eu.isas.peptideshaker.gui.tabpanels

Class OverviewPanel

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

javax.swing.JPanel

eu.isas.peptideshaker.gui.tabpanels.OverviewPanel

All Implemented Interfaces:

ProteinSequencePanelParent, ImageObserver, MenuContainer, Serializable, Accessible

public class OverviewPanel
extends JPanel
implements ProteinSequencePanelParent

The overview panel displaying the proteins, the peptides and the spectra.

Author:

Harald Barsnes, Marc Vaudel

See Also:

Serialized Form

Nested Class Summary

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

JPanel.AccessibleJPanel

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

JComponent.AccessibleJComponent

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 inherited from class javax.swing.JComponent

listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW

Fields inherited from class java.awt.Component

accessibleContext, BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

Constructors

Constructor and Description
OverviewPanel(PeptideShakerGUI parent) Creates a new OverviewPanel.

Method Summary

Modifier and Type	Method and Description
void	annotationClicked(ArrayList<ResidueAnnotation> allAnnotation, org.jfree.chart.ChartMouseEvent cme)
void	clearData() Clear all the data.
void	displayResults() Displays the results in the tables.
void	enableDarkTheme(boolean darkTheme) Enable or disable the dark theme.
Component	getBubblePlot() Returns the bubble plot.
long[]	getDisplayedPeptides() Returns a list of keys of the displayed peptides
long[]	getDisplayedProteins() Returns a list of keys of the displayed proteins
long[]	getDisplayedSpectrumMatches() Returns a list of keys of the displayed PSMs
com.compomics.util.gui.spectrum.IntensityHistogram	getIntensityHistogramPlot() Returns the intensity histogram plot panel.
com.compomics.util.gui.spectrum.MassErrorPlot	getMassErrorPlot() Returns the mass error plot panel.
JTable	getProteinTable() Returns the protein table.
HashMap<Long,ArrayList<com.compomics.util.experiment.identification.SpectrumIdentificationAssumption>>	getSelectedIdentificationAssumptions() Returns a map of the selected spectrum identification assumptions as a map: spectrum key | assumption
long[]	getSelectedPsmKeys() Returns the keys of the selected spectra in the PSM table.
int	getSelectedSpectrumTabIndex() Returns the current selected tab in the spectrum and fragment ions tabbed pane.
TreeMap<String,TreeSet<String>>	getSelectedSpectrumTitles() Returns the titles of the selected spectra in the PSM table in a map by file name.
Component	getSequenceFragmentationPlot() Returns the sequence fragmentation plot panel.
Component	getSpectrum() Returns the spectrum panel.
Component	getSpectrumAndPlots() Returns the extended spectrum panel.
boolean	isSpectrumEnabled() Returns true of the spectrum tab is enabled.
void	newItemSelection() Provides to the PeptideShakerGUI instance the currently selected protein, peptide and PSM.
void	selfUpdating(boolean selfUpdating) Deactivates the self updating tables.
void	setAccuracySliderValue(int value) Set the accuracy slider value.
void	setDisplayOptions(boolean displayProteins, boolean displayPeptidesAndPSMs, boolean displayCoverage, boolean displaySpectrum) Sets the whether the protein coverage and the spectrum shall be displayed.
void	setIntensitySliderValue(int value) Set the intensity slider value.
void	showSeparators(boolean showSeparators) Enable or disable the separators.
void	showSparkLines(boolean showSparkLines) Displays or hide sparklines in the tables.
void	showSpectrumAnnotationMenu() Makes sure that the annotation menu bar is shown in the currently visible spectrum and fragment ions tabbed pane.
void	updateBubblePlot() Updated the bubble plot with the current PSMs.
void	updateModificationColors() Update the PTM color coding.
void	updatePeptidePanelTitle() Updates the peptide panel title with the number of validated/confident proteins.
void	updatePeptideProteinInference(int proteinInferenceType) Update the protein inference type for the currently selected peptide.
void	updateProteinPanelTitle() Updates the protein panel title with the number of validated/confident proteins.
void	updateProteinTable() Updates the results in the protein table and reselect the desired protein.
void	updatePsmOrder() Update the PSM order in the PSM table.
void	updatePsmPanelTitle() Updates the PSM panel title with the number of validated/confident
void	updateScores() Hides or displays the score columns in the protein and peptide tables.
void	updateSelection(boolean scrollToVisible) Update the selected protein and peptide.
void	updateSeparators() Method called whenever the component is resized to maintain the look of the GUI.
void	updateSpectrum() Updates the spectrum annotation.
void	updateSurroundingAminoAcids() Update the number of surrounding amino acids displayed.

Methods inherited from class javax.swing.JPanel

getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, 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, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

OverviewPanel

public OverviewPanel(PeptideShakerGUI parent)

Creates a new OverviewPanel.

Parameters:

parent - the PeptideShaker parent frame.

Method Detail

updateProteinPanelTitle

public void updateProteinPanelTitle()

Updates the protein panel title with the number of validated/confident proteins.

updatePeptidePanelTitle

public void updatePeptidePanelTitle()

Updates the peptide panel title with the number of validated/confident proteins.

updatePsmPanelTitle

public void updatePsmPanelTitle()

Updates the PSM panel title with the number of validated/confident

showSparkLines

public void showSparkLines(boolean showSparkLines)

Displays or hide sparklines in the tables.

Parameters:

showSparkLines - boolean indicating whether sparklines shall be displayed or hidden

getDisplayedProteins

public long[] getDisplayedProteins()

Returns a list of keys of the displayed proteins

Returns:

a list of keys of the displayed proteins

getDisplayedPeptides

public long[] getDisplayedPeptides()

Returns a list of keys of the displayed peptides

Returns:

a list of keys of the displayed peptides

getDisplayedSpectrumMatches

public long[] getDisplayedSpectrumMatches()

Returns a list of keys of the displayed PSMs

Returns:

a list of keys of the displayed PSMs

updateSeparators

public void updateSeparators()

Method called whenever the component is resized to maintain the look of the GUI.

setDisplayOptions

public void setDisplayOptions(boolean displayProteins,
                              boolean displayPeptidesAndPSMs,
                              boolean displayCoverage,
                              boolean displaySpectrum)

Sets the whether the protein coverage and the spectrum shall be displayed.

Parameters:

displayProteins - boolean indicating whether the proteins shall be displayed

displayPeptidesAndPSMs - boolean indicating whether the peptides and PSMs shall be displayed

displayCoverage - boolean indicating whether the protein coverage shall be displayed

displaySpectrum - boolean indicating whether the spectrum shall be displayed

updateBubblePlot

public void updateBubblePlot()

Updated the bubble plot with the current PSMs.

updateSpectrum

public void updateSpectrum()

Updates the spectrum annotation. Used when the user updates the annotation accuracy.

displayResults

public void displayResults()

Displays the results in the tables.

updateProteinTable

public void updateProteinTable()

Updates the results in the protein table and reselect the desired protein.

getProteinTable

public JTable getProteinTable()

Returns the protein table.

Returns:

the protein table

getSelectedPsmKeys

public long[] getSelectedPsmKeys()

Returns the keys of the selected spectra in the PSM table.

Returns:

the keys of the selected spectra in the PSM table

getSelectedSpectrumTitles

public TreeMap<String,TreeSet<String>> getSelectedSpectrumTitles()

Returns the titles of the selected spectra in the PSM table in a map by file name.

Returns:

The titles of the selected spectra in the PSM table in a map by file name.

getSelectedIdentificationAssumptions

public HashMap<Long,ArrayList<com.compomics.util.experiment.identification.SpectrumIdentificationAssumption>> getSelectedIdentificationAssumptions()

Returns a map of the selected spectrum identification assumptions as a map: spectrum key | assumption

Returns:

an ArrayList of the keys of the selected spectra in the PSM table

getSpectrum

public Component getSpectrum()

Returns the spectrum panel.

Returns:

the spectrum panel, or null if the spectrum tab is not enabled

getSpectrumAndPlots

public Component getSpectrumAndPlots()

Returns the extended spectrum panel.

Returns:

the extended spectrum panel, or null if the spectrum tab is not enabled

getSequenceFragmentationPlot

public Component getSequenceFragmentationPlot()

Returns the sequence fragmentation plot panel.

Returns:

the sequence fragmentation plot panel, or null if the spectrum tab is not enabled

getIntensityHistogramPlot

public com.compomics.util.gui.spectrum.IntensityHistogram getIntensityHistogramPlot()

Returns the intensity histogram plot panel.

Returns:

the intensity histogram plot panel, or null if the spectrum tab is not enabled

getMassErrorPlot

public com.compomics.util.gui.spectrum.MassErrorPlot getMassErrorPlot()

Returns the mass error plot panel.

Returns:

the mass error plot panel, or null if the spectrum tab is not enabled or the the mass error plot is not showing

getBubblePlot

public Component getBubblePlot()

Returns the bubble plot.

Returns:

the bubble plot

isSpectrumEnabled

public boolean isSpectrumEnabled()

Returns true of the spectrum tab is enabled.

Returns:

true of the spectrum tab is enabled

showSeparators

public void showSeparators(boolean showSeparators)

Enable or disable the separators.

Parameters:

showSeparators - if true the separators are enabled

updateScores

public void updateScores()

Hides or displays the score columns in the protein and peptide tables.

enableDarkTheme

public void enableDarkTheme(boolean darkTheme)

Enable or disable the dark theme.

Parameters:

darkTheme - enable or disable the dark theme

getSelectedSpectrumTabIndex

public int getSelectedSpectrumTabIndex()

Returns the current selected tab in the spectrum and fragment ions tabbed pane.

Returns:

the current selected tab in the spectrum and fragment ions tabbed pane

showSpectrumAnnotationMenu

public void showSpectrumAnnotationMenu()

Makes sure that the annotation menu bar is shown in the currently visible spectrum and fragment ions tabbed pane.

setIntensitySliderValue

public void setIntensitySliderValue(int value)

Set the intensity slider value.

Parameters:

value - the intensity slider value

setAccuracySliderValue

public void setAccuracySliderValue(int value)

Set the accuracy slider value.

Parameters:

value - the accuracy slider value

updateModificationColors

public void updateModificationColors()

Update the PTM color coding.

updatePsmOrder

public void updatePsmOrder()

Update the PSM order in the PSM table.

updatePeptideProteinInference

public void updatePeptideProteinInference(int proteinInferenceType)

Update the protein inference type for the currently selected peptide.

Parameters:

proteinInferenceType - the protein inference type

updateSelection

public void updateSelection(boolean scrollToVisible)

Update the selected protein and peptide.

Parameters:

scrollToVisible - if true the table also scrolls to make the selected row visible

newItemSelection

public void newItemSelection()

Provides to the PeptideShakerGUI instance the currently selected protein, peptide and PSM.

clearData

public void clearData()

Clear all the data.

annotationClicked

public void annotationClicked(ArrayList<ResidueAnnotation> allAnnotation,
                              org.jfree.chart.ChartMouseEvent cme)

Specified by:

annotationClicked in interface ProteinSequencePanelParent

updateSurroundingAminoAcids

public void updateSurroundingAminoAcids()

Update the number of surrounding amino acids displayed.

selfUpdating

public void selfUpdating(boolean selfUpdating)

Deactivates the self updating tables.

Parameters:

selfUpdating - boolean indicating whether the tables should update their content