PeptideShakerGUI (PeptideShaker 2.2.2 API)

java.lang.Object
- java.awt.Component
- - java.awt.Container
  - - java.awt.Window
    - - java.awt.Frame
      - javax.swing.JFrame
        
        eu.isas.peptideshaker.gui.PeptideShakerGUI

All Implemented Interfaces:

com.compomics.software.dialogs.JavaHomeOrMemoryDialogParent, com.compomics.util.gui.error_handlers.notification.NotificationDialogParent, ClipboardOwner, ImageObserver, MenuContainer, Serializable, Accessible, RootPaneContainer, WindowConstants
```
public class PeptideShakerGUI
extends JFrame
implements ClipboardOwner, com.compomics.software.dialogs.JavaHomeOrMemoryDialogParent, com.compomics.util.gui.error_handlers.notification.NotificationDialogParent
```
The main PeptideShaker frame.

Author:

Harald Barsnes, Marc Vaudel

See Also:

Serialized Form

Nested Class Summary
- Nested classes/interfaces inherited from class javax.swing.JFrame
  JFrame.AccessibleJFrame
- Nested classes/interfaces inherited from class java.awt.Frame
  Frame.AccessibleAWTFrame
- Nested classes/interfaces inherited from class java.awt.Window
  Window.AccessibleAWTWindow, Window.Type
- Nested classes/interfaces inherited from class java.awt.Container
  Container.AccessibleAWTContainer
- Nested classes/interfaces inherited from class java.awt.Component
  Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`ANNOTATION_TAB_INDEX` The Annotation tab index.
`static Color`	`DARK_THEME_BACKGROUND_COLOR` The dark theme background color.
`static int`	`GO_ANALYSIS_TAB_INDEX` The GO Analysis tab index.
`static int`	`MODIFICATIONS_TAB_INDEX` The Modifications tab index.
`static int`	`OVER_VIEW_TAB_INDEX` The Overview tab index.
`static int`	`PROTEIN_FRACTIONS_TAB_INDEX` The Protein Fractions tab index.
`static int`	`QC_PLOTS_TAB_INDEX` The QC Plots tab index.
`static int`	`SPECTRUM_ID_TAB_INDEX` The SpectrumID tab index.
`static int`	`STRUCTURES_TAB_INDEX` The Structures tab index.
`static String`	`TITLED_BORDER_HORIZONTAL_PADDING` The horizontal padding used before and after the text in the titled borders.
`static String`	`TITLED_BORDER_HORIZONTAL_PADDING_HTML` The horizontal padding used before and after the text in the titled borders.
`static int`	`VALIDATION_TAB_INDEX` The Validation tab index.

Fields inherited from class javax.swing.JFrame
accessibleContext, EXIT_ON_CLOSE, rootPane, rootPaneCheckingEnabled

Fields inherited from class java.awt.Frame
CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, MAXIMIZED_BOTH, MAXIMIZED_HORIZ, MAXIMIZED_VERT, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSOR

Fields inherited from class java.awt.Component
BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface javax.swing.WindowConstants
DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, HIDE_ON_CLOSE

Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

Constructors
Constructor and Description
`PeptideShakerGUI()` Creates a new PeptideShaker frame.
`PeptideShakerGUI(File psdbFile, String zipURL, String zipUrlDownloadFolder, String pxAccession, boolean pxAccessionPrivate, boolean showWelcomeDialog)` Creates a new PeptideShaker frame.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addNote(String note)` Add a note to the current list of notes.
`void`	`addTip(String tip)` Add a tip to the current list of tips.
`void`	`catchException(Exception e)` Method called whenever an exception is caught.
`boolean`	`checkForNewVersion()` Check for new version.
`void`	`checkNewsFeed()` Displays a news feed at the bottom of the GUI.
`void`	`clearData(boolean clearDatabaseFolder, boolean updateGuiComponents)` Clear the data from the previous experiment.
`void`	`clearGeneMappings()` Clear the gene mappings.
`void`	`clearParameters()` Clears the project parameters.
`void`	`close()` Closes the frame by first checking if the project ought to be saved.
`void`	`disableSpectrumDisplay()` Method called to disable the spectrum display.
`void`	`displayResults()` This method will display results in all panels.
`void`	`editPathSettings(WelcomeDialog welcomeDialog)` Opens a dialog allowing the setting of paths.
`void`	`enableSpectrumExport(boolean enable)` Enable or disable the spectrum export in the overview panel.
`void`	`exportAnnotatedSpectrum()` Export the current spectrum annotation.
`void`	`exportBubblePlotAsFigure()` Export the current bubble plot as a figure.
`void`	`exportIntensityHistogramAsFigure()` Export the current intensity histogram as a figure.
`void`	`exportMassErrorPlotAsFigure()` Export the current mass error plot as a figure.
`void`	`exportProjectAsZip()` Export the project as a zip file.
`void`	`exportSelectedSpectraAsMgf()` Export the current spectrum as an mgf.
`void`	`exportSequenceFragmentationAsFigure()` Export the current sequence fragmentation as a figure.
`void`	`exportSpectrumAsFigure()` Export the current spectrum as a figure.
`JMenuBar`	`getAnnotationMenuBar()` Returns the annotation menu bar.
`double`	`getBubbleScale()` Returns the bubble plot scale value.
`HashMap<Double,String>`	`getCurrentMassDeltas()` Get the current delta masses for use when annotating the spectra.
`long`	`getDefaultPeptideSelection(long proteinKey)` Returns the default peptide, i.e., the "best" peptide for the given protein.
`long`	`getDefaultPsmSelection(long peptideKey)` Returns the default PSM, i.e., the "best" PSM for the given peptide.
`long[]`	`getDisplayedAssumptions()` Returns a list of keys of the currently displayed assumptions.
`long[]`	`getDisplayedPeptides()` Returns a list of keys of the currently displayed peptides.
`long[]`	`getDisplayedProteins()` Returns a list of keys of the currently displayed proteins.
`long[]`	`getDisplayedSpectrumMatches()` Returns a list of keys of the currently displayed spectrum matches.
`DisplayFeaturesGenerator`	`getDisplayFeaturesGenerator()` Returns the display features generator.
`DisplayParameters`	`getDisplayParameters()` Return the display parameters to use.
`com.compomics.util.exceptions.exception_handlers.FrameExceptionHandler`	`getExceptionHandler()` Returns the exception handler.
`String`	`getExtendedProjectReport()` Returns an extended HTML project report.
`com.compomics.util.gui.filtering.FilterParameters`	`getFilterParameters()` Return the filter parameters to use.
`com.compomics.util.experiment.biology.genes.GeneMaps`	`getGeneMaps()` Returns the gene maps.
`GOEAPanel`	`getGOPanel()` Returns the GO Panel.
`com.compomics.util.experiment.identification.Identification`	`getIdentification()` Returns the identification displayed.
`com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator`	`getIdentificationFeaturesGenerator()` Returns the identification features generator.
`com.compomics.util.parameters.identification.IdentificationParameters`	`getIdentificationParameters()` Returns the identification parameters.
`com.compomics.util.io.file.LastSelectedFolder`	`getLastSelectedFolder()` Returns the last selected folder.
`com.compomics.util.experiment.identification.peptide_shaker.Metrics`	`getMetrics()` Returns the metrics saved while loading the files.
`ModificationsPanel`	`getModificationsPanel()` Returns the modification panel.
`Image`	`getNormalIcon()` Returns the normal icon.
`OverviewPanel`	`getOverviewPanel()` Returns the OverviewPanel.
`int`	`getPreferredColumnWidth(JTable table, int colIndex, int margin)` Gets the preferred width of the column specified by colIndex.
`com.compomics.util.parameters.tools.ProcessingParameters`	`getProcessingParameters()` Returns the initial processing preferences.
`ProjectDetails`	`getProjectDetails()` Returns the project details.
`com.compomics.util.experiment.ProjectParameters`	`getProjectParameters()` Returns the project parameters.
`com.compomics.util.parameters.peptide_shaker.ProjectType`	`getProjectType()` Returns the project type.
`com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider`	`getProteinDetailsProvider()` Returns the protein details provider.
`ProteinFractionsPanel`	`getProteinFractionsPanel()` Returns the fractions panel.
`ProteinStructurePanel`	`getProteinStructurePanel()` Returns the ProteinStructurePanel.
`DecimalFormat`	`getScoreAndConfidenceDecimalFormat()` Returns the decimal format used for the score and confidence columns.
`long`	`getSelectedPeptideKey()` Returns the key of the selected peptide.
`long`	`getSelectedProteinKey()` Returns the key of the selected protein.
`String`	`getSelectedSpectrumFile()` Returns the currently selected spectrum file.
`String`	`getSelectedSpectrumTitle()` Returns the currently selected spectrum title.
`int`	`getSelectedTab()` Returns the selected tab as indexed by the static fields.
`com.compomics.util.experiment.io.biology.protein.SequenceProvider`	`getSequenceProvider()` Returns the sequence provider.
`Color`	`getSparklineColor()` Get the sparklines color.
`Color`	`getSparklineColorNonValidated()` Get the non-validated sparklines color.
`Color`	`getSparklineColorNotFound()` Get the not found sparklines color.
`Color`	`getSparklineColorPossible()` Get the possible sparklines color.
`com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters`	`getSpecificAnnotationParameters(String spectrumFile, String spectrumTitle, com.compomics.util.experiment.identification.SpectrumIdentificationAssumption spectrumIdentificationAssumption)` Returns the specific annotation parameters corresponding to the given spectrum, hit, and the menu selections.
`com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters`	`getSpectrumCountingParameters()` Returns the spectrum counting parameters.
`SpectrumIdentificationPanel`	`getSpectrumIdentificationPanel()` Returns the SpectrumIdentificationPanel.
`com.compomics.util.experiment.mass_spectrometry.SpectrumProvider`	`getSpectrumProvider()` Returns the spectrum provider.
`StarHider`	`getStarHider()` Returns the object responsible for starring/hiding matches.
`UserParameters`	`getUserParameters()` Returns the user parameters.
`File`	`getUserSelectedFile(String aSuggestedFileName, String aFileEnding, String aFileFormatDescription, String aDialogTitle, boolean openDialog)` Returns the file selected by the user, or null if no file was selected.
`com.compomics.util.parameters.UtilitiesUserParameters`	`getUtilitiesUserParameters()`
`ValidationPanel`	`getValidationPanel()` Returns the validation panel.
`Image`	`getWaitingIcon()` Returns the waiting icon.
`void`	`importPeptideShakerFile(File psFile, boolean importFromZip)` Imports information from a PeptideShaker file.
`void`	`importPeptideShakerZipFile(File zipFile)` Imports information from a PeptideShaker zip file.
`void`	`importPeptideShakerZipFromURL(String zipURL, String destinationFolder)` Imports a PeptideShaker zip file from a URL.
`void`	`initiateDisplay()` Initiate the display by displaying the data in the currently selected tab.
`void`	`jumpToTab(int tabIndex)` Jumps to the desired tab
`void`	`loadRecentProjectsList(JPopupMenu menu, WelcomeDialog welcomeDialog)` Add the list of recently used files to the file menu.
`void`	`loadUserParameters()` Loads the user parameters.
`void`	`lostOwnership(Clipboard clipboard, Transferable contents)`
`static void`	`main(String[] args)` The main method used to start PeptideShaker.
`void`	`notificationClicked(String notificationType)`
`void`	`openExampleFile()` Open the PeptideShaker example dataset.
`void`	`openProteinLinks(String links)` Opens one or more protein links in the default web browser.
`void`	`resetDisplayFeaturesGenerator()` Resets the display features generator.
`void`	`resetFrameTitle()` Reset the frame title.
`void`	`resetIdentificationFeaturesGenerator()` Resets the feature generator.
`void`	`resetModificationFactory()` Resets the modification factory.
`void`	`resetSelectedItems()` Resets the items selection.
`void`	`restart()` Closes and restarts PeptideShaker.
`void`	`saveProject(boolean aCloseWhenDone, boolean aExportToZipWhenDone)` Saves the modifications made to the project.
`void`	`saveProjectAs(boolean closeWhenDone, boolean aExportToZipWhenDone)` Save the project to a new location.
`void`	`setCurentNotes(ArrayList<String> currentNotes)` Set the list of current notes.
`void`	`setCurentTips(ArrayList<String> currentTips)` Set the list of current tips.
`void`	`setDataSaved(boolean dataSaved)` Set whether the current data has been saved to a psdb file or not.
`void`	`setDefaultParameters()` Set the default parameters.
`void`	`setDisplayOptions(boolean displayProteins, boolean displayPeptidesAndPsms, boolean displayCoverage, boolean displaySpectrum)` Update the display options for the overview tab.
`void`	`setDisplayParameters(DisplayParameters displayParameters)` Sets the display parameters to use.
`void`	`setFilterParameters(com.compomics.util.gui.filtering.FilterParameters filterParameters)` Sets the filter parameters to use.
`void`	`setGeneMaps(com.compomics.util.experiment.biology.genes.GeneMaps geneMaps)` Sets the gene maps.
`void`	`setIdentification(com.compomics.util.experiment.identification.Identification identification)` Sets the identification.
`void`	`setIdentificationFeaturesGenerator(com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator)` Sets the feature generator.
`void`	`setIdentificationParameters(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters)` Sets the identification parameters.
`void`	`setLastSelectedFolder(com.compomics.util.io.file.LastSelectedFolder lastSelectedFolder)` Set the last selected folder.
`void`	`setMetrics(com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics)` Sets the metrics saved while loading the files.
`void`	`setMsFileHandler(com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler msFileHandler)` Sets the mass spectrometry file handler.
`void`	`setProcessingParameters(com.compomics.util.parameters.tools.ProcessingParameters processingParameters)` Sets the initial processing preferences.
`void`	`setProject(com.compomics.util.experiment.ProjectParameters projectParameters)` Sets the project.
`void`	`setProjectDetails(ProjectDetails projectDetails)` Sets the project details.
`void`	`setProjectType(com.compomics.util.parameters.peptide_shaker.ProjectType projectType)` Sets the project type.
`void`	`setProteinDetailsProvider(com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider)` Sets the protein details provider.
`void`	`setSelectedItems()` Sets the selected item based on the selected tab.
`void`	`setSelectedItems(long proteinKey, long peptideKey, String spectrumFile, String spectrumTitle)` Sets the keys of the selected protein, peptide and PSM.
`void`	`setSequenceProvider(com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider)` Sets the sequence provider.
`void`	`setSparklineColor(Color sparklineColor)` Set the sparklines color.
`void`	`setSparklineColorNonValidated(Color sparklineColorNonValidated)` Set the non-validated sparklines color.
`void`	`setSparklineColorPossible(Color sparklineColorPossible)` Set the possible sparklines color.
`void`	`setSpectrumCountingParameters(com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingParameters)` Sets new spectrum counting parameters.
`void`	`setUpdated(int tabIndex, boolean updated)` Sets that the tab was updated.
`void`	`setUpLogFile(boolean redirectOutputStream)` Set up the log file.
`void`	`setUtilitiesUserParameters(com.compomics.util.parameters.UtilitiesUserParameters utilitiesUserParameters)` Set the utilities user parameters.
`void`	`showNotesNotification()` Show a note notification pop up.
`boolean`	`showSparklines()` Returns true if the sparklines are to be shown.
`void`	`showTipsNotification()` Show a tip notification pop up.
`void`	`spectrumFileSelectionChanged(String spectrumFile)` Sets the new spectrum file selected.
`void`	`updateAnnotationMenu()` Updates the ions used for fragment annotation.
`void`	`updateAnnotationMenuBarVisableOptions(boolean showSpectrumOptions, boolean showBubblePlotOptions, boolean showIonTableOptions, boolean showPtmPlotOptions, boolean showSingleSpectrumExportOptions)` Updates the visible menu items on the settings menu of the annotation menu bar.
`void`	`updateAnnotationMenus(com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters specificAnnotationParameters, int precursorCharge, HashSet<String> modNames)` Update the annotation menu bar with the current annotation preferences.
`void`	`updateFilterSettingsField(String text)` Update the filter settings field.
`void`	`updateFrameTitle()` Add the experiment title to the frame title.
`void`	`updateMainMatch(String mainMatch, int proteinInferenceType)` Update the protein match in the different tabs.
`void`	`updateModificationColorCoding()` Update the modification color coding in all tabs.
`void`	`updateNotesNotificationCounter()` Update the notification counter for the notes.
`void`	`updateRecentProjectsList()` Add the list of recently used files to the file menu.
`void`	`updateSelectionInCurrentTab()` Updates the selected items in the currently opened tab.
`void`	`updateSpectrumAnnotations()` Updates the annotations in the selected tab.
`void`	`updateSurroundingAminoAcids()` Update the number of surrounding amino acids displayed.
`void`	`updateTabbedPanes()` Update the tabbed panes.
`void`	`updateTipsNotificationCounter()` Update the notification counter for the tips.

Methods inherited from class java.awt.Frame
addNotify, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, remove, removeNotify, setBackground, setCursor, setExtendedState, setMaximizedBounds, setMenuBar, setOpacity, setResizable, setShape, setState, setTitle, setUndecorated

Methods inherited from class java.awt.Window
addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBackground, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getIconImages, getInputContext, getListeners, getLocale, getModalExclusionType, getMostRecentFocusOwner, getOpacity, getOwnedWindows, getOwner, getOwnerlessWindows, getShape, getToolkit, getType, getWarningString, getWindowFocusListeners, getWindowListeners, getWindows, getWindowStateListeners, hide, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isAutoRequestFocus, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isOpaque, isShowing, isValidateRoot, pack, paint, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setAutoRequestFocus, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImages, setLocation, setLocation, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, setType, setVisible, show, toBack, toFront

Methods inherited from class java.awt.Container
add, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, transferFocusDownCycle, validate, validateTree

Methods inherited from class java.awt.Component
action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resize, resize, revalidate, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setMaximumSize, setName, setPreferredSize, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.awt.MenuContainer
getFont, postEvent

- Field Detail
  - OVER_VIEW_TAB_INDEX
```
public static final int OVER_VIEW_TAB_INDEX
```
    The Overview tab index.
    
    See Also:
    
    Constant Field Values
  - SPECTRUM_ID_TAB_INDEX
```
public static final int SPECTRUM_ID_TAB_INDEX
```
    The SpectrumID tab index.
    
    See Also:
    
    Constant Field Values
  - PROTEIN_FRACTIONS_TAB_INDEX
```
public static final int PROTEIN_FRACTIONS_TAB_INDEX
```
    The Protein Fractions tab index.
    
    See Also:
    
    Constant Field Values
  - MODIFICATIONS_TAB_INDEX
```
public static final int MODIFICATIONS_TAB_INDEX
```
    The Modifications tab index.
    
    See Also:
    
    Constant Field Values
  - STRUCTURES_TAB_INDEX
```
public static final int STRUCTURES_TAB_INDEX
```
    The Structures tab index.
    
    See Also:
    
    Constant Field Values
  - ANNOTATION_TAB_INDEX
```
public static final int ANNOTATION_TAB_INDEX
```
    The Annotation tab index.
    
    See Also:
    
    Constant Field Values
  - GO_ANALYSIS_TAB_INDEX
```
public static final int GO_ANALYSIS_TAB_INDEX
```
    The GO Analysis tab index.
    
    See Also:
    
    Constant Field Values
  - VALIDATION_TAB_INDEX
```
public static final int VALIDATION_TAB_INDEX
```
    The Validation tab index.
    
    See Also:
    
    Constant Field Values
  - QC_PLOTS_TAB_INDEX
```
public static final int QC_PLOTS_TAB_INDEX
```
    The QC Plots tab index.
    
    See Also:
    
    Constant Field Values
  - TITLED_BORDER_HORIZONTAL_PADDING
```
public static String TITLED_BORDER_HORIZONTAL_PADDING
```
    The horizontal padding used before and after the text in the titled borders. (Needed to make it look as good in Java 7 as it did in Java 6...)
  - TITLED_BORDER_HORIZONTAL_PADDING_HTML
```
public static String TITLED_BORDER_HORIZONTAL_PADDING_HTML
```
    The horizontal padding used before and after the text in the titled borders. (Needed to make it look as good in Java 7 as it did in Java 6...)
  - DARK_THEME_BACKGROUND_COLOR
```
public static final Color DARK_THEME_BACKGROUND_COLOR
```
    The dark theme background color.
- Constructor Detail
  - PeptideShakerGUI
```
public PeptideShakerGUI()
```
    Creates a new PeptideShaker frame.
  - PeptideShakerGUI
```
public PeptideShakerGUI(File psdbFile,
                        String zipURL,
                        String zipUrlDownloadFolder,
                        String pxAccession,
                        boolean pxAccessionPrivate,
                        boolean showWelcomeDialog)
```
    Creates a new PeptideShaker frame.
    
    Parameters:
    
    psdbFile - the psdb file to load
    
    zipURL - the URL to a zipped psdb file to download and load, can be null
    
    zipUrlDownloadFolder - the folder to download the URL to, can be null
    
    pxAccession - a PX accession to open in the PRIDE Reshake, can be null
    
    pxAccessionPrivate - if true, the PX accession is private
    
    showWelcomeDialog - boolean indicating if the Welcome Dialog is to be shown
- Method Detail
  - main
```
public static void main(String[] args)
```
    The main method used to start PeptideShaker.
    
    Parameters:
    
    args - the arguments
  - loadUserParameters
```
public void loadUserParameters()
```
    Loads the user parameters.
  - setProject
```
public void setProject(com.compomics.util.experiment.ProjectParameters projectParameters)
```
    Sets the project.
    
    Parameters:
    
    projectParameters - the experiment
  - updateFrameTitle
```
public void updateFrameTitle()
```
    Add the experiment title to the frame title.
  - resetFrameTitle
```
public void resetFrameTitle()
```
    Reset the frame title.
  - getLastSelectedFolder
```
public com.compomics.util.io.file.LastSelectedFolder getLastSelectedFolder()
```
    Returns the last selected folder.
    
    Returns:
    
    the last selected folder
  - setLastSelectedFolder
```
public void setLastSelectedFolder(com.compomics.util.io.file.LastSelectedFolder lastSelectedFolder)
```
    Set the last selected folder.
    
    Parameters:
    
    lastSelectedFolder - the folder to set
  - editPathSettings
```
public void editPathSettings(WelcomeDialog welcomeDialog)
```
    Opens a dialog allowing the setting of paths.
    
    Parameters:
    
    welcomeDialog - reference to the Welcome dialog, can be null
  - initiateDisplay
```
public void initiateDisplay()
```
    Initiate the display by displaying the data in the currently selected tab. Was previously a part of the displayResults methods, but had to be split into a separate method due to threading issues.
  - displayResults
```
public void displayResults()
```
    This method will display results in all panels.
  - disableSpectrumDisplay
```
public void disableSpectrumDisplay()
```
    Method called to disable the spectrum display.
  - setUpLogFile
```
public void setUpLogFile(boolean redirectOutputStream)
```
    Set up the log file. Redirects the error and output streams to the log file.
    
    Parameters:
    
    redirectOutputStream - if true, redirects the output stream
  - getUserParameters
```
public UserParameters getUserParameters()
```
    Returns the user parameters.
    
    Returns:
    
    the user parameters
  - getUtilitiesUserParameters
```
public com.compomics.util.parameters.UtilitiesUserParameters getUtilitiesUserParameters()
```
    Specified by:
    
    getUtilitiesUserParameters in interface com.compomics.software.dialogs.JavaHomeOrMemoryDialogParent
  - setUtilitiesUserParameters
```
public void setUtilitiesUserParameters(com.compomics.util.parameters.UtilitiesUserParameters utilitiesUserParameters)
```
    Set the utilities user parameters.
    
    Parameters:
    
    utilitiesUserParameters - the utilities user parameters
  - setDefaultParameters
```
public void setDefaultParameters()
```
    Set the default parameters.
  - updateAnnotationMenu
```
public void updateAnnotationMenu()
```
    Updates the ions used for fragment annotation.
  - updateSpectrumAnnotations
```
public void updateSpectrumAnnotations()
```
    Updates the annotations in the selected tab.
  - updateModificationColorCoding
```
public void updateModificationColorCoding()
```
    Update the modification color coding in all tabs.
  - getProjectParameters
```
public com.compomics.util.experiment.ProjectParameters getProjectParameters()
```
    Returns the project parameters.
    
    Returns:
    
    the project parameters
  - getIdentification
```
public com.compomics.util.experiment.identification.Identification getIdentification()
```
    Returns the identification displayed.
    
    Returns:
    
    the identification displayed
  - getSequenceProvider
```
public com.compomics.util.experiment.io.biology.protein.SequenceProvider getSequenceProvider()
```
    Returns the sequence provider.
    
    Returns:
    
    the sequence provider
  - getSpectrumProvider
```
public com.compomics.util.experiment.mass_spectrometry.SpectrumProvider getSpectrumProvider()
```
    Returns the spectrum provider.
    
    Returns:
    
    the spectrum provider
  - setSequenceProvider
```
public void setSequenceProvider(com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider)
```
    Sets the sequence provider.
    
    Parameters:
    
    sequenceProvider - the sequence provider
  - getProteinDetailsProvider
```
public com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider getProteinDetailsProvider()
```
    Returns the protein details provider.
    
    Returns:
    
    the protein details provider
  - setProteinDetailsProvider
```
public void setProteinDetailsProvider(com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider)
```
    Sets the protein details provider.
    
    Parameters:
    
    proteinDetailsProvider - the protein details provider
  - setMsFileHandler
```
public void setMsFileHandler(com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler msFileHandler)
```
    Sets the mass spectrometry file handler.
    
    Parameters:
    
    msFileHandler - The mass spectrometry file handler.
  - setIdentification
```
public void setIdentification(com.compomics.util.experiment.identification.Identification identification)
```
    Sets the identification.
    
    Parameters:
    
    identification - the identification
  - getFilterParameters
```
public com.compomics.util.gui.filtering.FilterParameters getFilterParameters()
```
    Return the filter parameters to use.
    
    Returns:
    
    the filter parameters to use
  - getDisplayParameters
```
public DisplayParameters getDisplayParameters()
```
    Return the display parameters to use.
    
    Returns:
    
    the display parameters to use
  - setFilterParameters
```
public void setFilterParameters(com.compomics.util.gui.filtering.FilterParameters filterParameters)
```
    Sets the filter parameters to use.
    
    Parameters:
    
    filterParameters - the filter parameters to use
  - setDisplayParameters
```
public void setDisplayParameters(DisplayParameters displayParameters)
```
    Sets the display parameters to use.
    
    Parameters:
    
    displayParameters - the display parameters to use
  - getSpectrumCountingParameters
```
public com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters getSpectrumCountingParameters()
```
    Returns the spectrum counting parameters.
    
    Returns:
    
    the spectrum counting parameters
  - setSpectrumCountingParameters
```
public void setSpectrumCountingParameters(com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingParameters)
```
    Sets new spectrum counting parameters.
    
    Parameters:
    
    spectrumCountingParameters - new spectrum counting parameters
  - getIdentificationParameters
```
public com.compomics.util.parameters.identification.IdentificationParameters getIdentificationParameters()
```
    Returns the identification parameters.
    
    Returns:
    
    the identification parameters
  - setIdentificationParameters
```
public void setIdentificationParameters(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters)
```
    Sets the identification parameters.
    
    Parameters:
    
    identificationParameters - the identification parameters
  - getProcessingParameters
```
public com.compomics.util.parameters.tools.ProcessingParameters getProcessingParameters()
```
    Returns the initial processing preferences.
    
    Returns:
    
    the initial processing preferences
  - setProcessingParameters
```
public void setProcessingParameters(com.compomics.util.parameters.tools.ProcessingParameters processingParameters)
```
    Sets the initial processing preferences.
    
    Parameters:
    
    processingParameters - the initial processing preferences
  - resetModificationFactory
```
public void resetModificationFactory()
```
    Resets the modification factory.
  - getSparklineColor
```
public Color getSparklineColor()
```
    Get the sparklines color.
    
    Returns:
    
    the sparklineColor
  - setSparklineColor
```
public void setSparklineColor(Color sparklineColor)
```
    Set the sparklines color.
    
    Parameters:
    
    sparklineColor - the sparklineColor to set
  - getSparklineColorNonValidated
```
public Color getSparklineColorNonValidated()
```
    Get the non-validated sparklines color.
    
    Returns:
    
    the non-validated sparklineColor
  - setSparklineColorNonValidated
```
public void setSparklineColorNonValidated(Color sparklineColorNonValidated)
```
    Set the non-validated sparklines color.
    
    Parameters:
    
    sparklineColorNonValidated - the non-validated sparklineColor to set
  - getSparklineColorNotFound
```
public Color getSparklineColorNotFound()
```
    Get the not found sparklines color.
    
    Returns:
    
    the not found sparklineColor
  - getSparklineColorPossible
```
public Color getSparklineColorPossible()
```
    Get the possible sparklines color.
    
    Returns:
    
    the possible sparklineColor
  - setSparklineColorPossible
```
public void setSparklineColorPossible(Color sparklineColorPossible)
```
    Set the possible sparklines color.
    
    Parameters:
    
    sparklineColorPossible - the possible sparklineColor to set
  - getBubbleScale
```
public double getBubbleScale()
```
    Returns the bubble plot scale value.
    
    Returns:
    
    the bubble plot scale value
  - setSelectedItems
```
public void setSelectedItems(long proteinKey,
                             long peptideKey,
                             String spectrumFile,
                             String spectrumTitle)
```
    Sets the keys of the selected protein, peptide and PSM.
    
    Parameters:
    
    proteinKey - the key of the selected protein
    
    peptideKey - the key of the selected peptide
    
    spectrumFile - the file of the selected spectrum
    
    spectrumTitle - the title of the selected spectrum
  - updateSelectionInCurrentTab
```
public void updateSelectionInCurrentTab()
```
    Updates the selected items in the currently opened tab.
  - resetSelectedItems
```
public void resetSelectedItems()
```
    Resets the items selection.
  - setSelectedItems
```
public void setSelectedItems()
```
    Sets the selected item based on the selected tab.
  - getSelectedProteinKey
```
public long getSelectedProteinKey()
```
    Returns the key of the selected protein.
    
    Returns:
    
    the key of the selected protein
  - getSelectedPeptideKey
```
public long getSelectedPeptideKey()
```
    Returns the key of the selected peptide.
    
    Returns:
    
    the key of the selected peptide
  - getSelectedSpectrumFile
```
public String getSelectedSpectrumFile()
```
    Returns the currently selected spectrum file.
    
    Returns:
    
    the file of the selected spectrum
  - getSelectedSpectrumTitle
```
public String getSelectedSpectrumTitle()
```
    Returns the currently selected spectrum title.
    
    Returns:
    
    the title of the selected spectrum
  - clearData
```
public void clearData(boolean clearDatabaseFolder,
                      boolean updateGuiComponents)
```
    Clear the data from the previous experiment.
    
    Parameters:
    
    clearDatabaseFolder - decides if the database folder is to be cleared or not
    
    updateGuiComponents - true if the GUI components are to be updated
  - clearParameters
```
public void clearParameters()
```
    Clears the project parameters.
  - getOverviewPanel
```
public OverviewPanel getOverviewPanel()
```
    Returns the OverviewPanel.
    
    Returns:
    
    the OverviewPanel
  - getProteinFractionsPanel
```
public ProteinFractionsPanel getProteinFractionsPanel()
```
    Returns the fractions panel.
    
    Returns:
    
    the fractions panel
  - getValidationPanel
```
public ValidationPanel getValidationPanel()
```
    Returns the validation panel.
    
    Returns:
    
    the validation panel
  - getModificationsPanel
```
public ModificationsPanel getModificationsPanel()
```
    Returns the modification panel.
    
    Returns:
    
    the modification panel
  - getProteinStructurePanel
```
public ProteinStructurePanel getProteinStructurePanel()
```
    Returns the ProteinStructurePanel.
    
    Returns:
    
    the ProteinStructurePanel
  - getSpectrumIdentificationPanel
```
public SpectrumIdentificationPanel getSpectrumIdentificationPanel()
```
    Returns the SpectrumIdentificationPanel.
    
    Returns:
    
    the SpectrumIdentificationPanel
  - getGOPanel
```
public GOEAPanel getGOPanel()
```
    Returns the GO Panel.
    
    Returns:
    
    the GO Panel
  - getPreferredColumnWidth
```
public int getPreferredColumnWidth(JTable table,
                                   int colIndex,
                                   int margin)
```
    Gets the preferred width of the column specified by colIndex. The column will be just wide enough to show the column head and the widest cell in the column. Margin pixels are added to the left and right (resulting in an additional width of 2*margin pixels.
    Note that this method iterates all rows in the table to get the perfect width of the column!
    
    Parameters:
    
    table - the table
    
    colIndex - the colum index
    
    margin - the margin to add
    
    Returns:
    
    the preferred width of the column
  - enableSpectrumExport
```
public void enableSpectrumExport(boolean enable)
```
    Enable or disable the spectrum export in the overview panel.
    
    Parameters:
    
    enable - if true the spectrum export in the overview panel will be enabled
  - updateMainMatch
```
public void updateMainMatch(String mainMatch,
                            int proteinInferenceType)
```
    Update the protein match in the different tabs.
    
    Parameters:
    
    mainMatch - the protein match to use
    
    proteinInferenceType - the protein inference group type
  - setDataSaved
```
public void setDataSaved(boolean dataSaved)
```
    Set whether the current data has been saved to a psdb file or not.
    
    Parameters:
    
    dataSaved - whether the current data has been saved to a psdb file or not
  - getSelectedTab
```
public int getSelectedTab()
```
    Returns the selected tab as indexed by the static fields.
    
    Returns:
    
    the selected tab as indexed by the static fields
  - getDisplayedProteins
```
public long[] getDisplayedProteins()
```
    Returns a list of keys of the currently displayed proteins.
    
    Returns:
    
    a list of keys of the currently displayed proteins
  - getDisplayedPeptides
```
public long[] getDisplayedPeptides()
```
    Returns a list of keys of the currently displayed peptides.
    
    Returns:
    
    a list of keys of the currently displayed peptides
  - getDisplayedSpectrumMatches
```
public long[] getDisplayedSpectrumMatches()
```
    Returns a list of keys of the currently displayed spectrum matches.
    
    Returns:
    
    a list of keys of the currently displayed spectrum matches
  - getDisplayedAssumptions
```
public long[] getDisplayedAssumptions()
```
    Returns a list of keys of the currently displayed assumptions.
    
    Returns:
    
    a list of keys of the currently displayed assumptions
  - openProteinLinks
```
public void openProteinLinks(String links)
```
    Opens one or more protein links in the default web browser.
    
    Parameters:
    
    links - the links to open
  - getScoreAndConfidenceDecimalFormat
```
public DecimalFormat getScoreAndConfidenceDecimalFormat()
```
    Returns the decimal format used for the score and confidence columns.
    
    Returns:
    
    the decimal format used for the score and confidence columns
  - catchException
```
public void catchException(Exception e)
```
    Method called whenever an exception is caught.
    
    Parameters:
    
    e - the exception caught
  - getExceptionHandler
```
public com.compomics.util.exceptions.exception_handlers.FrameExceptionHandler getExceptionHandler()
```
    Returns the exception handler.
    
    Returns:
    
    the exception handler
  - close
```
public void close()
```
    Closes the frame by first checking if the project ought to be saved.
  - restart
```
public void restart()
```
    Closes and restarts PeptideShaker. Does not work inside the IDE of course.
    
    Specified by:
    
    restart in interface com.compomics.software.dialogs.JavaHomeOrMemoryDialogParent
  - updateAnnotationMenus
```
public void updateAnnotationMenus(com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters specificAnnotationParameters,
                                  int precursorCharge,
                                  HashSet<String> modNames)
```
    Update the annotation menu bar with the current annotation preferences.
    
    Parameters:
    
    specificAnnotationParameters - the specific annotation parameters
    
    precursorCharge - the precursor charges
    
    modNames - the names of the modifications
  - getSpecificAnnotationParameters
```
public com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters getSpecificAnnotationParameters(String spectrumFile,
                                                                                                                                     String spectrumTitle,
                                                                                                                                     com.compomics.util.experiment.identification.SpectrumIdentificationAssumption spectrumIdentificationAssumption)
```
    Returns the specific annotation parameters corresponding to the given spectrum, hit, and the menu selections.
    
    Parameters:
    
    spectrumFile - The file name of the spectrum.
    
    spectrumTitle - The title of the spectrum.
    
    spectrumIdentificationAssumption - The spectrum annotation preferences.
    
    Returns:
    
    the specific annotation parameters corresponding to the given spectrum, hit, and the menu selection
  - getAnnotationMenuBar
```
public JMenuBar getAnnotationMenuBar()
```
    Returns the annotation menu bar.
    
    Returns:
    
    the annotation menu bar
  - updateAnnotationMenuBarVisableOptions
```
public void updateAnnotationMenuBarVisableOptions(boolean showSpectrumOptions,
                                                  boolean showBubblePlotOptions,
                                                  boolean showIonTableOptions,
                                                  boolean showPtmPlotOptions,
                                                  boolean showSingleSpectrumExportOptions)
```
    Updates the visible menu items on the settings menu of the annotation menu bar.
    
    Parameters:
    
    showSpectrumOptions - if true, the spectrum options are shown
    
    showBubblePlotOptions - if true, the bubble plot options are shown
    
    showIonTableOptions - if true, the ion table options are shown
    
    showPtmPlotOptions - if true, the PTM plot option is shown
    
    showSingleSpectrumExportOptions - if true, the single spectrum export options are shown
  - updateRecentProjectsList
```
public void updateRecentProjectsList()
```
    Add the list of recently used files to the file menu.
  - loadRecentProjectsList
```
public void loadRecentProjectsList(JPopupMenu menu,
                                   WelcomeDialog welcomeDialog)
```
    Add the list of recently used files to the file menu.
    
    Parameters:
    
    menu - the menu to add the recent files list to
    
    welcomeDialog - the welcome dialog reference
  - getProjectDetails
```
public ProjectDetails getProjectDetails()
```
    Returns the project details.
    
    Returns:
    
    the project details
  - setProjectDetails
```
public void setProjectDetails(ProjectDetails projectDetails)
```
    Sets the project details.
    
    Parameters:
    
    projectDetails - the project details
  - importPeptideShakerZipFromURL
```
public void importPeptideShakerZipFromURL(String zipURL,
                                          String destinationFolder)
```
    Imports a PeptideShaker zip file from a URL.
    
    Parameters:
    
    zipURL - the PeptideShaker zip file to import
    
    destinationFolder - the folder to download and unzip the project in
  - importPeptideShakerZipFile
```
public void importPeptideShakerZipFile(File zipFile)
```
    Imports information from a PeptideShaker zip file.
    
    Parameters:
    
    zipFile - the PeptideShaker zip file to import
  - importPeptideShakerFile
```
public void importPeptideShakerFile(File psFile,
                                    boolean importFromZip)
```
    Imports information from a PeptideShaker file.
    
    Parameters:
    
    psFile - The PeptideShaker file to import.
    
    importFromZip - flag that determines if psdb was imported from a zip file
  - lostOwnership
```
public void lostOwnership(Clipboard clipboard,
                          Transferable contents)
```
    Specified by:
    
    lostOwnership in interface ClipboardOwner
  - exportSelectedSpectraAsMgf
```
public void exportSelectedSpectraAsMgf()
                                throws IOException
```
    Export the current spectrum as an mgf.
    
    Throws:
    
    IOException - Exception thrown whenever an error occurred while writing the mgf file
  - exportAnnotatedSpectrum
```
public void exportAnnotatedSpectrum()
                             throws IOException
```
    Export the current spectrum annotation.
    
    Throws:
    
    IOException - exception thrown whenever an error occurred while reading or writing a file
  - exportSpectrumAsFigure
```
public void exportSpectrumAsFigure()
```
    Export the current spectrum as a figure.
  - exportSequenceFragmentationAsFigure
```
public void exportSequenceFragmentationAsFigure()
```
    Export the current sequence fragmentation as a figure.
  - exportIntensityHistogramAsFigure
```
public void exportIntensityHistogramAsFigure()
```
    Export the current intensity histogram as a figure.
  - exportMassErrorPlotAsFigure
```
public void exportMassErrorPlotAsFigure()
```
    Export the current mass error plot as a figure.
  - exportBubblePlotAsFigure
```
public void exportBubblePlotAsFigure()
```
    Export the current bubble plot as a figure.
  - setDisplayOptions
```
public void setDisplayOptions(boolean displayProteins,
                              boolean displayPeptidesAndPsms,
                              boolean displayCoverage,
                              boolean displaySpectrum)
```
    Update the display options for the overview tab.
    
    Parameters:
    
    displayProteins - if the proteins panel is to be displayed
    
    displayPeptidesAndPsms - if the peptides and PSMs panel is to be displayed
    
    displayCoverage - if the protein coverage panel is to be displayed
    
    displaySpectrum - if the spectrum panel is to be displayed
  - getCurrentMassDeltas
```
public HashMap<Double,String> getCurrentMassDeltas()
```
    Get the current delta masses for use when annotating the spectra.
    
    Returns:
    
    the current delta masses
  - saveProject
```
public void saveProject(boolean aCloseWhenDone,
                        boolean aExportToZipWhenDone)
```
    Saves the modifications made to the project.
    
    Parameters:
    
    aCloseWhenDone - if true, PeptideShaker closes after saving
    
    aExportToZipWhenDone - if true, the project is also saved as a zip file
  - setUpdated
```
public void setUpdated(int tabIndex,
                       boolean updated)
```
    Sets that the tab was updated.
    
    Parameters:
    
    tabIndex - integer indicating which tab (according to the static indexing) was updated.
    
    updated - boolean indicating whether the tab is updated or not
  - updateTabbedPanes
```
public void updateTabbedPanes()
```
    Update the tabbed panes.
  - getStarHider
```
public StarHider getStarHider()
```
    Returns the object responsible for starring/hiding matches.
    
    Returns:
    
    the object responsible for starring/hiding matches
  - getIdentificationFeaturesGenerator
```
public com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator getIdentificationFeaturesGenerator()
```
    Returns the identification features generator.
    
    Returns:
    
    the identification features generator
  - resetIdentificationFeaturesGenerator
```
public void resetIdentificationFeaturesGenerator()
```
    Resets the feature generator.
  - setIdentificationFeaturesGenerator
```
public void setIdentificationFeaturesGenerator(com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator)
```
    Sets the feature generator.
    
    Parameters:
    
    identificationFeaturesGenerator - the identification features generator
  - resetDisplayFeaturesGenerator
```
public void resetDisplayFeaturesGenerator()
```
    Resets the display features generator.
  - getDisplayFeaturesGenerator
```
public DisplayFeaturesGenerator getDisplayFeaturesGenerator()
```
    Returns the display features generator.
    
    Returns:
    
    the display features generator
  - getMetrics
```
public com.compomics.util.experiment.identification.peptide_shaker.Metrics getMetrics()
```
    Returns the metrics saved while loading the files.
    
    Returns:
    
    the metrics saved while loading the files
  - setMetrics
```
public void setMetrics(com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics)
```
    Sets the metrics saved while loading the files.
    
    Parameters:
    
    metrics - the metrics saved while loading the files
  - getProjectType
```
public com.compomics.util.parameters.peptide_shaker.ProjectType getProjectType()
```
    Returns the project type.
    
    Returns:
    
    the project type
  - setProjectType
```
public void setProjectType(com.compomics.util.parameters.peptide_shaker.ProjectType projectType)
```
    Sets the project type.
    
    Parameters:
    
    projectType - the project type
  - getGeneMaps
```
public com.compomics.util.experiment.biology.genes.GeneMaps getGeneMaps()
```
    Returns the gene maps.
    
    Returns:
    
    the gene maps
  - setGeneMaps
```
public void setGeneMaps(com.compomics.util.experiment.biology.genes.GeneMaps geneMaps)
```
    Sets the gene maps.
    
    Parameters:
    
    geneMaps - the gene maps
  - spectrumFileSelectionChanged
```
public void spectrumFileSelectionChanged(String spectrumFile)
```
    Sets the new spectrum file selected.
    
    Parameters:
    
    spectrumFile - the name of the new spectrum file
  - saveProjectAs
```
public void saveProjectAs(boolean closeWhenDone,
                          boolean aExportToZipWhenDone)
```
    Save the project to a new location.
    
    Parameters:
    
    closeWhenDone - if true, PeptideShaker closes when done saving
    
    aExportToZipWhenDone - if true, the project is also saved as a zip file
  - getUserSelectedFile
```
public File getUserSelectedFile(String aSuggestedFileName,
                                String aFileEnding,
                                String aFileFormatDescription,
                                String aDialogTitle,
                                boolean openDialog)
```
    Returns the file selected by the user, or null if no file was selected.
    
    Parameters:
    
    aSuggestedFileName - the suggested file name, can be null
    
    aFileEnding - the file type, e.g., .txt
    
    aFileFormatDescription - the file format description, e.g., (Mascot Generic Format) *.mgf
    
    aDialogTitle - the title for the dialog
    
    openDialog - if true an open dialog is shown, false results in a save dialog
    
    Returns:
    
    the file selected by the user, or null if no file or folder was selected
  - jumpToTab
```
public void jumpToTab(int tabIndex)
```
    Jumps to the desired tab
    
    Parameters:
    
    tabIndex - index of the tab as indexed by the static fields
  - showSparklines
```
public boolean showSparklines()
```
    Returns true if the sparklines are to be shown.
    
    Returns:
    
    true if the sparklines are to be show
  - updateSurroundingAminoAcids
```
public void updateSurroundingAminoAcids()
```
    Update the number of surrounding amino acids displayed.
  - checkNewsFeed
```
public void checkNewsFeed()
```
    Displays a news feed at the bottom of the GUI.
  - openExampleFile
```
public void openExampleFile()
```
    Open the PeptideShaker example dataset.
  - updateFilterSettingsField
```
public void updateFilterSettingsField(String text)
```
    Update the filter settings field. (Interface method: not implemented in this class as it is not needed.)
    
    Parameters:
    
    text - the text to set
  - exportProjectAsZip
```
public void exportProjectAsZip()
```
    Export the project as a zip file.
  - getNormalIcon
```
public Image getNormalIcon()
```
    Returns the normal icon.
    
    Returns:
    
    the normal icon
  - getWaitingIcon
```
public Image getWaitingIcon()
```
    Returns the waiting icon.
    
    Returns:
    
    the waiting icon
  - getDefaultPsmSelection
```
public long getDefaultPsmSelection(long peptideKey)
```
    Returns the default PSM, i.e., the "best" PSM for the given peptide.
    
    Parameters:
    
    peptideKey - the peptide to get the PSM for
    
    Returns:
    
    the key of the default PSM
  - getDefaultPeptideSelection
```
public long getDefaultPeptideSelection(long proteinKey)
```
    Returns the default peptide, i.e., the "best" peptide for the given protein.
    
    Parameters:
    
    proteinKey - the protein to get the peptide for
    
    Returns:
    
    the key of the default peptide
  - clearGeneMappings
```
public void clearGeneMappings()
```
    Clear the gene mappings.
  - notificationClicked
```
public void notificationClicked(String notificationType)
```
    Specified by:
    
    notificationClicked in interface com.compomics.util.gui.error_handlers.notification.NotificationDialogParent
  - addNote
```
public void addNote(String note)
```
    Add a note to the current list of notes.
    
    Parameters:
    
    note - the note to add, can contain HTML formatting, but not the HTML start and end tags
  - setCurentNotes
```
public void setCurentNotes(ArrayList<String> currentNotes)
```
    Set the list of current notes.
    
    Parameters:
    
    currentNotes - the notes to set
  - updateNotesNotificationCounter
```
public void updateNotesNotificationCounter()
```
    Update the notification counter for the notes.
  - showNotesNotification
```
public void showNotesNotification()
```
    Show a note notification pop up.
  - addTip
```
public void addTip(String tip)
```
    Add a tip to the current list of tips.
    
    Parameters:
    
    tip - the tip to add, can contain HTML formatting, but not the HTML start and end tags
  - setCurentTips
```
public void setCurentTips(ArrayList<String> currentTips)
```
    Set the list of current tips.
    
    Parameters:
    
    currentTips - the tips to set
  - updateTipsNotificationCounter
```
public void updateTipsNotificationCounter()
```
    Update the notification counter for the tips.
  - showTipsNotification
```
public void showTipsNotification()
```
    Show a tip notification pop up.
  - getExtendedProjectReport
```
public String getExtendedProjectReport()
```
    Returns an extended HTML project report.
    
    Returns:
    
    an extended HTML project report
  - checkForNewVersion
```
public boolean checkForNewVersion()
```
    Check for new version.
    
    Returns:
    
    true if a new version is to be downloaded

Class PeptideShakerGUI

Nested Class Summary

Nested classes/interfaces inherited from class javax.swing.JFrame

Nested classes/interfaces inherited from class java.awt.Frame

Nested classes/interfaces inherited from class java.awt.Window

Nested classes/interfaces inherited from class java.awt.Container

Nested classes/interfaces inherited from class java.awt.Component

Field Summary

Fields inherited from class javax.swing.JFrame

Fields inherited from class java.awt.Frame

Fields inherited from class java.awt.Component

Fields inherited from interface javax.swing.WindowConstants

Fields inherited from interface java.awt.image.ImageObserver

Constructor Summary

Method Summary

Methods inherited from class javax.swing.JFrame

Methods inherited from class java.awt.Frame

Methods inherited from class java.awt.Window

Methods inherited from class java.awt.Container

Methods inherited from class java.awt.Component

Methods inherited from class java.lang.Object

Methods inherited from interface java.awt.MenuContainer

Field Detail

OVER_VIEW_TAB_INDEX

SPECTRUM_ID_TAB_INDEX

PROTEIN_FRACTIONS_TAB_INDEX

MODIFICATIONS_TAB_INDEX

STRUCTURES_TAB_INDEX

ANNOTATION_TAB_INDEX

GO_ANALYSIS_TAB_INDEX

VALIDATION_TAB_INDEX

QC_PLOTS_TAB_INDEX

TITLED_BORDER_HORIZONTAL_PADDING

TITLED_BORDER_HORIZONTAL_PADDING_HTML

DARK_THEME_BACKGROUND_COLOR

Constructor Detail

PeptideShakerGUI

PeptideShakerGUI

Method Detail

main

loadUserParameters

setProject

updateFrameTitle

resetFrameTitle

getLastSelectedFolder

setLastSelectedFolder

editPathSettings

initiateDisplay

displayResults

disableSpectrumDisplay

setUpLogFile

getUserParameters

getUtilitiesUserParameters

setUtilitiesUserParameters

setDefaultParameters

updateAnnotationMenu

updateSpectrumAnnotations

updateModificationColorCoding

getProjectParameters

getIdentification

getSequenceProvider

getSpectrumProvider

setSequenceProvider

getProteinDetailsProvider

setProteinDetailsProvider

setMsFileHandler

setIdentification

getFilterParameters

getDisplayParameters

setFilterParameters

setDisplayParameters

getSpectrumCountingParameters

setSpectrumCountingParameters

getIdentificationParameters

setIdentificationParameters

getProcessingParameters

setProcessingParameters

resetModificationFactory

getSparklineColor

setSparklineColor