Serialized Form (PeptideShaker 2.2.2 API)

Package eu.isas.peptideshaker.gui

Class eu.isas.peptideshaker.gui.FractionDetailsDialog extends JDialog implements Serializable
- Serialized Fields
  - peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
    The PeptideShakerGUI parent.
  - tableToolTips
```
ArrayList<E> tableToolTips
```
    The table column header tooltips.
  - backgroundPanel
```
JPanel backgroundPanel
```
  - cancelButton
```
JButton cancelButton
```
  - disclaimerLabel
```
JLabel disclaimerLabel
```
  - disclamierPanel
```
JPanel disclamierPanel
```
  - fractionJScrollPane
```
JScrollPane fractionJScrollPane
```
  - fractionTable
```
JTable fractionTable
```
  - fractionsPanel
```
JPanel fractionsPanel
```
  - helpLabel
```
JLabel helpLabel
```
  - importFractionRangesButton
```
JButton importFractionRangesButton
```
  - moveBottomButton
```
JButton moveBottomButton
```
  - moveDownButton
```
JButton moveDownButton
```
  - moveTopButton
```
JButton moveTopButton
```
  - moveUpButton
```
JButton moveUpButton
```
  - okButton
```
JButton okButton
```
  - orderSettingsPanel
```
JPanel orderSettingsPanel
```
Class eu.isas.peptideshaker.gui.IdToSpectrumFileMappingDialog extends JDialog implements Serializable
- Serialized Fields
  - missingFiles
```
HashMap<K,V> missingFiles
```
    Map of the missing mgf files indexed by ID file.
  - newFiles
```
HashMap<K,V> newFiles
```
    Map of the new mgf files indexed by the new ones.
  - idFiles
```
ArrayList<E> idFiles
```
    The list of id files presenting a missing mgf file.
  - lastSelectedFolder
```
File lastSelectedFolder
```
    The last selected folder.
  - waitingDialog
```
com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog waitingDialog
```
    The waiting dialog.
  - addButton
```
JButton addButton
```
  - backgroundPanel
```
JPanel backgroundPanel
```
  - browseButton
```
JButton browseButton
```
  - cancelButton
```
JButton cancelButton
```
  - fileList
```
JList<E> fileList
```
  - fileListScrollPane
```
JScrollPane fileListScrollPane
```
  - fileTable
```
JTable fileTable
```
  - fileTableScrollPane
```
JScrollPane fileTableScrollPane
```
  - folderLabel
```
JLabel folderLabel
```
  - folderTxt
```
JTextField folderTxt
```
  - helpTextLabel
```
JLabel helpTextLabel
```
  - okButton
```
JButton okButton
```
  - removeButton
```
JButton removeButton
```
Class eu.isas.peptideshaker.gui.ImageIconPanel extends JPanel implements Serializable
- Serialized Fields
  - imageIcon
```
ImageIcon imageIcon
```
    The image icon to display.
Class eu.isas.peptideshaker.gui.JumpToPanel extends JPanel implements Serializable
- Serialized Fields
  - selectedJumpType
```
JumpToPanel.JumpType selectedJumpType
```
    The type of data to jump to in that panel.
  - peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
    Instance of the main GUI class.
  - possibilities
```
EnumMap<K extends Enum<K>,V> possibilities
```
    Items matching the criterion for each type. Keys are in an array: protein, peptide, PSM.
  - currentSelection
```
EnumMap<K extends Enum<K>,V> currentSelection
```
    Currently selected item.
  - lastInput
```
EnumMap<K extends Enum<K>,V> lastInput
```
    The text to display by default.
  - lastLabel
```
EnumMap<K extends Enum<K>,V> lastLabel
```
    The text to display by default.
  - welcomeText
```
EnumMap<K extends Enum<K>,V> welcomeText
```
    The text to display by default.
  - spectrumfile
```
String spectrumfile
```
    The spectrum file inspected when jumping to spectra.
  - newInput
```
boolean newInput
```
    Counts the number of times the users has pressed a key on the keyboard in the search field.
  - searchMutex
```
com.compomics.util.threading.SimpleSemaphore searchMutex
```
    Semaphore for the synchronization of threads.
  - SPECTRUM_FILENAME_SPLITTER
```
String SPECTRUM_FILENAME_SPLITTER
```
    Splitter between spectrum file and spectrum title.
  - findJLabel
```
JLabel findJLabel
```
  - indexLabel
```
JLabel indexLabel
```
  - inputTxt
```
JTextField inputTxt
```
  - nextButton
```
JButton nextButton
```
  - previousButton
```
JButton previousButton
```

Class eu.isas.peptideshaker.gui.MatchValidationDialog extends JDialog implements Serializable

Serialized Fields

psParameter

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

The ps parameter of the match.

validationChanged
```
boolean validationChanged
```
Indicates whether the validation status of the match changed.
type
```
MatchValidationDialog.MatchType type
```
The type of match selected.

identificationParameters

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

the identification parameters used,

validationTableToolTips
```
ArrayList<E> validationTableToolTips
```
The filter table column header tooltips.
fastaFile
```
String fastaFile
```
The path to the FASTA file.
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
```
matchesBeforeFirstDecoyLbl
```
JLabel matchesBeforeFirstDecoyLbl
```
nTargetLbl
```
JLabel nTargetLbl
```
okButton
```
JButton okButton
```
qualityFiltersPanel
```
JPanel qualityFiltersPanel
```
qualityFiltersTable
```
JTable qualityFiltersTable
```

qualityFiltersTableScrollPane

JScrollPane qualityFiltersTableScrollPane

recommendedNumberOfTargetHitsLbl
```
JLabel recommendedNumberOfTargetHitsLbl
```
recommendedResolutionLbl
```
JLabel recommendedResolutionLbl
```
targetDecoyGroupPanel
```
JPanel targetDecoyGroupPanel
```
targetDecoyLbl
```
JLabel targetDecoyLbl
```
targetDecoyPanel
```
JPanel targetDecoyPanel
```
validationLevelJComboBox
```
JComboBox<E> validationLevelJComboBox
```
validationLevelPanel
```
JPanel validationLevelPanel
```
validationStatusLbl
```
JLabel validationStatusLbl
```
validationThresholdLbl
```
JLabel validationThresholdLbl
```
validationTypeLabel
```
JLabel validationTypeLabel
```

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

Class eu.isas.peptideshaker.gui.ModificationSiteInferenceDialog extends JDialog implements Serializable

Serialized Fields

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

ptm

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

The PTM investigated.

modificationFactory

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

The PTM factory.

peptidePtmScore

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

The peptide PTM scoring.

peptideMatch

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

The peptide match.

psms
```
ArrayList<E> psms
```
list of PSMs for this peptide.
mainSelection
```
boolean[] mainSelection
```
Main PTM site selection.
secondarySelection
```
boolean[] secondarySelection
```
Secondary PTM site selection.
ptmConfidenceTooltipMap
```
HashMap<K,V> ptmConfidenceTooltipMap
```
PTM confidence tooltip map, key: PTM confidence type, element: PTM confidence as a string.
backgroundPanel
```
JPanel backgroundPanel
```
cancelButton
```
JButton cancelButton
```
okButton
```
JButton okButton
```
openDialogHelpJButton
```
JButton openDialogHelpJButton
```
peptidePanel
```
JPanel peptidePanel
```
ptmSitePanel
```
JPanel ptmSitePanel
```
ptmSiteTable
```
JTable ptmSiteTable
```
ptmSiteTableScrollPane
```
JScrollPane ptmSiteTableScrollPane
```
ptmsTable
```
JTable ptmsTable
```
ptmsTableScrollPane
```
JScrollPane ptmsTableScrollPane
```
sequenceLabel
```
JLabel sequenceLabel
```

Class eu.isas.peptideshaker.gui.NewDialog extends JDialog implements Serializable

Serialized Fields

modificationFactory

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

The modification factory.

peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
A reference to the main frame.
idFiles
```
ArrayList<E> idFiles
```
The list of identification files.
modificationFiles
```
ArrayList<E> modificationFiles
```
The XML modification files found.
spectrumFiles
```
ArrayList<E> spectrumFiles
```
The list of spectrum files.
fastaFile
```
File fastaFile
```
The FASTA files.
peptideShaker
```
PeptideShaker peptideShaker
```
The peptide shaker class which will take care of the pre-processing.

progressDialog

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

The progress dialog.

identificationParameters

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

The parameters to use when loading the files.

processingParameters

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

The processing preferences.

displayPreferences
```
DisplayParameters displayPreferences
```
The display preferences.
welcomeDialog
```
WelcomeDialog welcomeDialog
```

spectrumCountingPreferences

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

The spectrum counting preferences.

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

identificationParametersFactory

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

The identification parameters factory.

msFileHandler

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

The handler for mass spectrometry files.

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
```
editProcessingButton
```
JButton editProcessingButton
```
editSettingsButton
```
JButton editSettingsButton
```
fastaFileTxt
```
JTextField fastaFileTxt
```
idFilesLabel
```
JLabel idFilesLabel
```
idFilesTxt
```
JTextField idFilesTxt
```
identificationParametersLabel
```
JLabel identificationParametersLabel
```
inputFilesPanel
```
JPanel inputFilesPanel
```
loadButton
```
JButton loadButton
```
peptideShakerPublicationLabel
```
JLabel peptideShakerPublicationLabel
```
processingLbl
```
JLabel processingLbl
```
processingParametersPanel
```
JPanel processingParametersPanel
```
processingTxt
```
JTextField processingTxt
```
projectDetailsPanel
```
JPanel projectDetailsPanel
```
projectNameIdTxt
```
JTextField projectNameIdTxt
```
projectReferenceLabel
```
JLabel projectReferenceLabel
```
projectSettingsButton
```
JButton projectSettingsButton
```
projectSettingsLabel
```
JLabel projectSettingsLabel
```
projectSettingsTxt
```
JTextField projectSettingsTxt
```
sampleDetailsPanel
```
JPanel sampleDetailsPanel
```
settingsComboBox
```
JComboBox<E> settingsComboBox
```
spectrumFilesLabel
```
JLabel spectrumFilesLabel
```
spectrumFilesTxt
```
JTextField spectrumFilesTxt
```
typeCmb
```
JComboBox<E> typeCmb
```

Class eu.isas.peptideshaker.gui.PeptideShakerGUI extends JFrame implements Serializable

Serialized Fields

EXAMPLE_DATASET_PATH
```
String EXAMPLE_DATASET_PATH
```
The path to the example dataset.
selectedProteinKey
```
long selectedProteinKey
```
The currently selected protein key.
selectedPeptideKey
```
long selectedPeptideKey
```
The currently selected peptide key.
selectedSpectrumFile
```
String selectedSpectrumFile
```
The currently selected spectrum file, null if none.
selectedSpectrumTitle
```
String selectedSpectrumTitle
```
The currently selected spectrum title, null if none.
updateNeeded
```
HashMap<K,V> 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.
scoreAndConfidenceDecimalFormat
```
DecimalFormat scoreAndConfidenceDecimalFormat
```
The decimal format use for the score and confidence columns.
dataSaved
```
boolean dataSaved
```
If true, the latest changes have been saved.
bubbleScale
```
double bubbleScale
```
The scaling value for the bubbles.
lastSelectedFolder
```
com.compomics.util.io.file.LastSelectedFolder lastSelectedFolder
```
The last folder opened by the user. Defaults to user.home.

modificationFactory

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

The modification factory.

utilitiesUserParameters

com.compomics.util.parameters.UtilitiesUserParameters utilitiesUserParameters

The utilities user preferences.

processingParameters

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

The processing preferences

progressDialog

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

A simple progress dialog.

overviewPanel
```
OverviewPanel overviewPanel
```
The overview panel.
proteinFractionsPanel
```
ProteinFractionsPanel proteinFractionsPanel
```
The protein fractions panel.
validationPanel
```
ValidationPanel validationPanel
```
The statistics panel.
modificationsPanel
```
ModificationsPanel modificationsPanel
```
The PTM panel.
annotationPanel
```
AnnotationPanel annotationPanel
```
The Annotation panel.

spectrumIdentificationPanel

SpectrumIdentificationPanel spectrumIdentificationPanel

The spectrum panel.

proteinStructurePanel
```
ProteinStructurePanel proteinStructurePanel
```
The protein structure panel.
qcPanel
```
QCPanel qcPanel
```
The QC panel.
goPanel
```
GOEAPanel goPanel
```
The GO Analysis panel.

exceptionHandler

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

The exception handler

jumpToPanel
```
JumpToPanel jumpToPanel
```
The Jump To panel.
displayFeaturesGenerator
```
DisplayFeaturesGenerator displayFeaturesGenerator
```
The class used to provide graphical features.
chargeMenus
```
HashMap<K,V> chargeMenus
```
The charge menus.
lossMenus
```
HashMap<K,V> lossMenus
```
The neutral loss menus.
publishedTweets
```
ArrayList<E> publishedTweets
```
The list of already published tweets.
newTweets
```
ArrayList<E> newTweets
```
The list of new tweets.
currentNotes
```
ArrayList<E> currentNotes
```
The list of current notes to the user.
currentTips
```
ArrayList<E> currentTips
```
The list of current tips to the user.
psdbParent
```
PsdbParent psdbParent
```
The psdb parent used to manage the data.
openingExistingProject
```
boolean openingExistingProject
```
True if an existing project is currently in the process of being opened.
starHider
```
StarHider starHider
```
Utility class to star or hide matches.
darkTheme
```
boolean darkTheme
```
Enable or disable the dark theme.
aIonCheckBoxMenuItem
```
JCheckBoxMenuItem aIonCheckBoxMenuItem
```
aboutJMenuItem
```
JMenuItem aboutJMenuItem
```
adaptCheckBoxMenuItem
```
JCheckBoxMenuItem adaptCheckBoxMenuItem
```
allCheckBoxMenuItem
```
JCheckBoxMenuItem allCheckBoxMenuItem
```
allTabsJTabbedPane
```
JTabbedPane allTabsJTabbedPane
```
annotationColorsJMenuItem
```
JMenuItem annotationColorsJMenuItem
```
annotationMenuBar
```
JMenuBar annotationMenuBar
```
annotationPreferencesMenu
```
JMenuItem annotationPreferencesMenu
```
annotationsJPanel
```
JPanel annotationsJPanel
```
bIonCheckBoxMenuItem
```
JCheckBoxMenuItem bIonCheckBoxMenuItem
```
backgroundLayeredPane
```
JLayeredPane backgroundLayeredPane
```
backgroundPanel
```
JPanel backgroundPanel
```
barsCheckBoxMenuItem
```
JCheckBoxMenuItem barsCheckBoxMenuItem
```
bubblePlotJMenuItem
```
JMenuItem bubblePlotJMenuItem
```
bubbleScaleJMenuItem
```
JMenuItem bubbleScaleJMenuItem
```
cIonCheckBoxMenuItem
```
JCheckBoxMenuItem cIonCheckBoxMenuItem
```
chargeMenu
```
JMenu chargeMenu
```
configurationFilesSettings
```
JMenuItem configurationFilesSettings
```

darkThemeCheckBoxMenuItem

JCheckBoxMenuItem darkThemeCheckBoxMenuItem

deNovoChargeButtonGroup
```
ButtonGroup deNovoChargeButtonGroup
```

deNovoChargeOneJRadioButtonMenuItem

JRadioButtonMenuItem deNovoChargeOneJRadioButtonMenuItem

deNovoChargeTwoJRadioButtonMenuItem

JRadioButtonMenuItem deNovoChargeTwoJRadioButtonMenuItem

deNovoMenu
```
JMenu deNovoMenu
```

defaultAnnotationCheckBoxMenuItem

JCheckBoxMenuItem defaultAnnotationCheckBoxMenuItem

editIdSettingsFilesMenuItem
```
JMenuItem editIdSettingsFilesMenuItem
```
editMenu
```
JMenu editMenu
```
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
```
helpJMenu
```
JMenu helpJMenu
```
helpJMenuItem
```
JMenuItem helpJMenuItem
```
helpMenu
```
JMenu helpMenu
```
helpMenuItem
```
JMenuItem helpMenuItem
```

highResAnnotationCheckBoxMenuItem

JCheckBoxMenuItem highResAnnotationCheckBoxMenuItem

identificationFeaturesMenuItem

JMenuItem identificationFeaturesMenuItem

immoniumIonsCheckMenu
```
JCheckBoxMenuItem immoniumIonsCheckMenu
```

intensityIonTableRadioButtonMenuItem

JRadioButtonMenuItem intensityIonTableRadioButtonMenuItem

ionTableButtonGroup
```
ButtonGroup ionTableButtonGroup
```
ionsMenu
```
JMenu ionsMenu
```
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
```
javaOptionsJMenuItem
```
JMenuItem javaOptionsJMenuItem
```
logReportMenu
```
JMenuItem logReportMenu
```
lossMenu
```
JMenu lossMenu
```
lossSplitter
```
JMenu lossSplitter
```
menuBar
```
JMenuBar menuBar
```
methodsSectionMenuItem
```
JMenuItem methodsSectionMenuItem
```
modificationJPanel
```
JPanel modificationJPanel
```

mzIonTableRadioButtonMenuItem

JRadioButtonMenuItem mzIonTableRadioButtonMenuItem

newJMenuItem
```
JMenuItem newJMenuItem
```
newsButton
```
JButton newsButton
```
notesButton
```
JButton notesButton
```
openExampleMenuItem
```
JMenuItem openExampleMenuItem
```
openJMenuItem
```
JMenuItem openJMenuItem
```
openRecentJMenu
```
JMenu openRecentJMenu
```
otherMenu
```
JMenu otherMenu
```
overViewTabViewMenu
```
JMenu overViewTabViewMenu
```
overviewJPanel
```
JPanel overviewJPanel
```

peptidesAndPsmsJCheckBoxMenuItem

JCheckBoxMenuItem peptidesAndPsmsJCheckBoxMenuItem

precursorCheckMenu
```
JCheckBoxMenuItem precursorCheckMenu
```
preferencesMenuItem
```
JMenuItem preferencesMenuItem
```
privacyMenuItem
```
JMenuItem privacyMenuItem
```
processingMenuItem
```
JMenuItem processingMenuItem
```
projectExportMenu
```
JMenu projectExportMenu
```
projectPropertiesMenuItem
```
JMenuItem projectPropertiesMenuItem
```
projectSettingsMenuItem
```
JMenuItem projectSettingsMenuItem
```
proteinFractionsJPanel
```
JPanel proteinFractionsJPanel
```
proteinStructureJPanel
```
JPanel proteinStructureJPanel
```

proteinsJCheckBoxMenuItem

JCheckBoxMenuItem proteinsJCheckBoxMenuItem

psmSortOrderButtonGroup
```
ButtonGroup psmSortOrderButtonGroup
```
psmSortOrderMenu
```
JMenu psmSortOrderMenu
```

psmSortRtRadioButtonMenuItem

JRadioButtonMenuItem psmSortRtRadioButtonMenuItem

psmSortScoreRadioButtonMenuItem

JRadioButtonMenuItem psmSortScoreRadioButtonMenuItem

qcJPanel
```
JPanel qcJPanel
```
quantifyMenuItem
```
JMenuItem quantifyMenuItem
```
relatedIonsCheckMenu
```
JCheckBoxMenuItem relatedIonsCheckMenu
```
reporterIonsCheckMenu
```
JCheckBoxMenuItem reporterIonsCheckMenu
```
reporterPreferencesJMenuItem
```
JMenuItem reporterPreferencesJMenuItem
```
resetAnnotationMenu
```
JMenu resetAnnotationMenu
```
reshakeMenuItem
```
JMenuItem reshakeMenuItem
```

rewindIonsDeNovoCheckBoxMenuItem

JCheckBoxMenuItem rewindIonsDeNovoCheckBoxMenuItem

saveMenuItem
```
JMenuItem saveMenuItem
```

scoresJCheckBoxMenuItem

JCheckBoxMenuItem scoresJCheckBoxMenuItem

searchGuiPreferencesJMenuItem
```
JMenuItem searchGuiPreferencesJMenuItem
```
searchParametersMenu
```
JMenuItem searchParametersMenu
```

sequenceCoverageJCheckBoxMenuItem

JCheckBoxMenuItem sequenceCoverageJCheckBoxMenuItem

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

sparklinesJCheckBoxMenuItem

JCheckBoxMenuItem sparklinesJCheckBoxMenuItem

speciesJMenuItem
```
JMenuItem speciesJMenuItem
```

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
```
statsJPanel
```
JPanel statsJPanel
```
tipsButton
```
JButton tipsButton
```
toolsMenu
```
JMenu toolsMenu
```

validatedProteinsOnlyJCheckBoxMenuItem

JCheckBoxMenuItem validatedProteinsOnlyJCheckBoxMenuItem

validationQcMenuItem
```
JMenuItem validationQcMenuItem
```
viewJMenu
```
JMenu viewJMenu
```
xIonCheckBoxMenuItem
```
JCheckBoxMenuItem xIonCheckBoxMenuItem
```
yIonCheckBoxMenuItem
```
JCheckBoxMenuItem yIonCheckBoxMenuItem
```
zIonCheckBoxMenuItem
```
JCheckBoxMenuItem zIonCheckBoxMenuItem
```

Class eu.isas.peptideshaker.gui.SaveDialog extends JDialog implements Serializable
- Serialized Fields
  - peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
    The PeptideShaker parent frame.
  - backgroundPanel
```
JPanel backgroundPanel
```
  - exportJButton
```
JButton exportJButton
```
  - exportPrideJButton
```
JButton exportPrideJButton
```
  - exportPrideLabel
```
JLabel exportPrideLabel
```
  - exportZipLabel
```
JLabel exportZipLabel
```
  - saveJButton
```
JButton saveJButton
```
  - saveLabel
```
JLabel saveLabel
```

Class eu.isas.peptideshaker.gui.WelcomeDialog extends JDialog implements Serializable

Serialized Fields

peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
The PeptideShaker parent frame.

progressDialog

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

The progress dialog.

aboutMenuItem
```
JMenuItem aboutMenuItem
```
backgroundPanel
```
JPanel backgroundPanel
```
bugReportMenuItem
```
JMenuItem bugReportMenuItem
```
compomicsButton
```
JButton compomicsButton
```
gettingStartedJButton1
```
JButton gettingStartedJButton1
```
gettingStartedMenuItem
```
JMenuItem gettingStartedMenuItem
```
helpMenu
```
JMenu helpMenu
```
isasButton
```
JButton isasButton
```
jSeparator1
```
JSeparator jSeparator1
```
jSeparator2
```
JPopupMenu.Separator jSeparator2
```
javaSettingsMenuItem
```
JMenuItem javaSettingsMenuItem
```
lowMemoryWarningLabel
```
JLabel lowMemoryWarningLabel
```
newJButton
```
JButton newJButton
```
openExampleDatasetJButton
```
JButton openExampleDatasetJButton
```
openJButton
```
JButton openJButton
```
pathSettingsMenu
```
JMenuItem pathSettingsMenu
```
probeButton
```
JButton probeButton
```
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 extends JDialog implements Serializable

Serialized Fields

peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
PeptideShaker main GUI.
exportFactory
```
PSExportFactory exportFactory
```
The export factory.
exportSchemesNames
```
ArrayList<E> exportSchemesNames
```
List of the available export schemes.
addReportLabel
```
JLabel addReportLabel
```
addReportMenuItem
```
JMenuItem addReportMenuItem
```
backgroundPanel
```
JPanel backgroundPanel
```
customReportsPanel
```
JPanel customReportsPanel
```
editReportMenuItem
```
JMenuItem editReportMenuItem
```
exitButton
```
JButton exitButton
```
exportReportButton
```
JButton exportReportButton
```
featuresPanel
```
JPanel featuresPanel
```
helpJButton
```
JButton helpJButton
```
helpLabel
```
JLabel helpLabel
```
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 extends JDialog implements Serializable

Serialized Fields

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

Class eu.isas.peptideshaker.gui.export.InclusionListExportDialog extends JDialog implements Serializable

Serialized Fields

followupPreferencesDialog
```
FollowUpExportDialog followupPreferencesDialog
```
References to the follow up export dialog.

exportFormat

InclusionListExport.ExportFormat exportFormat

The export format.

backgroundPanel
```
JPanel backgroundPanel
```
cancelButton
```
JButton cancelButton
```
degeneratedCheck
```
JCheckBox degeneratedCheck
```
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 extends JDialog implements Serializable

Serialized Fields

peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
The main PeptideShaker frame.
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
```
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 extends JDialog implements Serializable

Serialized Fields

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.

mzIdentMLVersion

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

The version of mzIdentML to use.

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
```
helpLabel
```
JLabel helpLabel
```
includeSequencesCheckBox
```
JCheckBox includeSequencesCheckBox
```
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
```

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

Package eu.isas.peptideshaker.gui.filtering

Class eu.isas.peptideshaker.gui.filtering.FiltersDialog extends JDialog implements Serializable

Serialized Fields

peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
The main GUI.
proteinStarFilters
```
HashMap<K,V> proteinStarFilters
```
The protein star filters.
proteinHideFilters
```
HashMap<K,V> proteinHideFilters
```
The protein hide filters.
peptideStarFilters
```
HashMap<K,V> peptideStarFilters
```
The peptide star filters.
peptideHideFilters
```
HashMap<K,V> peptideHideFilters
```
The peptide hide filters.
psmStarFilters
```
HashMap<K,V> psmStarFilters
```
The PSM star filters.
psmHideFilters
```
HashMap<K,V> psmHideFilters
```
The PSM hide filters.
allModifications
```
ArrayList<E> allModifications
```
All the modifications that can be used for filtering.
addHiddenPeptides
```
JButton addHiddenPeptides
```
addHiddenProtein
```
JButton addHiddenProtein
```
addHiddenPsm
```
JButton addHiddenPsm
```
addStarredPeptides
```
JButton addStarredPeptides
```
addStarredProtein
```
JButton addStarredProtein
```
addStarredPsm
```
JButton addStarredPsm
```
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
```
hiddenPsmTable
```
JTable hiddenPsmTable
```
hiddenPsmsPanel
```
JPanel hiddenPsmsPanel
```
hiddenPsmsScrollPane
```
JScrollPane hiddenPsmsScrollPane
```
okButton
```
JButton okButton
```
openDialogHelpJButton
```
JButton openDialogHelpJButton
```
peptidesSplitPane
```
JSplitPane peptidesSplitPane
```
proteinsSplitPane
```
JSplitPane proteinsSplitPane
```
psmsSplitPane
```
JSplitPane psmsSplitPane
```
starredPeptidesPanel
```
JPanel starredPeptidesPanel
```
starredPeptidesScrollPane
```
JScrollPane starredPeptidesScrollPane
```
starredPeptidesTable
```
JTable starredPeptidesTable
```
starredProteinsPanel
```
JPanel starredProteinsPanel
```
starredProteinsScrollPane
```
JScrollPane starredProteinsScrollPane
```
starredProteinsTable
```
JTable starredProteinsTable
```
starredPsmTable
```
JTable starredPsmTable
```
starredPsmsPanel
```
JPanel starredPsmsPanel
```
starredPsmsScrollPane
```
JScrollPane starredPsmsScrollPane
```
tabbedPane
```
JTabbedPane tabbedPane
```

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

Package eu.isas.peptideshaker.gui.tabpanels

Class eu.isas.peptideshaker.gui.tabpanels.AnnotationPanel extends JPanel implements Serializable

Serialized Fields

currentAccessionNumber
```
String currentAccessionNumber
```
The current protein accession number.
peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
The PeptideShakerGUI parent.
accessionNumberJTextField
```
JTextField accessionNumberJTextField
```
accessionNumberLabel
```
JLabel accessionNumberLabel
```
basicAnnotationJPanel
```
JPanel basicAnnotationJPanel
```
chromosomeJTextField
```
JTextField chromosomeJTextField
```
chromosomeLabel
```
JLabel chromosomeLabel
```
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
```
intActLinkJPanel
```
JPanel intActLinkJPanel
```
intactLabel
```
JLabel intactLabel
```
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
```
picrLinkJLabel
```
JLabel picrLinkJLabel
```

proteinDescriptionScrollPane

JScrollPane proteinDescriptionScrollPane

proteinDescriptionTextArea
```
JTextArea proteinDescriptionTextArea
```
quickGOLinkJPanel
```
JPanel quickGOLinkJPanel
```
quickGoLabel
```
JLabel quickGoLabel
```
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 extends JPanel implements Serializable

Serialized Fields

proteinTableToolTips
```
ArrayList<E> proteinTableToolTips
```
The protein table column header tooltips.

progressDialog

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

The progress dialog.

peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
PeptideShaker GUI parent.
mappingsTableToolTips
```
ArrayList<E> mappingsTableToolTips
```
The GO mappings table column header tooltips.
distributionChartPanel
```
org.jfree.chart.ChartPanel distributionChartPanel
```
The distribution chart panel.
signChartPanel
```
org.jfree.chart.ChartPanel signChartPanel
```
The significance chart panel.
currentGoMappingsColumn
```
String currentGoMappingsColumn
```
The currently selected column when opening the pop up menu for the GO table.

contextMenuMappingsBackgroundPanel

JPanel contextMenuMappingsBackgroundPanel

contextMenuPlotsBackgroundPanel
```
JPanel contextMenuPlotsBackgroundPanel
```
deselectAllMenuItem
```
JMenuItem deselectAllMenuItem
```
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
```
onePercentRadioButton
```
JRadioButton onePercentRadioButton
```
plotHelpJButton
```
JButton plotHelpJButton
```
plotLayeredPane
```
JLayeredPane plotLayeredPane
```
plotPanel
```
JPanel plotPanel
```
proteinGoMappingsScrollPane
```
JScrollPane proteinGoMappingsScrollPane
```
proteinTable
```
JTable proteinTable
```
proteinsPanel
```
JPanel proteinsPanel
```
proteinsScrollPane
```
JScrollPane proteinsScrollPane
```
selectAllMenuItem
```
JMenuItem selectAllMenuItem
```
selectSignificantMenuItem
```
JMenuItem selectSignificantMenuItem
```
selectTermsJPopupMenu
```
JPopupMenu selectTermsJPopupMenu
```
significanceJLabel
```
JLabel significanceJLabel
```

significanceLevelButtonGroup

ButtonGroup significanceLevelButtonGroup

statisticsMenuItem
```
JMenuItem statisticsMenuItem
```

Class eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel extends JPanel implements Serializable

Serialized Fields

progressDialog

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

The progress dialog.

currentModificationRow
```
int currentModificationRow
```
The currently selected row in the modification table.
selectedPeptidesTableToolTips
```
ArrayList<E> selectedPeptidesTableToolTips
```
The selected peptides table column header tooltips.
relatedPeptidesTableToolTips
```
ArrayList<E> relatedPeptidesTableToolTips
```
The related peptides table column header tooltips.
selectedPsmsTableToolTips
```
ArrayList<E> selectedPsmsTableToolTips
```
The selected PSMs table column header tooltips.
relatedPsmsTableToolTips
```
ArrayList<E> relatedPsmsTableToolTips
```
The related PSMs table column header tooltips.
modificationTableToolTips
```
ArrayList<E> modificationTableToolTips
```
Modification table column header tooltips.
peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
The main GUI.
peptideMap
```
HashMap<K,V> peptideMap
```
Map of all peptide keys indexed by their modification status.

identification

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

The displayed identification.

displayedPeptides
```
ArrayList<E> displayedPeptides
```
The keys of the peptides currently displayed.
relatedPeptides
```
ArrayList<E> relatedPeptides
```
The keys of the related peptides currently displayed.
relatedSelected
```
boolean relatedSelected
```
Boolean indicating whether the related peptide is selected.
spectrumPanel
```
com.compomics.util.gui.spectrum.SpectrumPanel spectrumPanel
```
The current spectrum panel for the selected PSM.
proteinInferenceTooltipMap
```
HashMap<K,V> proteinInferenceTooltipMap
```
Protein inference map, key: pi type, element: pi as a string.
modificationConfidenceTooltipMap
```
HashMap<K,V> 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.

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

contextMenuModPsmsBackgroundPanel

JPanel contextMenuModPsmsBackgroundPanel

contextMenuModificationBackgroundPanel

JPanel contextMenuModificationBackgroundPanel

contextMenuModifiedPeptidesBackgroundPanel

JPanel contextMenuModifiedPeptidesBackgroundPanel

contextMenuRelatedPeptidesBackgroundPanel

JPanel contextMenuRelatedPeptidesBackgroundPanel

contextMenuRelatedPsmsBackgroundPanel

JPanel contextMenuRelatedPsmsBackgroundPanel

contextMenuSpectrumBackgroundPanel

JPanel contextMenuSpectrumBackgroundPanel

deltaScoreGradientPanel
```
JPanel deltaScoreGradientPanel
```
deltaScoreMaxValueJLabel
```
JLabel deltaScoreMaxValueJLabel
```
deltaScoreMinValueJLabel
```
JLabel deltaScoreMinValueJLabel
```

exportModifiedPeptideProfileJButton

JButton exportModifiedPeptideProfileJButton

exportModifiedPsmsJButton
```
JButton exportModifiedPsmsJButton
```

exportRelatedPeptideProfileJButton

JButton exportRelatedPeptideProfileJButton

exportRelatedPsmsJButton
```
JButton exportRelatedPsmsJButton
```
exportSpectrumJButton
```
JButton exportSpectrumJButton
```
intensitySlider
```
JSlider intensitySlider
```
modPsmsPanel
```
JPanel modPsmsPanel
```

modificationAndPeptideSelectionPanel

JPanel modificationAndPeptideSelectionPanel

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

modifiedPeptidesLayeredPane

JLayeredPane modifiedPeptidesLayeredPane

modifiedPeptidesPanel
```
JPanel modifiedPeptidesPanel
```
modifiedPsmsHelpJButton
```
JButton modifiedPsmsHelpJButton
```
modsPsmsLayeredPanel
```
JPanel modsPsmsLayeredPanel
```
peptideTablesJSplitPane
```
JSplitPane peptideTablesJSplitPane
```
peptidesTable
```
JTable peptidesTable
```
peptidesTableJScrollPane
```
JScrollPane peptidesTableJScrollPane
```
psmAScoresJPanel
```
JPanel psmAScoresJPanel
```
psmAScoresScrollPane
```
JScrollPane psmAScoresScrollPane
```
psmAScoresTable
```
JTable psmAScoresTable
```
psmDeltaScoresJPanel
```
JPanel psmDeltaScoresJPanel
```
psmDeltaScoresTable
```
JTable psmDeltaScoresTable
```
psmDeltaScrollPane
```
JScrollPane psmDeltaScrollPane
```
psmSpectraSplitPane
```
JSplitPane psmSpectraSplitPane
```
psmSplitPane
```
JSplitPane psmSplitPane
```
psmsModPeptidesLayeredPane
```
JLayeredPane psmsModPeptidesLayeredPane
```

psmsModifiedTableJScrollPane

JScrollPane psmsModifiedTableJScrollPane

psmsRelatedPeptidesJLayeredPane

JLayeredPane psmsRelatedPeptidesJLayeredPane

psmsRelatedTableJScrollPane
```
JScrollPane psmsRelatedTableJScrollPane
```
relatedPeptidesJPanel
```
JPanel relatedPeptidesJPanel
```
relatedPeptidesJSplitPane
```
JSplitPane relatedPeptidesJSplitPane
```
relatedPeptidesPanel
```
JPanel relatedPeptidesPanel
```
relatedPeptidesTable
```
JTable relatedPeptidesTable
```

relatedPeptidesTableJScrollPane

JScrollPane relatedPeptidesTableJScrollPane

relatedPeptiesLayeredPane
```
JLayeredPane relatedPeptiesLayeredPane
```
relatedProfileHelpJButton
```
JButton relatedProfileHelpJButton
```
relatedPsmsHelpJButton
```
JButton relatedPsmsHelpJButton
```
relatedPsmsJPanel
```
JPanel relatedPsmsJPanel
```
relatedPsmsPanel
```
JPanel relatedPsmsPanel
```
relatedPsmsTable
```
JTable relatedPsmsTable
```
selectedPeptidesJPanel
```
JPanel selectedPeptidesJPanel
```
selectedPeptidesJSplitPane
```
JSplitPane selectedPeptidesJSplitPane
```
selectedPsmsTable
```
JTable selectedPsmsTable
```
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
```
spectrumTabbedPane
```
JTabbedPane spectrumTabbedPane
```

Class eu.isas.peptideshaker.gui.tabpanels.OverviewPanel extends JPanel implements Serializable

Serialized Fields

panelsShownUponMaximze
```
ArrayList<E> panelsShownUponMaximze
```
A list of the panels that where visible when the spectrum was maximized. The order is: protein, peptides and PSMs, coverage.

progressDialog

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

The progress dialog.

currentSpectrumMatchKey
```
long currentSpectrumMatchKey
```
The current spectrum key.
coverage
```
HashMap<K,V> coverage
```
The current sequence coverage in a map: likelihood to find the peptide > start end indexes > validation level
currentProteinAccession
```
String currentProteinAccession
```
The current protein accession number.
currentProteinSequence
```
String currentProteinSequence
```
The current protein sequence.

spectrumPanel

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

The current spectrum panel.

displaySpectrum
```
boolean displaySpectrum
```
Boolean indicating whether the spectrum shall be displayed.
displayCoverage
```
boolean displayCoverage
```
Boolean indicating whether the sequence coverage shall be displayed.
displayProteins
```
boolean displayProteins
```
Boolean indicating whether the protein table shall be displayed.
displayPeptidesAndPSMs
```
boolean displayPeptidesAndPSMs
```
Boolean indicating whether the PSMs shall be displayed.
proteinKeys
```
long[] proteinKeys
```
A list of proteins in the protein table.
peptideKeys
```
long[] peptideKeys
```
A list of the peptides in the peptide table.
psmKeys
```
long[] psmKeys
```
A list of PSMs in the PSM table.
peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
The main GUI.
proteinTableToolTips
```
ArrayList<E> proteinTableToolTips
```
The protein table column header tooltips.
peptideTableToolTips
```
ArrayList<E> peptideTableToolTips
```
The peptide table column header tooltips.
psmTableToolTips
```
ArrayList<E> psmTableToolTips
```
The PMS table column header tooltips.
coverageChart
```
org.jfree.chart.ChartPanel coverageChart
```
The sequence coverage chart.
ptmChart
```
org.jfree.chart.ChartPanel ptmChart
```
The sequence PTM chart.
peptideVariationsChart
```
org.jfree.chart.ChartPanel peptideVariationsChart
```
The sequence peptide variations chart.
proteinSequencePanel
```
ProteinSequencePanel proteinSequencePanel
```
The protein sequence panel.
ptmSequencePanel
```
ProteinSequencePanel ptmSequencePanel
```
The PTM sequence panel.
peptideVariationSequencePanel
```
ProteinSequencePanel peptideVariationSequencePanel
```
The peptide variation sequence panel.

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.

intensityHistogram

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

The intensity histogram.

sequenceFragmentationPanel

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

The sequence fragmentation panel.

lastMzMaximum
```
double lastMzMaximum
```
The last m/z maximum displayed.
spectrumSubPlotDividerLocation
```
int spectrumSubPlotDividerLocation
```
The location of the divider showing or hiding the spectrum sub plots.
coveragePanelDividerLocation
```
int coveragePanelDividerLocation
```
The location of the divider showing or hiding the coverage plot.
isSelfUpdating
```
boolean isSelfUpdating
```
Controls whether the component is selfupdating or not.
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

coverageJSplitPane
```
JSplitPane coverageJSplitPane
```

coveragePeptideTypesButtonGroup

ButtonGroup coveragePeptideTypesButtonGroup

coverageShowAllPeptidesJRadioButtonMenuItem

JRadioButtonMenuItem coverageShowAllPeptidesJRadioButtonMenuItem

coverageShowEnzymaticPeptidesOnlyJRadioButtonMenuItem

JRadioButtonMenuItem coverageShowEnzymaticPeptidesOnlyJRadioButtonMenuItem

coverageShowPossiblePeptidesJCheckBoxMenuItem

JCheckBoxMenuItem coverageShowPossiblePeptidesJCheckBoxMenuItem

coverageShowTruncatedPeptidesOnlyJRadioButtonMenuItem

JRadioButtonMenuItem coverageShowTruncatedPeptidesOnlyJRadioButtonMenuItem

deselectAllMenuItem
```
JMenuItem deselectAllMenuItem
```
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
```
intensitySlider
```
JSlider intensitySlider
```
ionTableAnnotationMenuPanel
```
JPanel ionTableAnnotationMenuPanel
```
ionTableJToolBar
```
JToolBar ionTableJToolBar
```
jSeparator1
```
JPopupMenu.Separator jSeparator1
```
maximizeSpectrumPanelJButton
```
JButton maximizeSpectrumPanelJButton
```
overviewJPanel
```
JPanel overviewJPanel
```
overviewJSplitPane
```
JSplitPane overviewJSplitPane
```
peptideScrollPane
```
JScrollPane peptideScrollPane
```
peptideTable
```
JTable peptideTable
```
peptidesHelpJButton
```
JButton peptidesHelpJButton
```
peptidesJPanel
```
JPanel peptidesJPanel
```
peptidesLayeredPane
```
JLayeredPane peptidesLayeredPane
```
peptidesPanel
```
JPanel peptidesPanel
```
peptidesPsmJSplitPane
```
JSplitPane peptidesPsmJSplitPane
```

peptidesPsmSpectrumFragmentIonsJSplitPane

JSplitPane peptidesPsmSpectrumFragmentIonsJSplitPane

proteinScrollPane
```
JScrollPane proteinScrollPane
```
proteinTable
```
JTable proteinTable
```
proteinsHelpJButton
```
JButton proteinsHelpJButton
```
proteinsJPanel
```
JPanel proteinsJPanel
```
proteinsLayeredPane
```
JLayeredPane proteinsLayeredPane
```
proteinsLayeredPanel
```
JPanel proteinsLayeredPanel
```
psmJPanel
```
JPanel psmJPanel
```
psmTable
```
JTable psmTable
```
psmsHelpJButton
```
JButton psmsHelpJButton
```
psmsLayeredPane
```
JLayeredPane psmsLayeredPane
```
psmsPanel
```
JPanel psmsPanel
```
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

sequenceCoverageTitledPanel
```
JPanel sequenceCoverageTitledPanel
```
sequenceCoveragetHelpJButton
```
JButton sequenceCoveragetHelpJButton
```
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
```
spectrumSplitPane
```
JSplitPane spectrumSplitPane
```
toolBar
```
JToolBar toolBar
```

Class eu.isas.peptideshaker.gui.tabpanels.ProteinFractionsPanel extends JPanel implements Serializable

Serialized Fields

peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
A reference to the main PeptideShakerGUI.
proteinKeys
```
long[] proteinKeys
```
The list of protein keys.
peptideKeys
```
long[] peptideKeys
```
A list of the peptides in the peptide table.
proteinTableToolTips
```
ArrayList<E> proteinTableToolTips
```
The protein table column header tooltips.
coverageTableToolTips
```
ArrayList<E> coverageTableToolTips
```
The coverage table column header tooltips.

progressDialog

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

The progress dialog.

fractionOrderSet
```
boolean fractionOrderSet
```
True if the fraction order has been okey'ed by the user.
LINE_WIDTH
```
int LINE_WIDTH
```
The default line width for the line plots.

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
```
exportPeptidesJButton
```
JButton exportPeptidesJButton
```
exportProteinsJButton
```
JButton exportProteinsJButton
```
fractionsPlotPanel
```
JPanel fractionsPlotPanel
```
intensityPlotOuterPanel
```
JPanel intensityPlotOuterPanel
```
intensityPlotPanel
```
JPanel intensityPlotPanel
```
mwPanel
```
JPanel mwPanel
```
mwPlotPanel
```
JPanel mwPlotPanel
```
peptidePlotOuterPanel
```
JPanel peptidePlotOuterPanel
```
peptidePlotPanel
```
JPanel peptidePlotPanel
```
peptidesHelpJButton
```
JButton peptidesHelpJButton
```
plotsLayeredPane
```
JLayeredPane plotsLayeredPane
```
plotsPanel
```
JPanel plotsPanel
```
plotsTabbedPane
```
JTabbedPane plotsTabbedPane
```
proteinPanel
```
JPanel proteinPanel
```
proteinPeptideSplitPane
```
JSplitPane proteinPeptideSplitPane
```
proteinTable
```
JTable proteinTable
```
proteinTableScrollPane
```
JScrollPane proteinTableScrollPane
```
proteinsHelpJButton
```
JButton proteinsHelpJButton
```
proteinsLayeredPane
```
JLayeredPane proteinsLayeredPane
```
sequenceCoverageJPopupMenu
```
JPopupMenu sequenceCoverageJPopupMenu
```
sequenceCoverageOptionsJButton
```
JButton sequenceCoverageOptionsJButton
```
spectraPlotOuterPanel
```
JPanel spectraPlotOuterPanel
```
spectraPlotPanel
```
JPanel spectraPlotPanel
```

totalPeptidesPerFractionPlotOuterPanel

JPanel totalPeptidesPerFractionPlotOuterPanel

Class eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel extends JPanel implements Serializable
- Serialized Fields
  - peptidePdbArray
```
ArrayList<E> peptidePdbArray
```
    Peptide keys that can be mapped to the current PDB file.
  - 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.
  - ribbonModel
```
boolean ribbonModel
```
    If true, the ribbon model is used.
  - backboneModel
```
boolean backboneModel
```
    If true, the backbone model is used.
  - currentlyDisplayedPdbFile
```
String currentlyDisplayedPdbFile
```
    The currently displayed PDB file.
  - progressDialog
```
com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog
```
    A simple progress dialog.
  - uniProtPdb
```
com.compomics.util.pdbfinder.FindPdbForUniprotAccessions uniProtPdb
```
    The UniProt to PDB finder.
  - peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
    The PeptideShaker main frame.
  - jmolPanel
```
ProteinStructurePanel.JmolPanel jmolPanel
```
    The Jmol panel.
  - proteinTableToolTips
```
ArrayList<E> proteinTableToolTips
```
    The protein table column header tooltips.
  - peptideTableToolTips
```
ArrayList<E> peptideTableToolTips
```
    The peptide table column header tooltips.
  - pdbTableToolTips
```
ArrayList<E> pdbTableToolTips
```
    The PDB files table column header tooltips.
  - pdbChainsTableToolTips
```
ArrayList<E> pdbChainsTableToolTips
```
    The PDB chains table column header tooltips.
  - peptideTableMap
```
HashMap<K,V> peptideTableMap
```
    A mapping of the peptide table entries.
  - jmolStructureShown
```
boolean jmolStructureShown
```
    If true, Jmol is currently displaying a structure.
  - chains
```
com.compomics.util.pdbfinder.pdb.PdbBlock[] chains
```
    The current PDB chains.
  - chainSequence
```
String chainSequence
```
    The amino acid sequence of the current chain.
  - proteinKeys
```
long[] proteinKeys
```
    A list of proteins in the protein table.
  - backboneJButton
```
JButton backboneJButton
```
  - contextMenuPdbChainsBackgroundPanel
```
JPanel contextMenuPdbChainsBackgroundPanel
```
  - contextMenuPdbMatchesBackgroundPanel
```
JPanel contextMenuPdbMatchesBackgroundPanel
```
  - contextMenuPdbStructureBackgroundPanel
```
JPanel contextMenuPdbStructureBackgroundPanel
```
  - contextMenuPeptidesBackgroundPanel
```
JPanel contextMenuPeptidesBackgroundPanel
```
  - contextMenuProteinsBackgroundPanel
```
JPanel contextMenuProteinsBackgroundPanel
```
  - exportPdbChainsJButton
```
JButton exportPdbChainsJButton
```
  - exportPdbMatchesJButton
```
JButton exportPdbMatchesJButton
```
  - exportPdbStructureJButton
```
JButton exportPdbStructureJButton
```
  - exportPeptidesJButton
```
JButton exportPeptidesJButton
```
  - exportProteinsJButton
```
JButton exportProteinsJButton
```
  - labelsJButton
```
JButton labelsJButton
```
  - pdbChainHelpJButton
```
JButton pdbChainHelpJButton
```
  - pdbChainsJPanel
```
JPanel pdbChainsJPanel
```
  - pdbChainsJScrollPane
```
JScrollPane pdbChainsJScrollPane
```
  - pdbChainsJTable
```
JTable pdbChainsJTable
```
  - pdbChainsLayeredPane
```
JLayeredPane pdbChainsLayeredPane
```
  - pdbChainsPanel
```
JPanel pdbChainsPanel
```
  - 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
```
  - peptideScrollPane
```
JScrollPane peptideScrollPane
```
  - peptideTable
```
JTable peptideTable
```
  - peptidesHelpJButton
```
JButton peptidesHelpJButton
```
  - peptidesJPanel
```
JPanel peptidesJPanel
```
  - peptidesLayeredPane
```
JLayeredPane peptidesLayeredPane
```
  - peptidesPanel
```
JPanel peptidesPanel
```
  - playJButton
```
JButton playJButton
```
  - proteinScrollPane
```
JScrollPane proteinScrollPane
```
  - proteinTable
```
JTable proteinTable
```
  - proteinsHelpJButton
```
JButton proteinsHelpJButton
```
  - proteinsJPanel
```
JPanel proteinsJPanel
```
  - proteinsLayeredPane
```
JLayeredPane proteinsLayeredPane
```
  - proteinsPanel
```
JPanel proteinsPanel
```
  - ribbonJButton
```
JButton ribbonJButton
```
Class eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel.JmolPanel extends JPanel implements Serializable
- Serialized Fields
  - viewer
```
org.jmol.api.JmolViewer viewer
```
    The JmolViewer.
  - currentSize
```
Dimension currentSize
```
    The current size of the JPanel.
  - rectClip
```
Rectangle rectClip
```
    The current rectangle of the JPanel.

Class eu.isas.peptideshaker.gui.tabpanels.QCPanel extends JPanel implements Serializable

Serialized Fields

peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
The main PeptideShaker GUI.
histogramColors
```
Color[] histogramColors
```
color for the plots (validated targets, validated decoy, non validated target, non validated decoy).
validatedValues
```
ArrayList<E> validatedValues
```
Values of the validated target hits.
validatedDoubtfulValues
```
ArrayList<E> validatedDoubtfulValues
```
Values of the doubtful validated target hits.
nonValidatedValues
```
ArrayList<E> nonValidatedValues
```
Values of the non validated target hits.
validatedDecoyValues
```
ArrayList<E> validatedDecoyValues
```
Values of the validated decoy hits.
nonValidatedDecoyValues
```
ArrayList<E> nonValidatedDecoyValues
```
Values of the non validated decoy hits.
maxValue
```
double maxValue
```
The current maximum value to be plotted.

currentProteinPlotType

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

The currently shown protein plot type.

currentPeptidePlotType

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

The currently shown peptide 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
```
peptideButtonGroup
```
ButtonGroup peptideButtonGroup
```
peptideLengthJRadioButton
```
JRadioButton peptideLengthJRadioButton
```

peptideMissedCleavagesJRadioButton

JRadioButton peptideMissedCleavagesJRadioButton

peptideModificationEfficiencyJRadioButton

JRadioButton peptideModificationEfficiencyJRadioButton

peptideModificationSpecificityJRadioButton

JRadioButton peptideModificationSpecificityJRadioButton

peptideModificationsJRadioButton

JRadioButton peptideModificationsJRadioButton

peptidePanel
```
JPanel peptidePanel
```
peptideQCPlotPanel
```
JPanel peptideQCPlotPanel
```

peptideValidatedPsmsJRadioButton

JRadioButton peptideValidatedPsmsJRadioButton

peptidesPlotHelpJButton
```
JButton peptidesPlotHelpJButton
```
peptidesPlotLayeredPane
```
JLayeredPane peptidesPlotLayeredPane
```
peptidesPlotTypePanel
```
JPanel peptidesPlotTypePanel
```
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
```

Class eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel extends JPanel implements Serializable

Serialized Fields

progressDialog

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

The progress dialog.

updateSelection
```
boolean updateSelection
```
Needed in order to not update the file selection too many times.
searchResultsTablePeptideTooltips
```
ArrayList<E> searchResultsTablePeptideTooltips
```
The peptide sequence tooltips for the search results table.
peptideShakerJTablePeptideTooltip
```
String peptideShakerJTablePeptideTooltip
```
The peptide sequence tooltips for the search results table.
idSoftwareTableToolTips
```
ArrayList<E> idSoftwareTableToolTips
```
The ID software table column header tooltips.
spectrumTableToolTips
```
ArrayList<E> spectrumTableToolTips
```
The spectrum table column header tooltips.
peptideShakerTableToolTips
```
ArrayList<E> peptideShakerTableToolTips
```
The peptide shaker table column header tooltips.
idResultsTableToolTips
```
ArrayList<E> idResultsTableToolTips
```
The ID results table column header tooltips.
currentAssumptionsList
```
ArrayList<E> currentAssumptionsList
```
The list of search results.
peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
The main GUI.

identification

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

The identification.

inputMap
```
InputMap inputMap
```
The PeptideShaker input map.
fileSelected
```
String fileSelected
```
The file currently selected.
advocatesUsed
```
ArrayList<E> advocatesUsed
```
The advocates used.
spectrumPanel
```
com.compomics.util.gui.spectrum.SpectrumPanel spectrumPanel
```
The current spectrum panel for the selected PSM.

numberPsmsPlot

org.jfree.chart.ChartPanel numberPsmsPlot

Number of PSMs plot.

uniquePsmsPlot

org.jfree.chart.ChartPanel uniquePsmsPlot

Number of unique PSMs plot.

unassignedPsmsPlot
```
org.jfree.chart.ChartPanel unassignedPsmsPlot
```
Number of unassigned PSMs plot.
idRatePlot
```
org.jfree.chart.ChartPanel idRatePlot
```
ID rate plot.
accuracySlider
```
JSlider accuracySlider
```
backgroundPanel
```
JPanel backgroundPanel
```
colorLegendLabel
```
JLabel colorLegendLabel
```

contextMenuIdSoftwareBackgroundPanel

JPanel contextMenuIdSoftwareBackgroundPanel

contextMenuPsmsBackgroundPanel
```
JPanel contextMenuPsmsBackgroundPanel
```

contextMenuSpectrumBackgroundPanel

JPanel contextMenuSpectrumBackgroundPanel

contextMenuSpectrumSelectionBackgroundPanel

JPanel contextMenuSpectrumSelectionBackgroundPanel

exportIdPerformancePerformanceJButton

JButton exportIdPerformancePerformanceJButton

exportPsmsJButton
```
JButton exportPsmsJButton
```
exportSpectrumJButton
```
JButton exportSpectrumJButton
```
exportSpectrumSelectionJButton
```
JButton exportSpectrumSelectionJButton
```
fileNamesCmb
```
JComboBox<E> fileNamesCmb
```
idPlotsPopupMenu
```
JPopupMenu idPlotsPopupMenu
```
idRateMenuItem
```
JMenuItem idRateMenuItem
```
idResultsPanel
```
JPanel idResultsPanel
```
idResultsTableJScrollPane
```
JScrollPane idResultsTableJScrollPane
```
idSoftwareHelpJButton
```
JButton idSoftwareHelpJButton
```
idSoftwareJLayeredPane
```
JLayeredPane idSoftwareJLayeredPane
```
idSoftwareJPanel
```
JPanel idSoftwareJPanel
```
idSoftwarePanel
```
JPanel idSoftwarePanel
```
intensitySlider
```
JSlider intensitySlider
```
numberPsmsPlotMenuItem
```
JMenuItem numberPsmsPlotMenuItem
```
overviewPlotsPanel
```
JPanel overviewPlotsPanel
```
peptideShakerJScrollPane
```
JScrollPane peptideShakerJScrollPane
```
peptideShakerJTable
```
JTable peptideShakerJTable
```
psmAndSpectrumSplitPane
```
JSplitPane psmAndSpectrumSplitPane
```
psmsHelpJButton
```
JButton psmsHelpJButton
```
psmsJPanel
```
JPanel psmsJPanel
```
psmsLayeredPane
```
JLayeredPane psmsLayeredPane
```
psmsPanel
```
JPanel psmsPanel
```
searchResultsTable
```
JTable searchResultsTable
```
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
```
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
```
unassignedPlotMenuItem
```
JMenuItem unassignedPlotMenuItem
```
uniquePsmsMenuItem
```
JMenuItem uniquePsmsMenuItem
```
vallidatedPsmsCheckBox
```
JCheckBox vallidatedPsmsCheckBox
```

Class eu.isas.peptideshaker.gui.tabpanels.ValidationPanel extends JPanel implements Serializable

Serialized Fields

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.

progressDialog

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

The progress dialog.

dataValidated
```
boolean dataValidated
```
If true the data has been (re-)loaded with the current threshold setting.
pepWindowApplied
```
boolean pepWindowApplied
```
If true the data has been (re-loaded) with the current PEP window size.
peptideShakerGUI
```
PeptideShakerGUI peptideShakerGUI
```
The main peptide shaker GUI.
LINE_WIDTH
```
int LINE_WIDTH
```
The default line width for the line plots.
currentTargetDecoyMap
```
TargetDecoyMap currentTargetDecoyMap
```
The currently displayed Target Decoy map.
targetDecoySeries
```
TargetDecoySeries targetDecoySeries
```
The Target Decoy metrics series of the currently displayed map.

confidencePlot

org.jfree.chart.plot.XYPlot confidencePlot

The confidence plot.

targetDecoyPlot

org.jfree.chart.plot.CategoryPlot targetDecoyPlot

The target/decoy plot.

costBenefitPlot

org.jfree.chart.plot.XYPlot costBenefitPlot

The benefit/cost plot.

lastThresholds
```
HashMap<K,V> lastThresholds
```
The last threshold input.
lastThresholdTypes
```
HashMap<K,V> lastThresholdTypes
```
The last threshold type 0 > confidence 1 > FDR 2 > FNR
originalThresholds
```
HashMap<K,V> originalThresholds
```
The original threshold input.
originalThresholdTypes
```
HashMap<K,V> originalThresholdTypes
```
The original threshold type 0 > confidence 1 > FDR 2 > FNR.

confidenceMarker

org.jfree.chart.plot.ValueMarker confidenceMarker

The confidence threshold marker.

modifiedMaps
```
HashMap<K,V> modifiedMaps
```
Map keeping track of probabilities modifications.

scoreAxis

org.jfree.chart.axis.NumberAxis scoreAxis

The score log axis.

fnrHighlightColor
```
Color fnrHighlightColor
```
The highlighting to use for FNR.
fdrHighlightColor
```
Color fdrHighlightColor
```
The highlighting to use for FDR.

modificationFactory

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

The compomics PTM factory.

advancedSettingsLabel
```
JLabel advancedSettingsLabel
```
applyButton
```
JButton applyButton
```
confidenceChartPanel
```
JPanel confidenceChartPanel
```
confidenceHelpJButton
```
JButton confidenceHelpJButton
```
confidenceLabel
```
JLabel confidenceLabel
```
confidencePanel
```
JPanel confidencePanel
```
confidencePlotExportJButton
```
JButton confidencePlotExportJButton
```
confidencePlotHelpJButton
```
JButton confidencePlotHelpJButton
```
confidencePlotLayeredPane
```
JLayeredPane confidencePlotLayeredPane
```
confidenceTxt
```
JTextField confidenceTxt
```
costBenefitChartPanel
```
JPanel costBenefitChartPanel
```
costBenefitPanel
```
JPanel costBenefitPanel
```
costBenefitPlotExportJButton
```
JButton costBenefitPlotExportJButton
```
costBenefitPlotHelpJButton
```
JButton costBenefitPlotHelpJButton
```
costBenefitPlotLayeredPane
```
JLayeredPane costBenefitPlotLayeredPane
```
datasetPropertiesLabel
```
JLabel datasetPropertiesLabel
```
estimatorHelpJButton
```
JButton estimatorHelpJButton
```
falsePositivesHelpJButton
```
JButton falsePositivesHelpJButton
```
fdrFnrPanel
```
JPanel fdrFnrPanel
```
fdrFnrPlotExportJButton
```
JButton fdrFnrPlotExportJButton
```
fdrFnrPlotHelpJButton
```
JButton fdrFnrPlotHelpJButton
```
fdrHelpJButton
```
JButton fdrHelpJButton
```
fdrLabel
```
JLabel fdrLabel
```
fdrPlotLayeredPane
```
JLayeredPane fdrPlotLayeredPane
```
fdrTxt
```
JTextField fdrTxt
```
fnrHelpJButton
```
JButton fnrHelpJButton
```
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
```
leftPlotSplitPane
```
JSplitPane leftPlotSplitPane
```
nFPTxt
```
JTextField nFPTxt
```
nMaxHelpJButton
```
JButton nMaxHelpJButton
```
nTPlTxt
```
JTextField nTPlTxt
```
nTotalTxt
```
JTextField nTotalTxt
```
nValidatedTxt
```
JTextField nValidatedTxt
```
optimizationJPanel
```
JPanel optimizationJPanel
```
parametersJPanel
```
JPanel parametersJPanel
```
pepBinSizeLabel
```
JLabel pepBinSizeLabel
```
resolutionLabel
```
JLabel resolutionLabel
```
resolutionTxt
```
JTextField resolutionTxt
```
rightPlotSplitPane
```
JSplitPane rightPlotSplitPane
```
targetDecoyChartPanel
```
JPanel targetDecoyChartPanel
```
thresholdHelpJButton
```
JButton thresholdHelpJButton
```
thresholdInput
```
JTextField thresholdInput
```
thresholdLabel
```
JLabel thresholdLabel
```
thresholdOptimizationLabel
```
JLabel thresholdOptimizationLabel
```
thresholdOptimizationTab
```
JPanel thresholdOptimizationTab
```
thresholdResetJButton
```
JButton thresholdResetJButton
```
thresholdTypeCmb
```
JComboBox<E> 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 extends com.compomics.util.experiment.personalization.ExperimentObject implements Serializable

Serialized Fields

identificationParameters

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

The identification parameters.

spectrumCountingPreferences

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

The spectrum counting preferences.

filterParameters

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

The GUI filter preferences.

displayParameters
```
DisplayParameters displayParameters
```
The display preferences.
projectDetails
```
ProjectDetails projectDetails
```
The project details.

metrics

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

The metrics saved when loading the files.

sequenceProvider

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

The sequence provider.

proteinDetailsProvider

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

The protein details provider.

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.

projectType

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

The type of project.

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

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

Serialized Form

Package eu.isas.peptideshaker.gui

Class eu.isas.peptideshaker.gui.FractionDetailsDialog extends JDialog implements Serializable

Serialized Fields

peptideShakerGUI

tableToolTips

backgroundPanel

cancelButton

disclaimerLabel

disclamierPanel

fractionJScrollPane

fractionTable

fractionsPanel

helpLabel

importFractionRangesButton

moveBottomButton

moveDownButton

moveTopButton

moveUpButton

okButton

orderSettingsPanel

Class eu.isas.peptideshaker.gui.IdToSpectrumFileMappingDialog extends JDialog implements Serializable

Serialized Fields

missingFiles

newFiles

idFiles

lastSelectedFolder

waitingDialog

addButton

backgroundPanel

browseButton

cancelButton

fileList

fileListScrollPane

fileTable

fileTableScrollPane

folderLabel

folderTxt

helpTextLabel

okButton

removeButton

Class eu.isas.peptideshaker.gui.ImageIconPanel extends JPanel implements Serializable

Serialized Fields

imageIcon

Class eu.isas.peptideshaker.gui.JumpToPanel extends JPanel implements Serializable

Serialized Fields

selectedJumpType

peptideShakerGUI

possibilities

currentSelection

lastInput

lastLabel

welcomeText

spectrumfile

newInput

searchMutex

SPECTRUM_FILENAME_SPLITTER

findJLabel

indexLabel

inputTxt

nextButton

previousButton

Class eu.isas.peptideshaker.gui.MatchValidationDialog extends JDialog implements Serializable

Serialized Fields

psParameter

validationChanged

type

identificationParameters

validationTableToolTips

fastaFile

backgroundPanel

bitLabel1

bitRecommendationLabel1

bitRecommendationLabel3

bitRecommendationLabel4

cancelButton

confidenceLbl

confidenceResolutionLbl

confidenceThresholdLbl

databaseSearchPanel