eu.isas.peptideshaker.gui.tabpanels

Class ModificationsPanel

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

javax.swing.JPanel

eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel

All Implemented Interfaces:

ImageObserver, MenuContainer, Serializable, Accessible

public class ModificationsPanel
extends JPanel

The Modifications tab.

Author:

Marc Vaudel, Harald Barsnes

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

Modifier and Type	Field and Description
static String	NO_MODIFICATION The modification name for no modification.

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
ModificationsPanel(PeptideShakerGUI peptideShakerGUI) Creates a new Modifications tab.

Method Summary

Modifier and Type	Method and Description
void	displayResults() Displays the results.
long[]	getDisplayedPeptides() Returns a list of the keys of the currently displayed peptides.
long[]	getDisplayedProteinMatches() Returns a list of the keys of the proteins of the currently displayed peptides.
long[]	getDisplayedSpectrumMatches() Returns a list of the PSM keys of the currently displayed assumptions.
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
String	getSelectedModification() Returns the selected modification name.
long[]	getSelectedPsmsKeys() Returns the keys of the selected PSMs.
TreeMap<String,TreeSet<String>>	getSelectedSpectrumTitles() Returns the titles of the selected spectra in the PSM table in a map by file name.
Component	getSpectrum() Returns the spectrum panel.
void	newItemSelection() Provides to the PeptideShakerGUI instance the currently selected peptide and PSM.
void	setAccuracySliderValue(int value) Set the accuracy slider value.
void	setIntensitySliderValue(int value) Set the intensity slider value.
void	showSparkLines(boolean showSparkLines) Displays or hide sparklines in tables.
void	showSpectrumAnnotationMenu() Makes sure that the annotation menu bar is visible.
void	updateGraphics(com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog) Updates the graphics components.
void	updateModificationColors() Update the modification color coding.
void	updateModificationProfiles(com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog) Redraws the modification profiles.
void	updatePeptideTable(com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog) Updates the peptide table.
void	updateRelatedPeptidesTable(com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog) Updates the related peptides table.
void	updateSelection() Tries to find the last selected peptide.
void	updateSeparators() Method called whenever the component is resized to maintain the look of the GUI.
void	updateSpectrum(long spectrumMatchKey, Long secondSpectrumMatchKey) Update the spectra according to the currently selected PSM.

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

Field Detail

NO_MODIFICATION

public static final String NO_MODIFICATION

The modification name for no modification.

See Also:

Constant Field Values

Constructor Detail

ModificationsPanel

public ModificationsPanel(PeptideShakerGUI peptideShakerGUI)

Creates a new Modifications tab.

Parameters:

peptideShakerGUI - the PeptideShaker parent frame

Method Detail

getDisplayedProteinMatches

public long[] getDisplayedProteinMatches()

Returns a list of the keys of the proteins of the currently displayed peptides.

Returns:

a list of the keys of the proteins of the currently displayed peptides

getDisplayedPeptides

public long[] getDisplayedPeptides()

Returns a list of the keys of the currently displayed peptides.

Returns:

a list of the keys of the currently displayed peptides

getDisplayedSpectrumMatches

public long[] getDisplayedSpectrumMatches()

Returns a list of the PSM keys of the currently displayed assumptions.

Returns:

a list of the PSM keys of the currently displayed assumptions

showSparkLines

public void showSparkLines(boolean showSparkLines)

Displays or hide sparklines in tables.

Parameters:

showSparkLines - boolean indicating whether sparklines shall be displayed or hidden

getSelectedModification

public String getSelectedModification()

Returns the selected modification name.

Returns:

the selected modification name

displayResults

public void displayResults()

Displays the results.

updateSelection

public void updateSelection()

Tries to find the last selected peptide.

updatePeptideTable

public void updatePeptideTable(com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog)

Updates the peptide table.

Parameters:

progressDialog - the progress dialog

updateRelatedPeptidesTable

public void updateRelatedPeptidesTable(com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog)

Updates the related peptides table.

Parameters:

progressDialog - a progress dialog

updateGraphics

public void updateGraphics(com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog)

Updates the graphics components.

Parameters:

progressDialog - the progress dialog

updateSpectrum

public void updateSpectrum(long spectrumMatchKey,
                           Long secondSpectrumMatchKey)

Update the spectra according to the currently selected PSM.

Parameters:

spectrumMatchKey - the main spectrum match key

secondSpectrumMatchKey - the secondary spectrum key

getSelectedPsmsKeys

public long[] getSelectedPsmsKeys()

Returns the keys of the selected PSMs.

Returns:

the keys of the selected PSMs

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

showSpectrumAnnotationMenu

public void showSpectrumAnnotationMenu()

Makes sure that the annotation menu bar is visible.

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 modification color coding.

updateModificationProfiles

public void updateModificationProfiles(com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog)

Redraws the modification profiles. For example if the modification colors are updated.

Parameters:

progressDialog - the progress dialog

updateSeparators

public void updateSeparators()

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

newItemSelection

public void newItemSelection()

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