    
    browseDatabaseSettings
    
    JButton browseDatabaseSettings
    
    cancelButton
    
    JButton cancelButton
    
    databaseHelpSettingsJLabel
    
    JLabel databaseHelpSettingsJLabel
    
    dataBasePanelSettings
    
    JPanel dataBasePanelSettings
    
    databaseSettingsLbl
    
    JLabel databaseSettingsLbl
    
    databaseSettingsTxt
    
    JTextField databaseSettingsTxt
    
    downloadUniProtJLabel
    
    JLabel downloadUniProtJLabel
    
    fastaParameters
    
    com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters
    
    The FASTA parameters.
    
    lastSelectedFolder
    
    com.compomics.util.io.file.LastSelectedFolder lastSelectedFolder
    
    The last selected folder.
    
    okButton
    
    JButton okButton
    
    selectedFastaFile
    
    String selectedFastaFile
    
    The path to the selected FASTA file.
    
    species
    
    String species
    
    The current species, can be null.
    
    speciesAndTaxonomyJPanel
    
    JPanel speciesAndTaxonomyJPanel
    
    speciesJTextField
    
    JTextField speciesJTextField
    
    speciesLabel
    
    JLabel speciesLabel
    
    targetDecoySettingsButton
    
    JButton targetDecoySettingsButton
    
    taxonomyJTextField
    
    JTextField taxonomyJTextField
    
    taxonomyLabel
    
    JLabel taxonomyLabel
    
    utilitiesUserParameters
    
    com.compomics.util.parameters.UtilitiesUserParameters utilitiesUserParameters
    
    The utilities user parameters.
- Class eu.isas.peptideshaker.gui.pride.PrideDataTypeSelectionDialog
  
  class PrideDataTypeSelectionDialog extends JDialog implements Serializable
  - Serialized Fields
    
    backgroundPanel
    
    JPanel backgroundPanel
    
    contentWarningLabel
    
    JLabel contentWarningLabel
    
    isCanceled
    
    boolean isCanceled
    
    True of the dialog was canceled by the user.
    
    loadPublicData
    
    boolean loadPublicData
    
    Set if public or private data is to be loaded.
    
    privateDataJButton
    
    JButton privateDataJButton
    
    publicDataJButton
    
    JButton publicDataJButton
    
    saveLabel
    
    JLabel saveLabel
    
    saveLabel1
    
    JLabel saveLabel1
- Class eu.isas.peptideshaker.gui.pride.PrideFreeTextSearchDialog
  
  class PrideFreeTextSearchDialog extends JDialog implements Serializable
  - Serialized Fields
    
    backgroundPanel
    
    JPanel backgroundPanel
    
    cancelButton
    
    JButton cancelButton
    
    helpLabel
    
    JLabel helpLabel
    
    okButton
    
    JButton okButton
    
    searchPanel
    
    JPanel searchPanel
    
    searchTextField
    
    JTextField searchTextField
- Class eu.isas.peptideshaker.gui.pride.PridePrivateDataDialog
  
  class PridePrivateDataDialog extends JDialog implements Serializable
  - Serialized Fields
    
    accessionLabel
    
    JLabel accessionLabel
    
    accessionTextField
    
    JTextField accessionTextField
    
    backgroundPanel
    
    JPanel backgroundPanel
    
    cancelButton
    
    JButton cancelButton
    
    okButton
    
    JButton okButton
    
    password
    
    String password
    
    The password.
    
    passwordField
    
    JPasswordField passwordField
    
    passwordLabel
    
    JLabel passwordLabel
    
    projectAccession
    
    String projectAccession
    
    The project accession.
    
    projectPanel
    
    JPanel projectPanel
    
    userDetailsPanel
    
    JPanel userDetailsPanel
    
    userName
    
    String userName
    
    The user name.
    
    userNameLabel
    
    JLabel userNameLabel
    
    userNameTextField
    
    JTextField userNameTextField
- Class eu.isas.peptideshaker.gui.pride.PrideReshakeGUI
  
  class PrideReshakeGUI extends JFrame implements Serializable
  - Serialized Fields
    
    aboutButton
    
    JButton aboutButton
    
    accessPrivateDataLabel
    
    JLabel accessPrivateDataLabel
    
    assayClusterAnnotation
    
    HashMap<String,Integer> assayClusterAnnotation
    
    The assay cluster annotation.
    
    assayHelpLabel
    
    JLabel assayHelpLabel
    
    assaysGreaterThanFiler
    
    boolean assaysGreaterThanFiler
    
    The assay number filter type. True means greater than, false means smaller than.
    
    assaysPanel
    
    JPanel assaysPanel
    
    assaysTable
    
    JTable assaysTable
    
    assaysTableToolTips
    
    ArrayList<String> assaysTableToolTips
    
    The assay table column header tooltips.
    
    assayTableScrollPane
    
    JScrollPane assayTableScrollPane
    
    backgroundPanel
    
    JPanel backgroundPanel
    
    browsePublicDataLabel
    
    JLabel browsePublicDataLabel
    
    clearProjectFiltersLabel
    
    JLabel clearProjectFiltersLabel
    
    currentFilterValues
    
    String[] currentFilterValues
    
    The current filter values.
    
    currentMgfFile
    
    File currentMgfFile
    
    The current mgf file.
    
    currentPrideDataFile
    
    File currentPrideDataFile
    
    The current PRIDE XML file.
    
    currentPrideDataFileUrl
    
    URL currentPrideDataFileUrl
    
    The URL of the current PRIDE project.
    
    currentSpecies
    
    String currentSpecies
    
    The currently selected species.
    
    currentZippedPrideDataFile
    
    File currentZippedPrideDataFile
    
    The current zipped PRIDE XML file.
    
    dataTypeSeparatorLabel
    
    JLabel dataTypeSeparatorLabel
    
    dateFormat
    
    SimpleDateFormat dateFormat
    
    The data format.
    
    downloadAllLabel
    
    JLabel downloadAllLabel
    
    downloadSelectedLabel
    
    JLabel downloadSelectedLabel
    
    editMenu
    
    JMenu editMenu
    
    exitMenuItem
    
    JMenuItem exitMenuItem
    
    fileMenu
    
    JMenu fileMenu
    
    filesHelpLabel
    
    JLabel filesHelpLabel
    
    filesPanel
    
    JPanel filesPanel
    
    filesTable
    
    JTable filesTable
    
    filesTableScrollPane
    
    JScrollPane filesTableScrollPane
    
    filesTableToolTips
    
    ArrayList<String> filesTableToolTips
    
    The files table column header tooltips.
    
    findMenuItem
    
    JMenuItem findMenuItem
    
    helpMenu
    
    JMenu helpMenu
    
    helpMenuItem
    
    JMenuItem helpMenuItem
    
    identificationParametersFactory
    
    com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory identificationParametersFactory
    
    The identification parameters factory.
    
    instrumentsAll
    
    ArrayList<String> instrumentsAll
    
    The list of all found instruments.
    
    maxPrecursorCharge
    
    Integer maxPrecursorCharge
    
    The maximum precursor charge detected in the PRIDE XML files.
    
    menuBar
    
    JMenuBar menuBar
    
    minPrecursorCharge
    
    Integer minPrecursorCharge
    
    The minimum precursor charge detected in the PRIDE XML files.
    
    outputFolder
    
    String outputFolder
    
    The output folder for the mgfs and spectrum properties.
    
    password
    
    String password
    
    The password.
    
    peptideShakerGUI
    
    PeptideShakerGUI peptideShakerGUI
    
    The PeptideShakerGUI parent.
    
    peptideShakerPublicationLabel
    
    JLabel peptideShakerPublicationLabel
    
    prideParametersReport
    
    String prideParametersReport
    
    The PRIDE search parameters report.
    
    prideReshakeSetupDialog
    
    PrideReshakeSetupDialog prideReshakeSetupDialog
    
    The Reshake setup dialog.
    
    progressDialog
    
    com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog
    
    The progress dialog.
    
    projectClusterAnnotation
    
    HashMap<String,Integer> projectClusterAnnotation
    
    The project cluster annotation.
    
    projectHelpLabel
    
    JLabel projectHelpLabel
    
    projectSearchLabel
    
    JLabel projectSearchLabel
    
    projectsPanel
    
    JPanel projectsPanel
    
    projectsScrollPane
    
    JScrollPane projectsScrollPane
    
    projectsTable
    
    JTable projectsTable
    
    projectsTableToolTips
    
    ArrayList<String> projectsTableToolTips
    
    The project table column header tooltips.
    
    projectTagsAll
    
    ArrayList<String> projectTagsAll
    
    The list of all found project tags.
    
    ptmFactory
    
    com.compomics.util.experiment.biology.modifications.ModificationFactory ptmFactory
    
    The PTM factory.
    
    ptmsAll
    
    ArrayList<String> ptmsAll
    
    The list of all found PTMs.
    
    reshakableCheckBox
    
    JCheckBox reshakableCheckBox
    
    reshakeableFiles
    
    HashMap<String,ArrayList<String>> reshakeableFiles
    
    The list of reshakeable files.
    
    reshakeButton
    
    JButton reshakeButton
    
    searchSettingsFiles
    
    HashMap<String,ArrayList<String>> searchSettingsFiles
    
    The list of files where search settings can be extracted.
    
    speciesAll
    
    ArrayList<String> speciesAll
    
    The list of all found species.
    
    tissuesAll
    
    ArrayList<String> tissuesAll
    
    The list of all found tissues.
    
    userName
    
    String userName
    
    The user name.
    
    welcomeDialog
    
    WelcomeDialog welcomeDialog
- Class eu.isas.peptideshaker.gui.pride.PrideReshakeSetupDialog
  
  class PrideReshakeSetupDialog extends JDialog implements Serializable
  - Serialized Fields
    
    aboutButton
    
    JButton aboutButton
    
    backgroundPanel
    
    JPanel backgroundPanel
    
    browseDatabaseSettingsButton
    
    JButton browseDatabaseSettingsButton
    
    browseWorkingFolderButton
    
    JButton browseWorkingFolderButton
    
    databasePanel
    
    JPanel databasePanel
    
    databaseSettingsLbl
    
    JLabel databaseSettingsLbl
    
    databaseSettingsTxt
    
    JTextField databaseSettingsTxt
    
    dataTypeSeparatorLabel
    
    JLabel dataTypeSeparatorLabel
    
    deselectAllLabel
    
    JLabel deselectAllLabel
    
    downloadUniProtJLabel
    
    JLabel downloadUniProtJLabel
    
    filesTableToolTips
    
    ArrayList<String> filesTableToolTips
    
    The files table column header tooltips.
    
    isFileBeingDownloaded
    
    boolean isFileBeingDownloaded
    
    True if a file is currently being downloaded.
    
    lastSelectedFolder
    
    com.compomics.util.io.file.LastSelectedFolder lastSelectedFolder
    
    The last selected folder.
    
    peptideShakerHomePageLabel
    
    JLabel peptideShakerHomePageLabel
    
    prideReShakeGUI
    
    PrideReshakeGUI prideReShakeGUI
    
    The PrideReshakeGUI parent.
    
    reshakeButton
    
    JButton reshakeButton
    
    searchSettingsLabel
    
    JLabel searchSettingsLabel
    
    searchSettingsPanel
    
    JPanel searchSettingsPanel
    
    searchSettingsScrollPane
    
    JScrollPane searchSettingsScrollPane
    
    searchSettingsTable
    
    JTable searchSettingsTable
    
    selectAllLabel
    
    JLabel selectAllLabel
    
    speciesJTextField
    
    JTextField speciesJTextField
    
    speciesLabel
    
    JLabel speciesLabel
    
    spectrumLabel
    
    JLabel spectrumLabel
    
    spectrumPanel
    
    JPanel spectrumPanel
    
    spectrumTable
    
    JTable spectrumTable
    
    spectrumTableScrollPane
    
    JScrollPane spectrumTableScrollPane
    
    workingFolderLbl
    
    JLabel workingFolderLbl
    
    workingFolderPanel
    
    JPanel workingFolderPanel
    
    workingFolderTxt
    
    JTextField workingFolderTxt
- Class eu.isas.peptideshaker.gui.pride.PrideSearchParametersDialog
  
  class PrideSearchParametersDialog extends JDialog implements Serializable
  - Serialized Fields
    
    backgroundPanel
    
    JPanel backgroundPanel
    
    cancelButton
    
    JButton cancelButton
    
    fastaFile
    
    File fastaFile
    
    The FASTA file.
    
    infoLabel
    
    JLabel infoLabel
    
    jSeparator1
    
    JSeparator jSeparator1
    
    okButton
    
    JButton okButton
    
    prideReShakeGUI
    
    PrideReshakeGUI prideReShakeGUI
    
    Reference to the main frame.
    
    prideSearchParametersFile
    
    File prideSearchParametersFile
    
    The extracted search parameters file.
    
    psProjectName
    
    String psProjectName
    
    The PeptideShaker project name.
    
    rawFiles
    
    ArrayList<File> rawFiles
    
    The raw files.
    
    searchParametersReportEditorPane
    
    JEditorPane searchParametersReportEditorPane
    
    searchParametersReportScrollPane
    
    JScrollPane searchParametersReportScrollPane
    
    species
    
    String species
    
    The species for the PRIDE project.
    
    speciesType
    
    String speciesType
    
    The species type for the PRIDE project.
    
    spectrumFiles
    
    ArrayList<File> spectrumFiles
    
    The spectrum files.
- Class eu.isas.peptideshaker.gui.pride.ProjectsFilterDialog
  
  class ProjectsFilterDialog extends JDialog implements Serializable
  - Serialized Fields
    
    accessionJTextField
    
    JTextField accessionJTextField
    
    accessionLabel
    
    JLabel accessionLabel
    
    assaysComboBox
    
    JComboBox assaysComboBox
    
    assaysJTextField
    
    JTextField assaysJTextField
    
    assaysLabel
    
    JLabel assaysLabel
    
    backgroundPanel
    
    JPanel backgroundPanel
    
    categoryComboBox
    
    JComboBox categoryComboBox
    
    categoryLabel
    
    JLabel categoryLabel
    
    clearJButton
    
    JButton clearJButton
    
    filterPanel
    
    JPanel filterPanel
    
    instrumentLabel
    
    JLabel instrumentLabel
    
    instrumentsComboBox
    
    JComboBox instrumentsComboBox
    
    keyPressedCounter
    
    int keyPressedCounter
    
    Counts the number of times the users has pressed a key on the keyboard in the search field.
    
    okJButton
    
    JButton okJButton
    
    prideReShakeGUI
    
    PrideReshakeGUI prideReShakeGUI
    
    The PrideReshakeGUI parent frame.
    
    projectSearchLabel
    
    JLabel projectSearchLabel
    
    projectsTable
    
    JTable projectsTable
    
    The projects table.
    
    ptmsComboBox
    
    JComboBox ptmsComboBox
    
    ptmsLabel
    
    JLabel ptmsLabel
    
    speciesComboBox
    
    JComboBox speciesComboBox
    
    speciesLabel
    
    JLabel speciesLabel
    
    tagsComboBox
    
    JComboBox tagsComboBox
    
    tagsLabel
    
    JLabel tagsLabel
    
    tissueLabel
    
    JLabel tissueLabel
    
    tissuesComboBox
    
    JComboBox tissuesComboBox
    
    titleJTextField
    
    JTextField titleJTextField
    
    titleLabel
    
    JLabel titleLabel
    
    typeComboBox
    
    JComboBox typeComboBox
    
    typeLabel
    
    JLabel typeLabel
    
    waitingTime
    
    int waitingTime
    
    The time to wait between keys typed before updating the search.
Package eu.isas.peptideshaker.gui.protein_inference
- Class eu.isas.peptideshaker.gui.protein_inference.ProteinInferenceDialog
  
  class ProteinInferenceDialog extends JDialog implements Serializable
  - Serialized Fields
    
    accessions
    
    String[] accessions
    
    The protein accessions.
    
    associatedMatches
    
    long[] associatedMatches
    
    Associated matches presenting the same proteins or a share.
    
    backgroundPanel
    
    JPanel backgroundPanel
    
    candidateProteinsTableToolTips
    
    ArrayList<String> candidateProteinsTableToolTips
    
    The candidate protein table column header tooltips.
    
    detailsPanel
    
    JPanel detailsPanel
    
    geneMaps
    
    com.compomics.util.experiment.biology.genes.GeneMaps geneMaps
    
    The gene maps
    
    graphInnerPanel
    
    JPanel graphInnerPanel
    
    graphPanel
    
    JPanel graphPanel
    
    groupClassJComboBox
    
    JComboBox groupClassJComboBox
    
    groupDetalsJPanel
    
    JPanel groupDetalsJPanel
    
    helpJButton
    
    JButton helpJButton
    
    identification
    
    com.compomics.util.experiment.identification.Identification identification
    
    The identification.
    
    inspectedMatch
    
    com.compomics.util.experiment.identification.matches.ProteinMatch inspectedMatch
    
    The inspected protein match.
    
    okButton
    
    JButton okButton
    
    peptideShakerGUI
    
    PeptideShakerGUI peptideShakerGUI
    
    The PeptideShaker parent frame.
    
    previousMainMatch
    
    String previousMainMatch
    
    The selected main match.
    
    proteinMatchJPanel
    
    JPanel proteinMatchJPanel
    
    proteinMatchJScrollPane
    
    JScrollPane proteinMatchJScrollPane
    
    proteinMatchTable
    
    JTable proteinMatchTable
    
    relatedHitsJPanel
    
    JPanel relatedHitsJPanel
    
    relatedHitsJScrollPane
    
    JScrollPane relatedHitsJScrollPane
    
    relatedHitsTable
    
    JTable relatedHitsTable
    
    relatedHitsTableToolTips
    
    ArrayList<String> relatedHitsTableToolTips
    
    The related hits table column header tooltips.
    
    tabbedPane
    
    JTabbedPane tabbedPane
    
    uniqueHitsJPanel
    
    JPanel uniqueHitsJPanel
    
    uniqueHitsJScrollPane
    
    JScrollPane uniqueHitsJScrollPane
    
    uniqueHitsTable
    
    JTable uniqueHitsTable
    
    uniqueHitsTableToolTips
    
    ArrayList<String> uniqueHitsTableToolTips
    
    The unique hits table column header tooltips.
    
    uniqueMatches
    
    long[] uniqueMatches
    
    The detected unique matches (if any).
- Class eu.isas.peptideshaker.gui.protein_inference.ProteinInferenceGraphLegendDialog
  
  class ProteinInferenceGraphLegendDialog extends JDialog implements Serializable
  - Serialized Fields
    
    backgroundPanel
    
    JPanel backgroundPanel
    
    legendButton
    
    JButton legendButton
- Class eu.isas.peptideshaker.gui.protein_inference.ProteinInferenceGraphPanel
  
  class ProteinInferenceGraphPanel extends JPanel implements Serializable
  - Serialized Fields
    
    allRadioButton
    
    JRadioButton allRadioButton
    
    annotationButtonGroup
    
    ButtonGroup annotationButtonGroup
    
    edgePaint
    
    org.apache.commons.collections15.Transformer<String,Paint> edgePaint
    
    The color formatting for the edges.
    
    edgeProperties
    
    HashMap<String,String> edgeProperties
    
    The edge properties: the keys are the edge names.
    
    edges
    
    HashMap<String,ArrayList<String>> edges
    
    The edges: the keys are the node labels and the elements the list of objects.
    
    edgeStroke
    
    org.apache.commons.collections15.Transformer<String,Stroke> edgeStroke
    
    The stroke type for the edges.
    
    evidenceRadioButton
    
    JRadioButton evidenceRadioButton
    
    exportLabel
    
    JLabel exportLabel
    
    graph
    
    edu.uci.ics.jung.graph.UndirectedSparseGraph<String,String> graph
    
    The graph.
    
    graphPanel
    
    JPanel graphPanel
    
    helpLabel
    
    JLabel helpLabel
    
    highlightCheckBox
    
    JCheckBox highlightCheckBox
    
    lastSelectedFolder
    
    com.compomics.util.io.file.LastSelectedFolder lastSelectedFolder
    
    The last folder opened by the user.
    
    layoutLabel
    
    JLabel layoutLabel
    
    legendLabel
    
    JLabel legendLabel
    
    nodeProperties
    
    HashMap<String,String> nodeProperties
    
    The node properties: the keys are the node names.
    
    nodes
    
    ArrayList<String> nodes
    
    The nodes.
    
    nodeToolTips
    
    HashMap<String,String> nodeToolTips
    
    The node tooltips: the keys are the node names.
    
    nodeTypeRadioButton
    
    JRadioButton nodeTypeRadioButton
    
    normalIcon
    
    Image normalIcon
    
    The normal icon.
    
    parentDialog
    
    JDialog parentDialog
    
    The parent dialog.
    
    parentPanel
    
    JPanel parentPanel
    
    The parent panel.
    
    peptideCountLabel
    
    JLabel peptideCountLabel
    
    peptideCountValueLabel
    
    JLabel peptideCountValueLabel
    
    proteinCountLabel
    
    JLabel proteinCountLabel
    
    proteinCountValueLabel
    
    JLabel proteinCountValueLabel
    
    selectAllLabel
    
    JLabel selectAllLabel
    
    selectedEdges
    
    ArrayList<String> selectedEdges
    
    The labels of the currently selected edges.
    
    selectedNeighborNodes
    
    ArrayList<String> selectedNeighborNodes
    
    The labels of the currently selected neighbor nodes.
    
    selectedNodes
    
    ArrayList<String> selectedNodes
    
    The labels of the currently selected nodes.
    
    selectionButtonGroup
    
    ButtonGroup selectionButtonGroup
    
    selectionPanel
    
    JPanel selectionPanel
    
    settingsPanel
    
    JPanel settingsPanel
    
    showPeptideLabels
    
    boolean showPeptideLabels
    
    Set if if the peptide labels are to be shown.
    
    showPeptideLabelsLabel
    
    JLabel showPeptideLabelsLabel
    
    showProteinLabels
    
    boolean showProteinLabels
    
    Set if if the protein labels are to be shown.
    
    showProteinLabelsLabel
    
    JLabel showProteinLabelsLabel
    
    uniqueRadioButton
    
    JRadioButton uniqueRadioButton
    
    validationStatusRadioButton
    
    JRadioButton validationStatusRadioButton
    
    visualizationViewer
    
    edu.uci.ics.jung.visualization.VisualizationViewer visualizationViewer
    
    The visualization viewer.
    
    waitingIcon
    
    Image waitingIcon
    
    The waiting icon.
- Class eu.isas.peptideshaker.gui.protein_inference.ProteinInferenceGraphSelectionDialog
  
  class ProteinInferenceGraphSelectionDialog extends JDialog implements Serializable
  - Serialized Fields
    
    backgroundPanel
    
    JPanel backgroundPanel
    
    okButton
    
    JButton okButton
    
    valuesEditorPane
    
    JEditorPane valuesEditorPane
    
    valuesPanel
    
    JPanel valuesPanel
    
    valuesScrollPane
    
    JScrollPane valuesScrollPane
- Class eu.isas.peptideshaker.gui.protein_inference.ProteinInferencePeptideLevelDialog
  
  class ProteinInferencePeptideLevelDialog extends JDialog implements Serializable
  - Serialized Fields
    
    backgroundPanel
    
    JPanel backgroundPanel
    
    detailsPanel
    
    JPanel detailsPanel
    
    graphInnerPanel
    
    JPanel graphInnerPanel
    
    graphPanel
    
    JPanel graphPanel
    
    helpJButton
    
    JButton helpJButton
    
    identification
    
    com.compomics.util.experiment.identification.Identification identification
    
    The identification object used to retrieve matches.
    
    okButton
    
    JButton okButton
    
    otherProteinJTable
    
    JTable otherProteinJTable
    
    otherProteinsJScrollPane
    
    JScrollPane otherProteinsJScrollPane
    
    otherProteinsPanel
    
    JPanel otherProteinsPanel
    
    otherProteinsTableToolTips
    
    ArrayList<String> otherProteinsTableToolTips
    
    The other proteins table column header tooltips.
    
    peptideDetailsPanel
    
    JPanel peptideDetailsPanel
    
    peptideMatchKey
    
    long peptideMatchKey
    
    The key of the peptide match of interest.
    
    peptideSequenceLabel
    
    JLabel peptideSequenceLabel
    
    peptideShakerGUI
    
    PeptideShakerGUI peptideShakerGUI
    
    The PeptideShakerGUI parent.
    
    peptidesPanel
    
    JPanel peptidesPanel
    
    proteinsJScrollPane
    
    JScrollPane proteinsJScrollPane
    
    protInferenceTypeCmb
    
    JComboBox protInferenceTypeCmb
    
    retainedProteinJTable
    
    JTable retainedProteinJTable
    
    retainedProteinsPanel
    
    JPanel retainedProteinsPanel
    
    retainedProteinsTableToolTips
    
    ArrayList<String> retainedProteinsTableToolTips
    
    The retained proteins table column header tooltips.
    
    tabbedPane
    
    JTabbedPane tabbedPane
Package eu.isas.peptideshaker.gui.start
- Class eu.isas.peptideshaker.gui.start.GettingStartedDialog
  
  class GettingStartedDialog extends JDialog implements Serializable
  - Serialized Fields
    
    backButton
    
    JButton backButton
    
    backgroundPanel
    
    JPanel backgroundPanel
    
    buttonsAndLinksPanel
    
    JPanel buttonsAndLinksPanel
    
    compomicsButton
    
    JButton compomicsButton
    
    currentDisplayPanelIndex
    
    int currentDisplayPanelIndex
    
    The index of the currently selected panel.
    
    displayPanel
    
    JPanel displayPanel
    
    displayPanels
    
    ArrayList<ImageIconPanel> displayPanels
    
    The panels containing the getting started information.
    
    isasButton
    
    JButton isasButton
    
    jSeparator
    
    JSeparator jSeparator
    
    nextButton
    
    JButton nextButton
    
    peptideShakerGUI
    
    PeptideShakerGUI peptideShakerGUI
    
    A reference to PeptideShakerGUI.
    
    probeButton
    
    JButton probeButton
    
    welcomeDialog
    
    WelcomeDialog welcomeDialog
    
    A reference to the WelcomeDialog, can be null.
Package eu.isas.peptideshaker.gui.tablemodels
- Class eu.isas.peptideshaker.gui.tablemodels.PeptideFractionTableModel
  
  class PeptideFractionTableModel extends DefaultTableModel implements Serializable
  - Serialized Fields
    
    displayFeaturesGenerator
    
    DisplayFeaturesGenerator displayFeaturesGenerator
    
    The display features generator.
    
    fileNames
    
    ArrayList<String> fileNames
    
    A list of ordered file names.
    
    identification
    
    com.compomics.util.experiment.identification.Identification identification
    
    The identification of this project.
    
    peptideKeys
    
    ArrayList<Long> peptideKeys
    
    A list of ordered peptide keys.
- Class eu.isas.peptideshaker.gui.tablemodels.PeptideTableModel
  
  class PeptideTableModel extends com.compomics.util.gui.tablemodels.SelfUpdatingTableModel implements Serializable
  - Serialized Fields
    
    displayFeaturesGenerator
    
    DisplayFeaturesGenerator displayFeaturesGenerator
    
    The display features generator.
    
    exceptionHandler
    
    com.compomics.util.exceptions.ExceptionHandler exceptionHandler
    
    The exception handler catches exceptions.
    
    identification
    
    com.compomics.util.experiment.identification.Identification identification
    
    The identification.
    
    identificationFeaturesGenerator
    
    com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator
    
    The identification features generator.
    
    peptideKeys
    
    long[] peptideKeys
    
    A list of ordered peptide keys.
    
    proteinAccession
    
    String proteinAccession
    
    The main accession of the protein match to which the list of peptides is attached.
    
    showScores
    
    boolean showScores
    
    Indicates whether the scores should be displayed instead of the confidence.
- Class eu.isas.peptideshaker.gui.tablemodels.ProteinFractionTableModel
  
  class ProteinFractionTableModel extends DefaultTableModel implements Serializable
  - Serialized Fields
    
    fileNames
    
    ArrayList<String> fileNames
    
    A list of ordered file names.
    
    identification
    
    com.compomics.util.experiment.identification.Identification identification
    
    The identification of this project.
    
    modelInitiated
    
    boolean modelInitiated
    
    Set to true as soon as the real model is initiated. False means that only the dummy constructor has been used.
    
    peptideShakerGUI
    
    PeptideShakerGUI peptideShakerGUI
    
    The main GUI class.
    
    proteinKeys
    
    long[] proteinKeys
    
    A list of ordered protein keys.
- Class eu.isas.peptideshaker.gui.tablemodels.ProteinGoTableModel
  
  class ProteinGoTableModel extends DefaultTableModel implements Serializable
  - Serialized Fields
    
    displayFeaturesGenerator
    
    DisplayFeaturesGenerator displayFeaturesGenerator
    
    The display features generator.
    
    identification
    
    com.compomics.util.experiment.identification.Identification identification
    
    The identification of this project.
    
    identificationFeaturesGenerator
    
    com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator
    
    The identification features generator.
    
    proteinDetailsProvider
    
    com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider
    
    The protein details provider.
    
    proteinGroupKeys
    
    ArrayList<Long> proteinGroupKeys
    
    A list of the protein keys.
    
    showScores
    
    boolean showScores
    
    Boolean indicating whether scores should be displayed.
- Class eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel
  
  class ProteinTableModel extends com.compomics.util.gui.tablemodels.SelfUpdatingTableModel implements Serializable
  - Serialized Fields
    
    displayFeaturesGenerator
    
    DisplayFeaturesGenerator displayFeaturesGenerator
    
    The display features generator provides display features.
    
    exceptionHandler
    
    com.compomics.util.exceptions.ExceptionHandler exceptionHandler
    
    The exception handler catches exceptions.
    
    geneMaps
    
    com.compomics.util.experiment.biology.genes.GeneMaps geneMaps
    
    The gene maps.
    
    identification
    
    com.compomics.util.experiment.identification.Identification identification
    
    The identification of this project.
    
    identificationFeaturesGenerator
    
    com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator
    
    The identification features generator provides identification information on the matches.
    
    proteinDetailsProvider
    
    com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider
    
    The protein details provider.
    
    proteinKeys
    
    long[] proteinKeys
    
    The list of the keys of the protein matches being displayed.
    
    sequenceProvider
    
    com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider
    
    The protein sequences provider.
    
    showScores
    
    boolean showScores
    
    If true the scores will be shown.
- Class eu.isas.peptideshaker.gui.tablemodels.PsmTableModel
  
  class PsmTableModel extends com.compomics.util.gui.tablemodels.SelfUpdatingTableModel implements Serializable
  - Serialized Fields
    
    displayFeaturesGenerator
    
    DisplayFeaturesGenerator displayFeaturesGenerator
    
    The display features generator.
    
    exceptionHandler
    
    com.compomics.util.exceptions.ExceptionHandler exceptionHandler
    
    The exception handler catches exceptions.
    
    identification
    
    com.compomics.util.experiment.identification.Identification identification
    
    The identification of this project.
    
    identificationParameters
    
    com.compomics.util.parameters.identification.IdentificationParameters identificationParameters
    
    The identification parameters.
    
    inputMap
    
    InputMap inputMap
    
    The ID input map.
    
    psmKeys
    
    long[] psmKeys
    
    A list of ordered PSM keys.
    
    showScores
    
    boolean showScores
    
    Indicates whether the scores should be displayed instead of the confidence
    
    spectrumProvider
    
    com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider
    
    The spectrum provider.

Package eu.isas.peptideshaker.gui.tabpanels

Class eu.isas.peptideshaker.gui.tabpanels.AnnotationPanel

class AnnotationPanel extends JPanel implements Serializable

Serialized Fields

accessionNumberJTextField
```
JTextField accessionNumberJTextField
```
accessionNumberLabel
```
JLabel accessionNumberLabel
```
basicAnnotationJPanel
```
JPanel basicAnnotationJPanel
```
chromosomeJTextField
```
JTextField chromosomeJTextField
```
chromosomeLabel
```
JLabel chromosomeLabel
```
currentAccessionNumber
```
String currentAccessionNumber
```
The current protein accession number.
dastyLabel
```
JLabel dastyLabel
```
dastyLinkJPanel
```
JPanel dastyLinkJPanel
```
databaseJTextField
```
JTextField databaseJTextField
```
databaseLabel
```
JLabel databaseLabel
```
davidLabel
```
JLabel davidLabel
```
davidLinkJPanel
```
JPanel davidLinkJPanel
```
descriptionLabel
```
JLabel descriptionLabel
```
geneNameJTextField
```
JTextField geneNameJTextField
```
geneNameLabel
```
JLabel geneNameLabel
```
helpEditorPane
```
JEditorPane helpEditorPane
```
helpPanel
```
JPanel helpPanel
```
helpScrollPane
```
JScrollPane helpScrollPane
```
intactLabel
```
JLabel intactLabel
```
intActLinkJPanel
```
JPanel intActLinkJPanel
```
interProLabel
```
JLabel interProLabel
```
interProLinkJPanel
```
JPanel interProLinkJPanel
```
loadDastyJButton
```
JButton loadDastyJButton
```
loadDavidJButton
```
JButton loadDavidJButton
```
loadIntActJButton
```
JButton loadIntActJButton
```
loadInterProJButton
```
JButton loadInterProJButton
```
loadNextProtJButton
```
JButton loadNextProtJButton
```
loadPdbJButton
```
JButton loadPdbJButton
```
loadQuickGOJButton
```
JButton loadQuickGOJButton
```
loadReactomeJButton
```
JButton loadReactomeJButton
```
loadStringJButton
```
JButton loadStringJButton
```
loadUniProtJButton
```
JButton loadUniProtJButton
```
nextProtLabel
```
JLabel nextProtLabel
```
nextProtLinkJPanel
```
JPanel nextProtLinkJPanel
```
pdbLabel
```
JLabel pdbLabel
```
pdbLinkJPanel
```
JPanel pdbLinkJPanel
```
peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
The PeptideShakerGUI parent.
picrLinkJLabel
```
JLabel picrLinkJLabel
```

proteinDescriptionScrollPane

JScrollPane proteinDescriptionScrollPane

proteinDescriptionTextArea
```
JTextArea proteinDescriptionTextArea
```
quickGoLabel
```
JLabel quickGoLabel
```
quickGOLinkJPanel
```
JPanel quickGOLinkJPanel
```
reactomeLabel
```
JLabel reactomeLabel
```
reactomeLinkJPanel
```
JPanel reactomeLinkJPanel
```
stringLabel
```
JLabel stringLabel
```
stringLinkJPanel
```
JPanel stringLinkJPanel
```
taxonomyJTextField
```
JTextField taxonomyJTextField
```
texonomyLabel
```
JLabel texonomyLabel
```
uniprotLabel
```
JLabel uniprotLabel
```
uniprotLinkJPanel
```
JPanel uniprotLinkJPanel
```
webDastyLabel
```
JLabel webDastyLabel
```
webDavidLabel
```
JLabel webDavidLabel
```
webIntActLabel
```
JLabel webIntActLabel
```
webInterProLabel
```
JLabel webInterProLabel
```
webNextProtLabel
```
JLabel webNextProtLabel
```
webPdbLabel
```
JLabel webPdbLabel
```
webQuickGOLabel
```
JLabel webQuickGOLabel
```
webReactomeLabel
```
JLabel webReactomeLabel
```
webStringLabel
```
JLabel webStringLabel
```
webUniProtLabel
```
JLabel webUniProtLabel
```

Class eu.isas.peptideshaker.gui.tabpanels.GOEAPanel

class GOEAPanel extends JPanel implements Serializable

Serialized Fields

contextMenuMappingsBackgroundPanel

JPanel contextMenuMappingsBackgroundPanel

contextMenuPlotsBackgroundPanel
```
JPanel contextMenuPlotsBackgroundPanel
```
currentGoMappingsColumn
```
String currentGoMappingsColumn
```
The currently selected column when opening the pop up menu for the GO table.
deselectAllMenuItem
```
JMenuItem deselectAllMenuItem
```
distributionChartPanel
```
org.jfree.chart.ChartPanel distributionChartPanel
```
The distribution chart panel.
exportMappingsJButton
```
JButton exportMappingsJButton
```
exportPlotsJButton
```
JButton exportPlotsJButton
```
fivePercentRadioButton
```
JRadioButton fivePercentRadioButton
```
goFrequencyPlotPanel
```
JPanel goFrequencyPlotPanel
```
goMappingsTable
```
JTable goMappingsTable
```
goPlotsTabbedPane
```
JTabbedPane goPlotsTabbedPane
```
goProteinCountLabel
```
JLabel goProteinCountLabel
```
goSignificancePlotPanel
```
JPanel goSignificancePlotPanel
```
jSeparator1
```
JPopupMenu.Separator jSeparator1
```
mappingsHelpJButton
```
JButton mappingsHelpJButton
```
mappingsPanel
```
JPanel mappingsPanel
```
mappingsTableLayeredPane
```
JLayeredPane mappingsTableLayeredPane
```
mappingsTableToolTips
```
ArrayList<String> mappingsTableToolTips
```
The GO mappings table column header tooltips.
onePercentRadioButton
```
JRadioButton onePercentRadioButton
```
peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
PeptideShaker GUI parent.
plotHelpJButton
```
JButton plotHelpJButton
```
plotLayeredPane
```
JLayeredPane plotLayeredPane
```
plotPanel
```
JPanel plotPanel
```

progressDialog

com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog

The progress dialog.

proteinGoMappingsScrollPane
```
JScrollPane proteinGoMappingsScrollPane
```
proteinsPanel
```
JPanel proteinsPanel
```
proteinsScrollPane
```
JScrollPane proteinsScrollPane
```
proteinTable
```
JTable proteinTable
```
proteinTableToolTips
```
ArrayList<String> proteinTableToolTips
```
The protein table column header tooltips.
selectAllMenuItem
```
JMenuItem selectAllMenuItem
```
selectSignificantMenuItem
```
JMenuItem selectSignificantMenuItem
```
selectTermsJPopupMenu
```
JPopupMenu selectTermsJPopupMenu
```
signChartPanel
```
org.jfree.chart.ChartPanel signChartPanel
```
The significance chart panel.
significanceJLabel
```
JLabel significanceJLabel
```

significanceLevelButtonGroup

ButtonGroup significanceLevelButtonGroup

speciesFactory

com.compomics.util.experiment.biology.taxonomy.SpeciesFactory speciesFactory

The species factory.

statisticsMenuItem
```
JMenuItem statisticsMenuItem
```

Class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel

class ModificationsPanel extends JPanel implements Serializable

Serialized Fields

accuracySlider
```
JSlider accuracySlider
```
aScoreGradientPanel
```
JPanel aScoreGradientPanel
```
aScoreMaxValueJLabel
```
JLabel aScoreMaxValueJLabel
```
aScoreMinValueJLabel
```
JLabel aScoreMinValueJLabel
```

contextMenuModificationBackgroundPanel

JPanel contextMenuModificationBackgroundPanel

contextMenuModifiedPeptidesBackgroundPanel

JPanel contextMenuModifiedPeptidesBackgroundPanel

contextMenuModPsmsBackgroundPanel

JPanel contextMenuModPsmsBackgroundPanel

contextMenuRelatedPeptidesBackgroundPanel

JPanel contextMenuRelatedPeptidesBackgroundPanel

contextMenuRelatedPsmsBackgroundPanel

JPanel contextMenuRelatedPsmsBackgroundPanel

contextMenuSpectrumBackgroundPanel

JPanel contextMenuSpectrumBackgroundPanel

currentModificationRow
```
int currentModificationRow
```
The currently selected row in the modification table.
deltaScoreGradientPanel
```
JPanel deltaScoreGradientPanel
```
deltaScoreMaxValueJLabel
```
JLabel deltaScoreMaxValueJLabel
```
deltaScoreMinValueJLabel
```
JLabel deltaScoreMinValueJLabel
```
displayedPeptides
```
ArrayList<Long> displayedPeptides
```
The keys of the peptides currently displayed.

exportModifiedPeptideProfileJButton

JButton exportModifiedPeptideProfileJButton

exportModifiedPsmsJButton
```
JButton exportModifiedPsmsJButton
```

exportRelatedPeptideProfileJButton

JButton exportRelatedPeptideProfileJButton

exportRelatedPsmsJButton
```
JButton exportRelatedPsmsJButton
```
exportSpectrumJButton
```
JButton exportSpectrumJButton
```

identification

com.compomics.util.experiment.identification.Identification identification

The displayed identification.

intensitySlider
```
JSlider intensitySlider
```

modificationAndPeptideSelectionPanel

JPanel modificationAndPeptideSelectionPanel

modificationConfidenceTooltipMap
```
HashMap<Integer,String> modificationConfidenceTooltipMap
```
Modification confidence tooltip map, key: modification confidence type, element: modification confidence as a string.

modificationFactory

com.compomics.util.experiment.biology.modifications.ModificationFactory modificationFactory

The modification factory.

modificationJScrollPane
```
JScrollPane modificationJScrollPane
```
modificationJTable
```
JTable modificationJTable
```

modificationLayeredLayeredPane

JLayeredPane modificationLayeredLayeredPane

modificationLayeredPanel
```
JPanel modificationLayeredPanel
```
modificationPanel
```
JPanel modificationPanel
```
modificationProfileHelpJButton
```
JButton modificationProfileHelpJButton
```

modificationProfileRelatedPeptideJPanel

JPanel modificationProfileRelatedPeptideJPanel

modificationProfileSelectedPeptideJPanel

JPanel modificationProfileSelectedPeptideJPanel

modificationSelectionHelpJButton

JButton modificationSelectionHelpJButton

modificationTableToolTips
```
ArrayList<String> modificationTableToolTips
```
Modification table column header tooltips.

modifiedPeptidesLayeredPane

JLayeredPane modifiedPeptidesLayeredPane

modifiedPeptidesPanel
```
JPanel modifiedPeptidesPanel
```
modifiedPsmsHelpJButton
```
JButton modifiedPsmsHelpJButton
```
modPsmsPanel
```
JPanel modPsmsPanel
```
modsPsmsLayeredPanel
```
JPanel modsPsmsLayeredPanel
```
peptideMap
```
HashMap<String,HashSet<Long>> peptideMap
```
Map of all peptide keys indexed by their modification status.
peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
The main GUI.
peptidesTable
```
JTable peptidesTable
```
peptidesTableJScrollPane
```
JScrollPane peptidesTableJScrollPane
```
peptideTablesJSplitPane
```
JSplitPane peptideTablesJSplitPane
```

progressDialog

com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog

The progress dialog.

proteinInferenceTooltipMap
```
HashMap<Integer,String> proteinInferenceTooltipMap
```
Protein inference map, key: pi type, element: pi as a string.
psmAScoresJPanel
```
JPanel psmAScoresJPanel
```
psmAScoresScrollPane
```
JScrollPane psmAScoresScrollPane
```
psmAScoresTable
```
JTable psmAScoresTable
```
psmDeltaScoresJPanel
```
JPanel psmDeltaScoresJPanel
```
psmDeltaScoresTable
```
JTable psmDeltaScoresTable
```
psmDeltaScrollPane
```
JScrollPane psmDeltaScrollPane
```

psmsModifiedTableJScrollPane

JScrollPane psmsModifiedTableJScrollPane

psmsModPeptidesLayeredPane
```
JLayeredPane psmsModPeptidesLayeredPane
```
psmSpectraSplitPane
```
JSplitPane psmSpectraSplitPane
```
psmSplitPane
```
JSplitPane psmSplitPane
```

psmsRelatedPeptidesJLayeredPane

JLayeredPane psmsRelatedPeptidesJLayeredPane

psmsRelatedTableJScrollPane
```
JScrollPane psmsRelatedTableJScrollPane
```
relatedPeptides
```
ArrayList<Long> relatedPeptides
```
The keys of the related peptides currently displayed.
relatedPeptidesJPanel
```
JPanel relatedPeptidesJPanel
```
relatedPeptidesJSplitPane
```
JSplitPane relatedPeptidesJSplitPane
```
relatedPeptidesPanel
```
JPanel relatedPeptidesPanel
```
relatedPeptidesTable
```
JTable relatedPeptidesTable
```

relatedPeptidesTableJScrollPane

JScrollPane relatedPeptidesTableJScrollPane

relatedPeptidesTableToolTips
```
ArrayList<String> relatedPeptidesTableToolTips
```
The related peptides table column header tooltips.
relatedPeptiesLayeredPane
```
JLayeredPane relatedPeptiesLayeredPane
```
relatedProfileHelpJButton
```
JButton relatedProfileHelpJButton
```
relatedPsmsHelpJButton
```
JButton relatedPsmsHelpJButton
```
relatedPsmsJPanel
```
JPanel relatedPsmsJPanel
```
relatedPsmsPanel
```
JPanel relatedPsmsPanel
```
relatedPsmsTable
```
JTable relatedPsmsTable
```
relatedPsmsTableToolTips
```
ArrayList<String> relatedPsmsTableToolTips
```
The related PSMs table column header tooltips.
relatedSelected
```
boolean relatedSelected
```
Boolean indicating whether the related peptide is selected.
selectedPeptidesJPanel
```
JPanel selectedPeptidesJPanel
```
selectedPeptidesJSplitPane
```
JSplitPane selectedPeptidesJSplitPane
```
selectedPeptidesTableToolTips
```
ArrayList<String> selectedPeptidesTableToolTips
```
The selected peptides table column header tooltips.
selectedPsmsTable
```
JTable selectedPsmsTable
```
selectedPsmsTableToolTips
```
ArrayList<String> selectedPsmsTableToolTips
```
The selected PSMs table column header tooltips.
sliderPanel
```
JPanel sliderPanel
```
slidersSplitPane
```
JSplitPane slidersSplitPane
```
spectrumAndFragmentIonJPanel
```
JPanel spectrumAndFragmentIonJPanel
```
spectrumAndFragmentIonPanel
```
JPanel spectrumAndFragmentIonPanel
```
spectrumAnnotationMenuPanel
```
JPanel spectrumAnnotationMenuPanel
```
spectrumChartJPanel
```
JPanel spectrumChartJPanel
```
spectrumHelpJButton
```
JButton spectrumHelpJButton
```
spectrumJPanel
```
JPanel spectrumJPanel
```
spectrumJToolBar
```
JToolBar spectrumJToolBar
```
spectrumLayeredPane
```
JLayeredPane spectrumLayeredPane
```
spectrumPanel
```
com.compomics.util.gui.spectrum.SpectrumPanel spectrumPanel
```
The current spectrum panel for the selected PSM.
spectrumTabbedPane
```
JTabbedPane spectrumTabbedPane
```

Class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel

class OverviewPanel extends JPanel implements Serializable

Serialized Fields

accuracySlider
```
JSlider accuracySlider
```
backgroundLayeredPane
```
JLayeredPane backgroundLayeredPane
```
bubbleAnnotationMenuPanel
```
JPanel bubbleAnnotationMenuPanel
```
bubbleJPanel
```
JPanel bubbleJPanel
```
bubblePlotJToolBar
```
JToolBar bubblePlotJToolBar
```
bubblePlotTabJPanel
```
JPanel bubblePlotTabJPanel
```

contextMenuPeptidesBackgroundPanel

JPanel contextMenuPeptidesBackgroundPanel

contextMenuProteinsBackgroundPanel

JPanel contextMenuProteinsBackgroundPanel

contextMenuPsmsBackgroundPanel
```
JPanel contextMenuPsmsBackgroundPanel
```

contextMenuSequenceCoverageBackgroundPanel

JPanel contextMenuSequenceCoverageBackgroundPanel

contextMenuSpectrumBackgroundPanel

JPanel contextMenuSpectrumBackgroundPanel

coverage
```
HashMap<Double,HashMap<int[],Integer>> coverage
```
The current sequence coverage in a map: likelihood to find the peptide > start end indexes > validation level
coverageChart
```
org.jfree.chart.ChartPanel coverageChart
```
The sequence coverage chart.
coverageJSplitPane
```
JSplitPane coverageJSplitPane
```
coveragePanelDividerLocation
```
int coveragePanelDividerLocation
```
The location of the divider showing or hiding the coverage plot.

coveragePeptideTypesButtonGroup

ButtonGroup coveragePeptideTypesButtonGroup

coverageShowAllPeptidesJRadioButtonMenuItem

JRadioButtonMenuItem coverageShowAllPeptidesJRadioButtonMenuItem

coverageShowEnzymaticPeptidesOnlyJRadioButtonMenuItem

JRadioButtonMenuItem coverageShowEnzymaticPeptidesOnlyJRadioButtonMenuItem

coverageShowPossiblePeptidesJCheckBoxMenuItem

JCheckBoxMenuItem coverageShowPossiblePeptidesJCheckBoxMenuItem

coverageShowTruncatedPeptidesOnlyJRadioButtonMenuItem

JRadioButtonMenuItem coverageShowTruncatedPeptidesOnlyJRadioButtonMenuItem

currentProteinAccession
```
String currentProteinAccession
```
The current protein accession number.
currentProteinSequence
```
String currentProteinSequence
```
The current protein sequence.
currentSpectrumMatchKey
```
long currentSpectrumMatchKey
```
The current spectrum key.
deselectAllMenuItem
```
JMenuItem deselectAllMenuItem
```
displayCoverage
```
boolean displayCoverage
```
Boolean indicating whether the sequence coverage shall be displayed.
displayPeptidesAndPSMs
```
boolean displayPeptidesAndPSMs
```
Boolean indicating whether the PSMs shall be displayed.
displayProteins
```
boolean displayProteins
```
Boolean indicating whether the protein table shall be displayed.
displaySpectrum
```
boolean displaySpectrum
```
Boolean indicating whether the spectrum shall be displayed.
exportPeptidesJButton
```
JButton exportPeptidesJButton
```
exportProteinsJButton
```
JButton exportProteinsJButton
```
exportPsmsJButton
```
JButton exportPsmsJButton
```

exportSequenceCoverageContextJButton

JButton exportSequenceCoverageContextJButton

exportSpectrumJButton
```
JButton exportSpectrumJButton
```
fragmentIonJPanel
```
JPanel fragmentIonJPanel
```
fragmentIonsJScrollPane
```
JScrollPane fragmentIonsJScrollPane
```
hideCoverageJButton
```
JButton hideCoverageJButton
```
hidePeptideAndPsmsJButton
```
JButton hidePeptideAndPsmsJButton
```
hidePeptideAndPsmsJButton2
```
JButton hidePeptideAndPsmsJButton2
```
hideProteinsJButton
```
JButton hideProteinsJButton
```
hideSpectrumPanelJButton
```
JButton hideSpectrumPanelJButton
```

intensityHistogram

com.compomics.util.gui.spectrum.IntensityHistogram intensityHistogram

The intensity histogram.

intensitySlider
```
JSlider intensitySlider
```
ionTableAnnotationMenuPanel
```
JPanel ionTableAnnotationMenuPanel
```
ionTableJToolBar
```
JToolBar ionTableJToolBar
```
isSelfUpdating
```
boolean isSelfUpdating
```
Controls whether the component is selfupdating or not.
jSeparator1
```
JPopupMenu.Separator jSeparator1
```
lastMzMaximum
```
double lastMzMaximum
```
The last m/z maximum displayed.

massErrorBubblePlot

com.compomics.util.gui.spectrum.MassErrorBubblePlot massErrorBubblePlot

The mass error bubble plot.

massErrorPlot

com.compomics.util.gui.spectrum.MassErrorPlot massErrorPlot

The mass error plot.

maximizeSpectrumPanelJButton
```
JButton maximizeSpectrumPanelJButton
```
overviewJPanel
```
JPanel overviewJPanel
```
overviewJSplitPane
```
JSplitPane overviewJSplitPane
```
panelsShownUponMaximze
```
ArrayList<Boolean> panelsShownUponMaximze
```
A list of the panels that where visible when the spectrum was maximized. The order is: protein, peptides and PSMs, coverage.
peptideKeys
```
long[] peptideKeys
```
A list of the peptides in the peptide table.
peptideScrollPane
```
JScrollPane peptideScrollPane
```
peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
The main GUI.
peptidesHelpJButton
```
JButton peptidesHelpJButton
```
peptidesJPanel
```
JPanel peptidesJPanel
```
peptidesLayeredPane
```
JLayeredPane peptidesLayeredPane
```
peptidesPanel
```
JPanel peptidesPanel
```
peptidesPsmJSplitPane
```
JSplitPane peptidesPsmJSplitPane
```

peptidesPsmSpectrumFragmentIonsJSplitPane

JSplitPane peptidesPsmSpectrumFragmentIonsJSplitPane

peptideTable
```
JTable peptideTable
```
peptideTableToolTips
```
ArrayList<String> peptideTableToolTips
```
The peptide table column header tooltips.
peptideVariationsChart
```
org.jfree.chart.ChartPanel peptideVariationsChart
```
The sequence peptide variations chart.
peptideVariationSequencePanel
```
ProteinSequencePanel peptideVariationSequencePanel
```
The peptide variation sequence panel.

progressDialog

com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog

The progress dialog.

proteinKeys
```
long[] proteinKeys
```
A list of proteins in the protein table.
proteinScrollPane
```
JScrollPane proteinScrollPane
```
proteinSequencePanel
```
ProteinSequencePanel proteinSequencePanel
```
The protein sequence panel.
proteinsHelpJButton
```
JButton proteinsHelpJButton
```
proteinsJPanel
```
JPanel proteinsJPanel
```
proteinsLayeredPane
```
JLayeredPane proteinsLayeredPane
```
proteinsLayeredPanel
```
JPanel proteinsLayeredPanel
```
proteinTable
```
JTable proteinTable
```
proteinTableToolTips
```
ArrayList<String> proteinTableToolTips
```
The protein table column header tooltips.
psmJPanel
```
JPanel psmJPanel
```
psmKeys
```
long[] psmKeys
```
A list of PSMs in the PSM table.
psmsHelpJButton
```
JButton psmsHelpJButton
```
psmsLayeredPane
```
JLayeredPane psmsLayeredPane
```
psmsPanel
```
JPanel psmsPanel
```
psmTable
```
JTable psmTable
```
psmTableToolTips
```
ArrayList<String> psmTableToolTips
```
The PMS table column header tooltips.
ptmChart
```
org.jfree.chart.ChartPanel ptmChart
```
The sequence PTM chart.
ptmSequencePanel
```
ProteinSequencePanel ptmSequencePanel
```
The PTM sequence panel.
secondarySpectrumPlotsJPanel
```
JPanel secondarySpectrumPlotsJPanel
```
selectAllMenuItem
```
JMenuItem selectAllMenuItem
```
selectJPopupMenu
```
JPopupMenu selectJPopupMenu
```

sequenceCoverageExportPopupMenu

JPopupMenu sequenceCoverageExportPopupMenu

sequenceCoverageInnerPanel
```
JPanel sequenceCoverageInnerPanel
```
sequenceCoverageJPanel
```
JPanel sequenceCoverageJPanel
```
sequenceCoverageJPopupMenu
```
JPopupMenu sequenceCoverageJPopupMenu
```

sequenceCoverageLayeredPane

JLayeredPane sequenceCoverageLayeredPane

sequenceCoverageOptionsJButton
```
JButton sequenceCoverageOptionsJButton
```

sequenceCoveragePlotExportMenuItem

JMenuItem sequenceCoveragePlotExportMenuItem

sequenceCoverageSequenceExportMenuItem

JMenuItem sequenceCoverageSequenceExportMenuItem

sequenceCoveragetHelpJButton
```
JButton sequenceCoveragetHelpJButton
```
sequenceCoverageTitledPanel
```
JPanel sequenceCoverageTitledPanel
```

sequenceFragmentationPanel

com.compomics.util.gui.spectrum.SequenceFragmentationPanel sequenceFragmentationPanel

The sequence fragmentation panel.

sequencePtmsPanel
```
JPanel sequencePtmsPanel
```
sequenceVariationsPanel
```
JPanel sequenceVariationsPanel
```

showCoverageAfterSeparator

JPopupMenu.Separator showCoverageAfterSeparator

showCoverageJButton
```
JButton showCoverageJButton
```

showPeptidesAfterSeparator

JPopupMenu.Separator showPeptidesAfterSeparator

showPeptidesAndPsmsJButton
```
JButton showPeptidesAndPsmsJButton
```

showProteinsAfterSeparator

JPopupMenu.Separator showProteinsAfterSeparator

showProteinsBeforeSeparator

JPopupMenu.Separator showProteinsBeforeSeparator

showProteinsJButton
```
JButton showProteinsJButton
```

showSpectrumAfterSeparator

JPopupMenu.Separator showSpectrumAfterSeparator

showSpectrumJButton
```
JButton showSpectrumJButton
```
slidersPanel
```
JPanel slidersPanel
```
slidersSplitPane
```
JSplitPane slidersSplitPane
```
spectraScrollPane
```
JScrollPane spectraScrollPane
```
spectrumAnnotationMenuPanel
```
JPanel spectrumAnnotationMenuPanel
```
spectrumContainerJPanel
```
JPanel spectrumContainerJPanel
```
spectrumHelpJButton
```
JButton spectrumHelpJButton
```
spectrumJPanel
```
JPanel spectrumJPanel
```
spectrumJTabbedPane
```
JTabbedPane spectrumJTabbedPane
```
spectrumJToolBar
```
JToolBar spectrumJToolBar
```
spectrumLayeredPane
```
JLayeredPane spectrumLayeredPane
```
spectrumMainJPanel
```
JPanel spectrumMainJPanel
```
spectrumMainPanel
```
JPanel spectrumMainPanel
```
spectrumOuterJPanel
```
JPanel spectrumOuterJPanel
```
spectrumPaddingPanel
```
JPanel spectrumPaddingPanel
```

spectrumPanel

com.compomics.util.gui.spectrum.SpectrumPanel spectrumPanel

The current spectrum panel.

spectrumSplitPane
```
JSplitPane spectrumSplitPane
```
spectrumSubPlotDividerLocation
```
int spectrumSubPlotDividerLocation
```
The location of the divider showing or hiding the spectrum sub plots.
toolBar
```
JToolBar toolBar
```

Class eu.isas.peptideshaker.gui.tabpanels.ProteinFractionsPanel

class ProteinFractionsPanel extends JPanel implements Serializable

Serialized Fields

contextMenuPeptidesBackgroundPanel

JPanel contextMenuPeptidesBackgroundPanel

contextMenuProteinsBackgroundPanel

JPanel contextMenuProteinsBackgroundPanel

coveragePeptideTypesButtonGroup

ButtonGroup coveragePeptideTypesButtonGroup

coverageShowAllPeptidesJRadioButtonMenuItem

JRadioButtonMenuItem coverageShowAllPeptidesJRadioButtonMenuItem

coverageShowEnzymaticPeptidesOnlyJRadioButtonMenuItem

JRadioButtonMenuItem coverageShowEnzymaticPeptidesOnlyJRadioButtonMenuItem

coverageShowTruncatedPeptidesOnlyJRadioButtonMenuItem

JRadioButtonMenuItem coverageShowTruncatedPeptidesOnlyJRadioButtonMenuItem

coverageTable
```
JTable coverageTable
```
coverageTablePanel
```
JPanel coverageTablePanel
```
coverageTableScrollPane
```
JScrollPane coverageTableScrollPane
```
coverageTableToolTips
```
ArrayList<String> coverageTableToolTips
```
The coverage table column header tooltips.
exportPeptidesJButton
```
JButton exportPeptidesJButton
```
exportProteinsJButton
```
JButton exportProteinsJButton
```
fractionOrderSet
```
boolean fractionOrderSet
```
True if the fraction order has been okey'ed by the user.
fractionsPlotPanel
```
JPanel fractionsPlotPanel
```
intensityPlotOuterPanel
```
JPanel intensityPlotOuterPanel
```
intensityPlotPanel
```
JPanel intensityPlotPanel
```
LINE_WIDTH
```
int LINE_WIDTH
```
The default line width for the line plots.
mwPanel
```
JPanel mwPanel
```
mwPlotPanel
```
JPanel mwPlotPanel
```
peptideKeys
```
long[] peptideKeys
```
A list of the peptides in the peptide table.
peptidePlotOuterPanel
```
JPanel peptidePlotOuterPanel
```
peptidePlotPanel
```
JPanel peptidePlotPanel
```
peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
A reference to the main PeptideShakerGUI.
peptidesHelpJButton
```
JButton peptidesHelpJButton
```
plotsLayeredPane
```
JLayeredPane plotsLayeredPane
```
plotsPanel
```
JPanel plotsPanel
```
plotsTabbedPane
```
JTabbedPane plotsTabbedPane
```

progressDialog

com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog

The progress dialog.

proteinKeys
```
long[] proteinKeys
```
The list of protein keys.
proteinPanel
```
JPanel proteinPanel
```
proteinPeptideSplitPane
```
JSplitPane proteinPeptideSplitPane
```
proteinsHelpJButton
```
JButton proteinsHelpJButton
```
proteinsLayeredPane
```
JLayeredPane proteinsLayeredPane
```
proteinTable
```
JTable proteinTable
```
proteinTableScrollPane
```
JScrollPane proteinTableScrollPane
```
proteinTableToolTips
```
ArrayList<String> proteinTableToolTips
```
The protein table column header tooltips.
sequenceCoverageJPopupMenu
```
JPopupMenu sequenceCoverageJPopupMenu
```
sequenceCoverageOptionsJButton
```
JButton sequenceCoverageOptionsJButton
```
spectraPlotOuterPanel
```
JPanel spectraPlotOuterPanel
```
spectraPlotPanel
```
JPanel spectraPlotPanel
```

totalPeptidesPerFractionPlotOuterPanel

JPanel totalPeptidesPerFractionPlotOuterPanel

Class eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel

class ProteinStructurePanel extends JPanel implements Serializable
- Serialized Fields
  - backboneJButton
    
    JButton backboneJButton
  - backboneModel
    
    boolean backboneModel
    
    If true, the backbone model is used.
  - chains
    
    com.compomics.util.pdbfinder.pdb.PdbBlock[] chains
    
    The current PDB chains.
  - chainSequence
    
    String chainSequence
    
    The amino acid sequence of the current chain.
  - contextMenuPdbChainsBackgroundPanel
    
    JPanel contextMenuPdbChainsBackgroundPanel
  - contextMenuPdbMatchesBackgroundPanel
    
    JPanel contextMenuPdbMatchesBackgroundPanel
  - contextMenuPdbStructureBackgroundPanel
    
    JPanel contextMenuPdbStructureBackgroundPanel
  - contextMenuPeptidesBackgroundPanel
    
    JPanel contextMenuPeptidesBackgroundPanel
  - contextMenuProteinsBackgroundPanel
    
    JPanel contextMenuProteinsBackgroundPanel
  - currentlyDisplayedPdbFile
    
    String currentlyDisplayedPdbFile
    
    The currently displayed PDB file.
  - exportPdbChainsJButton
    
    JButton exportPdbChainsJButton
  - exportPdbMatchesJButton
    
    JButton exportPdbMatchesJButton
  - exportPdbStructureJButton
    
    JButton exportPdbStructureJButton
  - exportPeptidesJButton
    
    JButton exportPeptidesJButton
  - exportProteinsJButton
    
    JButton exportProteinsJButton
  - jmolPanel
    
    ProteinStructurePanel.JmolPanel jmolPanel
    
    The Jmol panel.
  - jmolStructureShown
    
    boolean jmolStructureShown
    
    If true, Jmol is currently displaying a structure.
  - labelsJButton
    
    JButton labelsJButton
  - pdbChainHelpJButton
    
    JButton pdbChainHelpJButton
  - pdbChainsJPanel
    
    JPanel pdbChainsJPanel
  - pdbChainsJScrollPane
    
    JScrollPane pdbChainsJScrollPane
  - pdbChainsJTable
    
    JTable pdbChainsJTable
  - pdbChainsLayeredPane
    
    JLayeredPane pdbChainsLayeredPane
  - pdbChainsPanel
    
    JPanel pdbChainsPanel
  - pdbChainsTableToolTips
    
    ArrayList<String> pdbChainsTableToolTips
    
    The PDB chains table column header tooltips.
  - pdbJScrollPane
    
    JScrollPane pdbJScrollPane
  - pdbLayeredPane
    
    JLayeredPane pdbLayeredPane
  - pdbMatchesHelpJButton
    
    JButton pdbMatchesHelpJButton
  - pdbMatchesJPanel
    
    JPanel pdbMatchesJPanel
  - pdbMatchesJTable
    
    JTable pdbMatchesJTable
  - pdbMatchesLayeredPane
    
    JLayeredPane pdbMatchesLayeredPane
  - pdbMatchesPanel
    
    JPanel pdbMatchesPanel
  - pdbOuterPanel
    
    JPanel pdbOuterPanel
  - pdbPanel
    
    JPanel pdbPanel
  - pdbStructureHelpJButton
    
    JButton pdbStructureHelpJButton
  - pdbStructureJPanel
    
    JPanel pdbStructureJPanel
  - pdbStructureLayeredPane
    
    JLayeredPane pdbStructureLayeredPane
  - pdbTableToolTips
    
    ArrayList<String> pdbTableToolTips
    
    The PDB files table column header tooltips.
  - peptidePdbArray
    
    ArrayList<Long> peptidePdbArray
    
    Peptide keys that can be mapped to the current PDB file.
  - peptideScrollPane
    
    JScrollPane peptideScrollPane
  - peptideShakerGUI
    
    PeptideShakerGUI peptideShakerGUI
    
    The PeptideShaker main frame.
  - peptidesHelpJButton
    
    JButton peptidesHelpJButton
  - peptidesJPanel
    
    JPanel peptidesJPanel
  - peptidesLayeredPane
    
    JLayeredPane peptidesLayeredPane
  - peptidesPanel
    
    JPanel peptidesPanel
  - peptideTable
    
    JTable peptideTable
  - peptideTableMap
    
    HashMap<Integer,Long> peptideTableMap
    
    A mapping of the peptide table entries.
  - peptideTableToolTips
    
    ArrayList<String> peptideTableToolTips
    
    The peptide table column header tooltips.
  - playJButton
    
    JButton playJButton
  - progressDialog
    
    com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog
    
    A simple progress dialog.
  - proteinKeys
    
    long[] proteinKeys
    
    A list of proteins in the protein table.
  - proteinScrollPane
    
    JScrollPane proteinScrollPane
  - proteinsHelpJButton
    
    JButton proteinsHelpJButton
  - proteinsJPanel
    
    JPanel proteinsJPanel
  - proteinsLayeredPane
    
    JLayeredPane proteinsLayeredPane
  - proteinsPanel
    
    JPanel proteinsPanel
  - proteinTable
    
    JTable proteinTable
  - proteinTableToolTips
    
    ArrayList<String> proteinTableToolTips
    
    The protein table column header tooltips.
  - ribbonJButton
    
    JButton ribbonJButton
  - ribbonModel
    
    boolean ribbonModel
    
    If true, the ribbon model is used.
  - showModificationLabels
    
    boolean showModificationLabels
    
    If true, labels are shown for the modifications in the 3D structure.
  - spinModel
    
    boolean spinModel
    
    If true, the 3D model will be spinning.
  - uniProtPdb
    
    com.compomics.util.pdbfinder.FindPdbForUniprotAccessions uniProtPdb
    
    The UniProt to PDB finder.
Class eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel.JmolPanel

class JmolPanel extends JPanel implements Serializable
- Serialized Fields
  - currentSize
    
    Dimension currentSize
    
    The current size of the JPanel.
  - rectClip
    
    Rectangle rectClip
    
    The current rectangle of the JPanel.
  - viewer
    
    org.jmol.api.JmolViewer viewer
    
    The JmolViewer.

Class eu.isas.peptideshaker.gui.tabpanels.QCPanel

class QCPanel extends JPanel implements Serializable

Serialized Fields

currentPeptidePlotType

eu.isas.peptideshaker.gui.tabpanels.QCPanel.PlotType currentPeptidePlotType

The currently shown peptide plot type.

currentProteinPlotType

eu.isas.peptideshaker.gui.tabpanels.QCPanel.PlotType currentProteinPlotType

The currently shown protein plot type.

currentPsmPlotType

eu.isas.peptideshaker.gui.tabpanels.QCPanel.PlotType currentPsmPlotType

The currently shown PSM plot type.

exportPeptidesPlotJButton
```
JButton exportPeptidesPlotJButton
```
exportProteinsPlotJButton
```
JButton exportProteinsPlotJButton
```
exportPsmPlotJButton
```
JButton exportPsmPlotJButton
```
histogramColors
```
Color[] histogramColors
```
color for the plots (validated targets, validated decoy, non validated target, non validated decoy).
maxValue
```
double maxValue
```
The current maximum value to be plotted.
nonValidatedDecoyValues
```
ArrayList<Double> nonValidatedDecoyValues
```
Values of the non validated decoy hits.
nonValidatedValues
```
ArrayList<Double> nonValidatedValues
```
Values of the non validated target hits.
peptideButtonGroup
```
ButtonGroup peptideButtonGroup
```

peptideCleavageSitesJRadioButton

JRadioButton peptideCleavageSitesJRadioButton

peptideLengthJRadioButton
```
JRadioButton peptideLengthJRadioButton
```

peptideMissedCleavagesJRadioButton

JRadioButton peptideMissedCleavagesJRadioButton

peptideModificationEfficiencyJRadioButton

JRadioButton peptideModificationEfficiencyJRadioButton

peptideModificationsJRadioButton

JRadioButton peptideModificationsJRadioButton

peptideModificationSpecificityJRadioButton

JRadioButton peptideModificationSpecificityJRadioButton

peptidePanel
```
JPanel peptidePanel
```
peptideQCPlotPanel
```
JPanel peptideQCPlotPanel
```
peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
The main PeptideShaker GUI.
peptidesPlotHelpJButton
```
JButton peptidesPlotHelpJButton
```
peptidesPlotLayeredPane
```
JLayeredPane peptidesPlotLayeredPane
```
peptidesPlotTypePanel
```
JPanel peptidesPlotTypePanel
```

peptideValidatedPsmsJRadioButton

JRadioButton peptideValidatedPsmsJRadioButton

proteinButtonGroup
```
ButtonGroup proteinButtonGroup
```

proteinNumberValidatedPeptidesJRadioButton

JRadioButton proteinNumberValidatedPeptidesJRadioButton

proteinPanel
```
JPanel proteinPanel
```
proteinPlotTypePanel
```
JPanel proteinPlotTypePanel
```
proteinQCPlotPanel
```
JPanel proteinQCPlotPanel
```

proteinSequenceCoverageJRadioButton

JRadioButton proteinSequenceCoverageJRadioButton

proteinSequenceLengthJRadioButton

JRadioButton proteinSequenceLengthJRadioButton

proteinSpectrumCountingScoreJRadioButton

JRadioButton proteinSpectrumCountingScoreJRadioButton

proteinsPlotHelpJButton
```
JButton proteinsPlotHelpJButton
```
proteinsPlotLayeredPane
```
JLayeredPane proteinsPlotLayeredPane
```
psmButtonGroup
```
ButtonGroup psmButtonGroup
```
psmPanel
```
JPanel psmPanel
```
psmPlotHelpJButton
```
JButton psmPlotHelpJButton
```
psmPlotLayeredPane
```
JLayeredPane psmPlotLayeredPane
```
psmPlotTypePanel
```
JPanel psmPlotTypePanel
```

psmPrecursorChargeJRadioButton

JRadioButton psmPrecursorChargeJRadioButton

psmPrecursorMassErrorJRadioButton

JRadioButton psmPrecursorMassErrorJRadioButton

psmQCPlotPanel
```
JPanel psmQCPlotPanel
```
qcPanel
```
JPanel qcPanel
```
tabbedPane
```
JTabbedPane tabbedPane
```
validatedDecoyValues
```
ArrayList<Double> validatedDecoyValues
```
Values of the validated decoy hits.
validatedDoubtfulValues
```
ArrayList<Double> validatedDoubtfulValues
```
Values of the doubtful validated target hits.
validatedValues
```
ArrayList<Double> validatedValues
```
Values of the validated target hits.

Class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel

class SpectrumIdentificationPanel extends JPanel implements Serializable

Serialized Fields

accuracySlider
```
JSlider accuracySlider
```
advocatesUsed
```
ArrayList<Integer> advocatesUsed
```
The advocates used.
backgroundPanel
```
JPanel backgroundPanel
```
colorLegendLabel
```
JLabel colorLegendLabel
```

contextMenuIdSoftwareBackgroundPanel

JPanel contextMenuIdSoftwareBackgroundPanel

contextMenuPsmsBackgroundPanel
```
JPanel contextMenuPsmsBackgroundPanel
```

contextMenuSpectrumBackgroundPanel

JPanel contextMenuSpectrumBackgroundPanel

contextMenuSpectrumSelectionBackgroundPanel

JPanel contextMenuSpectrumSelectionBackgroundPanel

currentAssumptionsList

ArrayList<com.compomics.util.experiment.identification.SpectrumIdentificationAssumption> currentAssumptionsList

The list of search results.

exportIdPerformancePerformanceJButton

JButton exportIdPerformancePerformanceJButton

exportPsmsJButton
```
JButton exportPsmsJButton
```
exportSpectrumJButton
```
JButton exportSpectrumJButton
```
exportSpectrumSelectionJButton
```
JButton exportSpectrumSelectionJButton
```
fileNamesCmb
```
JComboBox fileNamesCmb
```
fileSelected
```
String fileSelected
```
The file currently selected.

identification

com.compomics.util.experiment.identification.Identification identification

The identification.

idPlotsPopupMenu
```
JPopupMenu idPlotsPopupMenu
```
idRateMenuItem
```
JMenuItem idRateMenuItem
```
idRatePlot
```
org.jfree.chart.ChartPanel idRatePlot
```
ID rate plot.
idResultsPanel
```
JPanel idResultsPanel
```
idResultsTableJScrollPane
```
JScrollPane idResultsTableJScrollPane
```
idResultsTableToolTips
```
ArrayList<String> idResultsTableToolTips
```
The ID results table column header tooltips.
idSoftwareHelpJButton
```
JButton idSoftwareHelpJButton
```
idSoftwareJLayeredPane
```
JLayeredPane idSoftwareJLayeredPane
```
idSoftwareJPanel
```
JPanel idSoftwareJPanel
```
idSoftwarePanel
```
JPanel idSoftwarePanel
```
idSoftwareTableToolTips
```
ArrayList<String> idSoftwareTableToolTips
```
The ID software table column header tooltips.
inputMap
```
InputMap inputMap
```
The PeptideShaker input map.
intensitySlider
```
JSlider intensitySlider
```

numberPsmsPlot

org.jfree.chart.ChartPanel numberPsmsPlot

Number of PSMs plot.

numberPsmsPlotMenuItem
```
JMenuItem numberPsmsPlotMenuItem
```
overviewPlotsPanel
```
JPanel overviewPlotsPanel
```
peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
The main GUI.
peptideShakerJScrollPane
```
JScrollPane peptideShakerJScrollPane
```
peptideShakerJTable
```
JTable peptideShakerJTable
```
peptideShakerJTablePeptideTooltip
```
String peptideShakerJTablePeptideTooltip
```
The peptide sequence tooltips for the search results table.
peptideShakerTableToolTips
```
ArrayList<String> peptideShakerTableToolTips
```
The peptide shaker table column header tooltips.

progressDialog

com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog

The progress dialog.

psmAndSpectrumSplitPane
```
JSplitPane psmAndSpectrumSplitPane
```
psmsHelpJButton
```
JButton psmsHelpJButton
```
psmsJPanel
```
JPanel psmsJPanel
```
psmsLayeredPane
```
JLayeredPane psmsLayeredPane
```
psmsPanel
```
JPanel psmsPanel
```
searchResultsTable
```
JTable searchResultsTable
```
searchResultsTablePeptideTooltips
```
ArrayList<String> searchResultsTablePeptideTooltips
```
The peptide sequence tooltips for the search results table.
slidersPanel
```
JPanel slidersPanel
```
slidersSplitPane
```
JSplitPane slidersSplitPane
```
spectrumAnnotationMenuPanel
```
JPanel spectrumAnnotationMenuPanel
```
spectrumChartPanel
```
JPanel spectrumChartPanel
```
spectrumHelpJButton
```
JButton spectrumHelpJButton
```
spectrumIdResultsLabel
```
JLabel spectrumIdResultsLabel
```
spectrumJPanel
```
JPanel spectrumJPanel
```
spectrumJPanel1
```
JPanel spectrumJPanel1
```
spectrumJToolBar
```
JToolBar spectrumJToolBar
```
spectrumLayeredPane
```
JLayeredPane spectrumLayeredPane
```
spectrumPanel
```
com.compomics.util.gui.spectrum.SpectrumPanel spectrumPanel
```
The current spectrum panel for the selected PSM.
spectrumPanelPanel
```
JPanel spectrumPanelPanel
```
spectrumSelectionDialog
```
JDialog spectrumSelectionDialog
```
spectrumSelectionHelpJButton
```
JButton spectrumSelectionHelpJButton
```
spectrumSelectionJPanel
```
JPanel spectrumSelectionJPanel
```

spectrumSelectionLayeredPane

JLayeredPane spectrumSelectionLayeredPane

spectrumSelectionOptionsJButton
```
JButton spectrumSelectionOptionsJButton
```
spectrumSelectionPanel
```
JPanel spectrumSelectionPanel
```

spectrumSelectionPsmSplitPane

JSplitPane spectrumSelectionPsmSplitPane

spectrumTable
```
JTable spectrumTable
```
spectrumTableJScrollPane
```
JScrollPane spectrumTableJScrollPane
```
spectrumTableToolTips
```
ArrayList<String> spectrumTableToolTips
```
The spectrum table column header tooltips.
unassignedPlotMenuItem
```
JMenuItem unassignedPlotMenuItem
```
unassignedPsmsPlot
```
org.jfree.chart.ChartPanel unassignedPsmsPlot
```
Number of unassigned PSMs plot.
uniquePsmsMenuItem
```
JMenuItem uniquePsmsMenuItem
```

uniquePsmsPlot

org.jfree.chart.ChartPanel uniquePsmsPlot

Number of unique PSMs plot.

updateSelection
```
boolean updateSelection
```
Needed in order to not update the file selection too many times.
vallidatedPsmsCheckBox
```
JCheckBox vallidatedPsmsCheckBox
```

Class eu.isas.peptideshaker.gui.tabpanels.ValidationPanel

class ValidationPanel extends JPanel implements Serializable

Serialized Fields

advancedSettingsLabel
```
JLabel advancedSettingsLabel
```
applyButton
```
JButton applyButton
```
confidenceChartPanel
```
JPanel confidenceChartPanel
```
confidenceHelpJButton
```
JButton confidenceHelpJButton
```
confidenceLabel
```
JLabel confidenceLabel
```

confidenceMarker

org.jfree.chart.plot.ValueMarker confidenceMarker

The confidence threshold marker.

confidencePanel
```
JPanel confidencePanel
```

confidencePlot

org.jfree.chart.plot.XYPlot confidencePlot

The confidence plot.

confidencePlotExportJButton
```
JButton confidencePlotExportJButton
```
confidencePlotHelpJButton
```
JButton confidencePlotHelpJButton
```
confidencePlotLayeredPane
```
JLayeredPane confidencePlotLayeredPane
```
confidenceTxt
```
JTextField confidenceTxt
```
costBenefitChartPanel
```
JPanel costBenefitChartPanel
```
costBenefitPanel
```
JPanel costBenefitPanel
```

costBenefitPlot

org.jfree.chart.plot.XYPlot costBenefitPlot

The benefit/cost plot.

costBenefitPlotExportJButton
```
JButton costBenefitPlotExportJButton
```
costBenefitPlotHelpJButton
```
JButton costBenefitPlotHelpJButton
```
costBenefitPlotLayeredPane
```
JLayeredPane costBenefitPlotLayeredPane
```
currentTargetDecoyMap
```
TargetDecoyMap currentTargetDecoyMap
```
The currently displayed Target Decoy map.
datasetPropertiesLabel
```
JLabel datasetPropertiesLabel
```
dataValidated
```
boolean dataValidated
```
If true the data has been (re-)loaded with the current threshold setting.
estimatorHelpJButton
```
JButton estimatorHelpJButton
```
falsePositivesHelpJButton
```
JButton falsePositivesHelpJButton
```
fdrFnrPanel
```
JPanel fdrFnrPanel
```
fdrFnrPlotExportJButton
```
JButton fdrFnrPlotExportJButton
```
fdrFnrPlotHelpJButton
```
JButton fdrFnrPlotHelpJButton
```
fdrHelpJButton
```
JButton fdrHelpJButton
```
fdrHighlightColor
```
Color fdrHighlightColor
```
The highlighting to use for FDR.
fdrLabel
```
JLabel fdrLabel
```
fdrPlotLayeredPane
```
JLayeredPane fdrPlotLayeredPane
```
fdrTxt
```
JTextField fdrTxt
```
fnrHelpJButton
```
JButton fnrHelpJButton
```
fnrHighlightColor
```
Color fnrHighlightColor
```
The highlighting to use for FNR.
fnrLabel
```
JLabel fnrLabel
```
fnrTxt
```
JTextField fnrTxt
```
fpLabel
```
JLabel fpLabel
```
groupListJPanel
```
JPanel groupListJPanel
```
groupSelectionHelpJButton
```
JButton groupSelectionHelpJButton
```
groupSelectionLayeredPane
```
JLayeredPane groupSelectionLayeredPane
```

groupSelectionScrollPaneScrollPane

JScrollPane groupSelectionScrollPaneScrollPane

groupSelectionTable
```
JTable groupSelectionTable
```
idSummaryJPanel
```
JPanel idSummaryJPanel
```
lastThresholds
```
HashMap<String,Double> lastThresholds
```
The last threshold input.
lastThresholdTypes
```
HashMap<String,Integer> lastThresholdTypes
```
The last threshold type 0 > confidence 1 > FDR 2 > FNR
leftPlotSplitPane
```
JSplitPane leftPlotSplitPane
```
LINE_WIDTH
```
int LINE_WIDTH
```
The default line width for the line plots.

modificationFactory

com.compomics.util.experiment.biology.modifications.ModificationFactory modificationFactory

The compomics PTM factory.

modifiedMaps
```
HashMap<String,Boolean> modifiedMaps
```
Map keeping track of probabilities modifications.
nFPTxt
```
JTextField nFPTxt
```
nMaxHelpJButton
```
JButton nMaxHelpJButton
```
nTotalTxt
```
JTextField nTotalTxt
```
nTPlTxt
```
JTextField nTPlTxt
```
nValidatedTxt
```
JTextField nValidatedTxt
```
optimizationJPanel
```
JPanel optimizationJPanel
```
originalThresholds
```
HashMap<String,Double> originalThresholds
```
The original threshold input.
originalThresholdTypes
```
HashMap<String,Integer> originalThresholdTypes
```
The original threshold type 0 > confidence 1 > FDR 2 > FNR.
parametersJPanel
```
JPanel parametersJPanel
```
pepBinSizeLabel
```
JLabel pepBinSizeLabel
```
peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
The main peptide shaker GUI.
pepWindowApplied
```
boolean pepWindowApplied
```
If true the data has been (re-loaded) with the current PEP window size.

progressDialog

com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog

The progress dialog.

resolutionLabel
```
JLabel resolutionLabel
```
resolutionTxt
```
JTextField resolutionTxt
```
rightPlotSplitPane
```
JSplitPane rightPlotSplitPane
```

scoreAxis

org.jfree.chart.axis.NumberAxis scoreAxis

The score log axis.

tabInitiated
```
boolean tabInitiated
```
It true the tab has been initiated, i.e., the data has been displayed at least once. False means that the tab has to be loaded from scratch.
targetDecoyChartPanel
```
JPanel targetDecoyChartPanel
```

targetDecoyPlot

org.jfree.chart.plot.CategoryPlot targetDecoyPlot

The target/decoy plot.

targetDecoySeries
```
TargetDecoySeries targetDecoySeries
```
The Target Decoy metrics series of the currently displayed map.
thresholdHelpJButton
```
JButton thresholdHelpJButton
```
thresholdInput
```
JTextField thresholdInput
```
thresholdLabel
```
JLabel thresholdLabel
```
thresholdOptimizationLabel
```
JLabel thresholdOptimizationLabel
```
thresholdOptimizationTab
```
JPanel thresholdOptimizationTab
```
thresholdResetJButton
```
JButton thresholdResetJButton
```
thresholdTypeCmb
```
JComboBox thresholdTypeCmb
```
thresholdTypeLabel
```
JLabel thresholdTypeLabel
```
totalTPHelpJButton
```
JButton totalTPHelpJButton
```
totalTpLabel
```
JLabel totalTpLabel
```
tpLabel
```
JLabel tpLabel
```
truePositivesHelpJButton
```
JButton truePositivesHelpJButton
```
validateButton
```
JButton validateButton
```
validatedHitsHelpJButton
```
JButton validatedHitsHelpJButton
```
validatedHitsLabel
```
JLabel validatedHitsLabel
```
validationResultsLabel
```
JLabel validationResultsLabel
```
windowTxt
```
JTextField windowTxt
```

Package eu.isas.peptideshaker.parameters

Class eu.isas.peptideshaker.parameters.PeptideShakerParameters

class PeptideShakerParameters extends com.compomics.util.experiment.personalization.ExperimentObject implements Serializable

Serialized Fields

displayParameters
```
DisplayParameters displayParameters
```
The display preferences.

filterParameters

com.compomics.util.gui.filtering.FilterParameters filterParameters

The GUI filter preferences.

fmIndexPath
```
String fmIndexPath
```
The path for the FM index.

geneMaps

com.compomics.util.experiment.biology.genes.GeneMaps geneMaps

The gene maps.

identificationFeaturesCache

com.compomics.util.experiment.identification.features.IdentificationFeaturesCache identificationFeaturesCache

The identification features generator with features in cache.

identificationParameters

com.compomics.util.parameters.identification.IdentificationParameters identificationParameters

The identification parameters.

metrics

com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics

The metrics saved when loading the files.

projectDetails
```
ProjectDetails projectDetails
```
The project details.

projectType

com.compomics.util.parameters.peptide_shaker.ProjectType projectType

The type of project.

proteinDetailsProvider

com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider

The protein details provider.

sequenceProvider

com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider

The sequence provider.

spectrumCountingPreferences

com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences

The spectrum counting preferences.

Package eu.isas.peptideshaker.preferences
- Class eu.isas.peptideshaker.preferences.DisplayParameters
  
  class DisplayParameters extends com.compomics.util.experiment.personalization.ExperimentObject implements Serializable
  - Serialized Fields
    
    displayedPTMs
    
    HashMap<String,Boolean> displayedPTMs
    
    The displayed PTMs.
    
    intensityIonTable
    
    boolean intensityIonTable
    
    If true, the ion table is shown as an intensity version, false displays the standard Mascot version.
    
    nAASurroundingPeptides
    
    int nAASurroundingPeptides
    
    The number of amino acids surrounding a peptide.
    
    showBars
    
    boolean showBars
    
    If true, bars are shown in the bubble plot highlighting the ions.
    
    showHiddenProteins
    
    boolean showHiddenProteins
    
    Show/hide the hidden proteins.
    
    showScores
    
    boolean showScores
    
    Show/hide the hidden scores.
    
    showValidatedProteinsOnly
    
    boolean showValidatedProteinsOnly
    
    If true, only the validated proteins are shown.
- Class eu.isas.peptideshaker.preferences.ProjectDetails
  
  class ProjectDetails extends com.compomics.util.experiment.personalization.ExperimentObject implements Serializable
  - Serialized Fields
    
    contactAddress
    
    String contactAddress
    
    The address of the contact for the mzIdentML dataset.
    
    contactEmail
    
    String contactEmail
    
    The e-mail of the contact for the mzIdentML dataset.
    
    contactFirstName
    
    String contactFirstName
    
    The first name of the contact for the mzIdentML dataset.
    
    contactLastName
    
    String contactLastName
    
    The last name of the contact for the mzIdentML dataset.
    
    contactUrl
    
    String contactUrl
    
    The URL of the contact for the mzIdentML dataset.
    
    creationDate
    
    Date creationDate
    
    When the project was created.
    
    fastaFilePath
    
    String fastaFilePath
    
    The path to the FASTA file.
    
    identificationAlgorithms
    
    HashMap<String,HashMap<String,ArrayList<String>>> identificationAlgorithms
    
    Map of the identification algorithms names and versions used to generate the identification files. identification file name > Advocate Ids > identification algorithm versions used.
    
    identificationFiles
    
    ArrayList<String> identificationFiles
    
    List of the identification file paths loaded.
    
    includeProteinSequences
    
    Boolean includeProteinSequences
    
    If true, the protein sequences are included in the mzid file.
    
    mzIdentMLOutputFile
    
    String mzIdentMLOutputFile
    
    The mzIdentML output file.
    
    organizationAddress
    
    String organizationAddress
    
    The address of the organization for the mzIdentML dataset.
    
    organizationEmail
    
    String organizationEmail
    
    The e-mail of the organization for the mzIdentML dataset.
    
    organizationName
    
    String organizationName
    
    The name of the organization for the mzIdentML dataset.
    
    organizationUrl
    
    String organizationUrl
    
    The URL of the organization for the mzIdentML dataset.
    
    peptideShakerVersion
    
    String peptideShakerVersion
    
    The PeptideShaker version used to create the project.
    
    prideContactGroup
    
    com.compomics.util.pride.prideobjects.ContactGroup prideContactGroup
    
    The PRIDE contact group.
    
    prideExperimentDescription
    
    String prideExperimentDescription
    
    The PRIDE experiment description.
    
    prideExperimentLabel
    
    String prideExperimentLabel
    
    The PRIDE experiment label.
    
    prideExperimentProjectTitle
    
    String prideExperimentProjectTitle
    
    The PRIDE experiment project title.
    
    prideExperimentTitle
    
    String prideExperimentTitle
    
    The PRIDE experiment title.
    
    prideInstrument
    
    com.compomics.util.pride.prideobjects.Instrument prideInstrument
    
    The PRIDE instrument details.
    
    prideOutputFolder
    
    String prideOutputFolder
    
    The PRIDE output folder.
    
    prideProtocol
    
    com.compomics.util.pride.prideobjects.Protocol prideProtocol
    
    The PRIDE protocol details.
    
    prideReferenceGroup
    
    com.compomics.util.pride.prideobjects.ReferenceGroup prideReferenceGroup
    
    The PRIDE reference group.
    
    prideSample
    
    com.compomics.util.pride.prideobjects.Sample prideSample
    
    The PRIDE sample details.
    
    report
    
    String report
    
    The report created during the loading of the tool.
    
    spectrumFiles
    
    HashMap<String,String> spectrumFiles
    
    Map of the spectrum files paths indexed by name without extension.
    
    userAdvocateMapping
    
    HashMap<Integer,com.compomics.util.experiment.identification.Advocate> userAdvocateMapping
    
    The user advocates mapping of this project.
- Class eu.isas.peptideshaker.preferences.UserParameters
  
  class UserParameters extends Object implements Serializable
  
  serialVersionUID:
  
  3298905131097982664L
  - Serialized Fields
    
    recentProjects
    
    ArrayList<String> recentProjects
    
    The recent projects.
    
    showSliders
    
    boolean showSliders
    
    Show/hide sliders.
Package eu.isas.peptideshaker.ptm
- Class eu.isas.peptideshaker.ptm.ModificationLocalizationScorer
  
  class ModificationLocalizationScorer extends com.compomics.util.experiment.personalization.ExperimentObject implements Serializable
  - Serialized Fields
    
    CONFIDENT_OFFSET
    
    int CONFIDENT_OFFSET
    
    Localization score offset for modification that are confidently localized.
    
    INFERRED_OFFSET
    
    int INFERRED_OFFSET
    
    Localization score offset for modification that are inferred.
    
    modificationFactory
    
    com.compomics.util.experiment.biology.modifications.ModificationFactory modificationFactory
    
    The compomics modification factory.
Package eu.isas.peptideshaker.scoring
- Class eu.isas.peptideshaker.scoring.PSMaps
  
  class PSMaps extends com.compomics.util.experiment.personalization.ExperimentObject implements Serializable
  
  serialVersionUID:
  
  -7582248988590322280L
  - Serialized Fields
    
    inputMap
    
    InputMap inputMap
    
    The target decoy map of all search engine scores.
    
    peptideMap
    
    TargetDecoyMap peptideMap
    
    The peptide level map.
    
    proteinMap
    
    TargetDecoyMap proteinMap
    
    The protein level map.
    
    psmMap
    
    TargetDecoyMap psmMap
    
    The PSM level map.
Package eu.isas.peptideshaker.scoring.maps
- Class eu.isas.peptideshaker.scoring.maps.InputMap
  
  class InputMap extends Object implements Serializable
  
  serialVersionUID:
  
  1117083720476649996L
  - Serialized Fields
    
    advocateContribution
    
    HashMap<Integer,HashMap<String,Integer>> advocateContribution
    
    Map of the search engine contribution. Advocate Id > Spectrum file name > number of validated hits.
    
    advocateUniqueContribution
    
    HashMap<Integer,HashMap<String,Integer>> advocateUniqueContribution
    
    Map of the search engine contribution. Advocate Id > Spectrum file name > number of validated hits found by this advocate only.
    
    fileIdRate
    
    HashMap<String,Integer> fileIdRate
    
    The PeptideShaker number of validated hits for every file.
    
    inputMap
    
    HashMap<Integer,TargetDecoyMap> inputMap
    
    Map of the hits as imported. One target/decoy map per identification advocate (referenced by their compomics utilities index).
    
    inputSpecificMap
    
    HashMap<Integer,HashMap<String,TargetDecoyMap>> inputSpecificMap
    
    Map of the hits per file as imported. advocate index > file name > target decoy map
    
    intermediateScores
    
    HashMap<String,HashMap<Integer,HashMap<Integer,TargetDecoyMap>>> intermediateScores
    
    Map of the intermediate scores. Name of the file > advocate index > score index
    
    peptideShakerUniqueContribution
    
    HashMap<String,Integer> peptideShakerUniqueContribution
    
    PeptideShaker unique contribution.
- Class eu.isas.peptideshaker.scoring.maps.SpecificTargetDecoyMap
  
  class SpecificTargetDecoyMap extends com.compomics.util.experiment.personalization.ExperimentObject implements Serializable
  
  serialVersionUID:
  
  746516685643358198L
  - Serialized Fields
    
    fileSpecificGrouping
    
    HashMap<Integer,HashSet<String>> fileSpecificGrouping
    
    Map used to group keys together per file.
    
    fileSpecificMaps
    
    HashMap<Integer,HashMap<String,TargetDecoyMap>> fileSpecificMaps
    
    The map of the target decoy maps indexed by file and category.
    
    groupedMaps
    
    HashMap<Integer,TargetDecoyMap> groupedMaps
    
    The map of the target decoy maps indexed by category.
    
    grouping
    
    HashMap<Integer,Integer> grouping
    
    Map used to group keys together in the grouped maps.
Package eu.isas.peptideshaker.scoring.maps.specific
- Class eu.isas.peptideshaker.scoring.maps.specific.ModificationSpecificMap
  
  class ModificationSpecificMap extends SpecificTargetDecoyMap implements Serializable
- Class eu.isas.peptideshaker.scoring.maps.specific.SimpleSpecificMap
  
  class SimpleSpecificMap extends SpecificTargetDecoyMap implements Serializable
Package eu.isas.peptideshaker.scoring.targetdecoy
- Class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap
  
  class TargetDecoyMap extends com.compomics.util.experiment.personalization.ExperimentObject implements Serializable
  
  serialVersionUID:
  
  7333389442377322662L
  - Serialized Fields
    
    hitMap
    
    HashMap<Double,TargetDecoyPoint> hitMap
    
    The hit map containing the indexed target/decoy points.
    
    minDecoysInBin
    
    Integer minDecoysInBin
    
    The number of decoy matches to include in the first bin to set the bin size nmax. Two means that two consecutive decoys will be used.
    
    minFDR
    
    double minFDR
    
    The minimal FDR which can be achieved on the dataset.
    
    nmax
    
    Integer nmax
    
    The bin size, by default the maximal number of target hits comprised between minDecoysInBin subsequent decoy hits.
    
    nTargetOnly
    
    Integer nTargetOnly
    
    The number of target hits found before the first decoy hit.
    
    scores
    
    ArrayList<Double> scores
    
    The scores imported in the map.
    
    targetDecoyResults
    
    TargetDecoyResults targetDecoyResults
    
    The results computed on this map.
    
    windowSize
    
    Integer windowSize
    
    The window size for pep estimation.
- Class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyPoint
  
  class TargetDecoyPoint extends Object implements Serializable
  
  serialVersionUID:
  
  1030681250987827768L
  - Serialized Fields
    
    nDecoy
    
    int nDecoy
    
    The number of decoy hits at this point.
    
    nTarget
    
    int nTarget
    
    The number of target hits at this point.
    
    p
    
    double p
    
    The posterior error probability associated to this point.
- Class eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyResults
  
  class TargetDecoyResults extends com.compomics.util.experiment.personalization.ExperimentObject implements Serializable
  
  serialVersionUID:
  
  -8387463582045627644L
  - Serialized Fields
    
    confidenceLimit
    
    double confidenceLimit
    
    The confidence limit.
    
    fdrLimit
    
    double fdrLimit
    
    The FDR limit.
    
    fnrLimit
    
    double fnrLimit
    
    The FNR limit.
    
    inputType
    
    int inputType
    
    The type of input 0 > confidence 1 > FDR 2 > FNR.
    
    n
    
    double n
    
    The estimated number of true positives.
    
    nFP
    
    double nFP
    
    The estimated number of false positives.
    
    noValidated
    
    Boolean noValidated
    
    A boolean indicating that everything was validated.
    
    nTPTotal
    
    double nTPTotal
    
    The estimated number of true positives reachable.
    
    scoreLimit
    
    double scoreLimit
    
    The corresponding score limit.
    
    userInput
    
    double userInput
    
    The user input which gave the displayed results.
Package eu.isas.peptideshaker.utils
- Class eu.isas.peptideshaker.utils.ExportFactoryMarshaller
  
  class ExportFactoryMarshaller extends com.compomics.util.io.json.JsonMarshaller implements Serializable

Serialized Form

Package eu.isas.peptideshaker.gui

Class eu.isas.peptideshaker.gui.FractionDetailsDialog

Serialized Fields

backgroundPanel

cancelButton

disclaimerLabel

disclamierPanel

fractionJScrollPane

fractionsPanel

fractionTable

helpLabel

importFractionRangesButton

moveBottomButton

moveDownButton

moveTopButton

moveUpButton

okButton

orderSettingsPanel

peptideShakerGUI

tableToolTips

Class eu.isas.peptideshaker.gui.IdToSpectrumFileMappingDialog

Serialized Fields

addButton

backgroundPanel

browseButton

cancelButton

fileList

fileListScrollPane

fileTable

fileTableScrollPane

folderLabel

folderTxt

helpTextLabel

idFiles

lastSelectedFolder

missingFiles

newFiles

okButton

removeButton

waitingDialog

Class eu.isas.peptideshaker.gui.ImageIconPanel

Serialized Fields

imageIcon

Class eu.isas.peptideshaker.gui.JumpToPanel

Serialized Fields

currentSelection

findJLabel

indexLabel

inputTxt

lastInput

lastLabel

newInput

nextButton

peptideShakerGUI

possibilities

previousButton

searchMutex

selectedJumpType

SPECTRUM_FILENAME_SPLITTER

spectrumfile

welcomeText

Class eu.isas.peptideshaker.gui.MatchValidationDialog

Serialized Fields

backgroundPanel

bitLabel1

bitRecommendationLabel1

bitRecommendationLabel3

bitRecommendationLabel4

cancelButton

confidenceLbl

confidenceResolutionLbl

confidenceThresholdLbl

databaseSearchPanel

editLbl

fastaFile

identificationParameters

matchesBeforeFirstDecoyLbl

nTargetLbl

okButton