Package eu.isas.peptideshaker.gui.tabpanels

Class SpectrumIdentificationPanel

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

javax.swing.JPanel

eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel

All Implemented Interfaces:

ImageObserver, MenuContainer, Serializable, Accessible

public class SpectrumIdentificationPanel
extends JPanel

The Spectrum ID panel.

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	Description
static final int	AGREEMENT	Static index for the ID software agreement: the ID softwares all have the same top ranking peptide without accounting for modification localization.
static final int	AGREEMENT_WITH_MODS	Static index for the ID software agreement: the ID softwares all have the same top ranking peptide.
static final int	CONFLICT	Static index for the ID software agreement: the ID software have different top ranking peptides.
static final int	NO_ID	Static index for the ID software agreement: no psm found.
static final int	PARTIALLY_MISSING	Static index for the ID software agreement: one or more of the softwares did not identify the spectrum, while one or more of the others did.

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	Description
SpectrumIdentificationPanel(PeptideShakerGUI peptideShakerGUI)	Create a new SpectrumIdentificationPanel.

Method Summary

Modifier and Type	Method	Description
void	displayResults()	Displays the results in the panel.
Component	getBubblePlot()	Returns the bubble plot.
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	getSelectedSpectrumTitle()	Returns the title of the currently selected spectrum.
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.
static int	isBestPsmEqualForAllIdSoftware(com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingPreferences, Integer numberOfAdvocatesUsed)	Returns true if all the used id software tools agree on the top PSM without accounting for modification localization, false otherwise.
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 the tables.
void	showSpectrumAnnotationMenu()	Makes sure that the annotation menu bar is visible.
void	updateModificationColors()	Update the PTM color coding.
void	updateScores()	Hides or displays the search engine scores in the spectrum identifications table.
void	updateSelection()	Updates the spectrum selected according to the user's last selection.
void	updateSeparators()	Method called whenever the component is resized to maintain the look of the GUI.
void	updateSpectrum()	Update the spectrum based on 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, 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, requestFocus, requestFocus, requestFocusInWindow, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setMixingCutoutShape, 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 Details

NO_ID

public static final int NO_ID

Static index for the ID software agreement: no psm found.

See Also:

• Constant Field Values

CONFLICT

public static final int CONFLICT

Static index for the ID software agreement: the ID software have different top ranking peptides.

See Also:

• Constant Field Values

PARTIALLY_MISSING

public static final int PARTIALLY_MISSING

Static index for the ID software agreement: one or more of the softwares did not identify the spectrum, while one or more of the others did.

See Also:

• Constant Field Values

AGREEMENT

public static final int AGREEMENT

Static index for the ID software agreement: the ID softwares all have the same top ranking peptide without accounting for modification localization.

See Also:

• Constant Field Values

AGREEMENT_WITH_MODS

public static final int AGREEMENT_WITH_MODS

Static index for the ID software agreement: the ID softwares all have the same top ranking peptide.

See Also:

• Constant Field Values

Constructor Details

SpectrumIdentificationPanel

public SpectrumIdentificationPanel(PeptideShakerGUI peptideShakerGUI)

Create a new SpectrumIdentificationPanel.

Parameters:

peptideShakerGUI - the PeptideShaker parent frame

Method Details

showSparkLines

public void showSparkLines(boolean showSparkLines)

Displays or hide sparklines in the tables.

Parameters:

showSparkLines - boolean indicating whether sparklines shall be displayed or hidden

displayResults

public void displayResults()

Displays the results in the panel.

getSelectedSpectrumTitle

public String getSelectedSpectrumTitle()

Returns the title of the currently selected spectrum.

Returns:

the title of the currently selected spectrum

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

updateSelection

public void updateSelection()

Updates the spectrum selected according to the user's last selection.

updateSpectrum

public void updateSpectrum()

Update the spectrum based on the currently selected PSM.

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.

getBubblePlot

public Component getBubblePlot()

Returns the bubble plot.

Returns:

the bubble plot

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.

updateSeparators

public void updateSeparators()

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

isBestPsmEqualForAllIdSoftware

public static int isBestPsmEqualForAllIdSoftware(com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch,
 com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingPreferences,
 Integer numberOfAdvocatesUsed)

Returns true if all the used id software tools agree on the top PSM without accounting for modification localization, false otherwise.

Parameters:

spectrumMatch - the PSM to check

sequenceMatchingPreferences - the sequence matching preferences

numberOfAdvocatesUsed - the total number of advocates used for the search

Returns:

true if all the used id software agree on the top PSM

updateScores

public void updateScores()

Hides or displays the search engine scores in the spectrum identifications table.