Package com.compomics.util.gui.spectrum

Class SequenceFragmentationPanel

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

javax.swing.JPanel

com.compomics.util.gui.spectrum.SequenceFragmentationPanel

All Implemented Interfaces:

ImageObserver, MenuContainer, Serializable, Accessible

public class SequenceFragmentationPanel
extends JPanel

This class was imported from the Peptizer and MascotDatfile parser, and was developed to display fragmentation information on the modified sequence as inspired by X!Tandem.

Author:

Kenny Helsens, Lennart Martens, 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	Description
SequenceFragmentationPanel()	Empty default constructor
SequenceFragmentationPanel(String aSequence, IonMatch[] aIonMatches, boolean boolModifiedSequence, boolean aHighlightModifications, ModificationParameters modificationProfile, int forwardIon, int rewindIon)	Creates a new SequenceFragmentationPanel working with B and Y ions.
SequenceFragmentationPanel(String taggedModifiedSequence, IonMatch[] aIonMatches, boolean aHighlightModifications, ModificationParameters modificationProfile, int forwardIon, int rewindIon)	Creates a new SequenceFragmentationPanel working with B and Y ions.

Method Summary

Modifier and Type	Method	Description
void	paint(Graphics g)	Paints the SequenceFragmentationPanel.
void	setFontColor(Color fontColor)	Set the color for the font of the peptide sequence.
void	setIonMatches(IonMatch[] lIonMatches)	Set the ArrayList with FragmentIon matches.
void	setPeptideSequenceFont(Font peptideSequenceFont)	Set the font to use for the peptide sequence.
void	setSequence(String lSequence, boolean boolModifiedSequence)	Set the Sequence for the SequenceFragmentationPanel.

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, 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

Constructor Details

SequenceFragmentationPanel

public SequenceFragmentationPanel()

Empty default constructor

SequenceFragmentationPanel

public SequenceFragmentationPanel(String aSequence,
 IonMatch[] aIonMatches,
 boolean boolModifiedSequence,
 boolean aHighlightModifications,
 ModificationParameters modificationProfile,
 int forwardIon,
 int rewindIon)

Creates a new SequenceFragmentationPanel working with B and Y ions.

Parameters:

aSequence - String with the Modified Sequence of an peptide identification.

aIonMatches - Array with fragment ion matches.

boolModifiedSequence - boolean describing the sequence. This constructor can be used to enter a ModifiedSequence or a normal sequence.

aHighlightModifications - boolean decides whether the modification are highlighted by adding a star above the modified residue instead if displaying the PTM short name

modificationProfile - the modification profile

forwardIon - the forward ion type (for instance B ion) as indexed by the PeptideFragmentIon static fields

rewindIon - the rewind ion type (for instance Y ion) as indexed by the PeptideFragmentIon static fields

See Also:

• GraphicsEnvironment.isHeadless()
• JComponent.getDefaultLocale()

SequenceFragmentationPanel

public SequenceFragmentationPanel(String taggedModifiedSequence,
 IonMatch[] aIonMatches,
 boolean aHighlightModifications,
 ModificationParameters modificationProfile,
 int forwardIon,
 int rewindIon)
                           throws HeadlessException

Creates a new SequenceFragmentationPanel working with B and Y ions.

Parameters:

taggedModifiedSequence - the tagged modified peptide sequence

aIonMatches - Array with fragment ion matches.

aHighlightModifications - boolean decides whether the modification are highlighted by adding a star above the modified residue instead if displaying the PTM short name

modificationProfile - the modification profile

forwardIon - the forward ion type (for instance B ion) as indexed by the PeptideFragmentIon static fields

rewindIon - the rewind ion type (for instance Y ion) as indexed by the PeptideFragmentIon static fields

Throws:

HeadlessException - if GraphicsEnvironment.isHeadless() returns true.

See Also:

• GraphicsEnvironment.isHeadless()
• JComponent.getDefaultLocale()

Method Details

setPeptideSequenceFont

public void setPeptideSequenceFont(Font peptideSequenceFont)

Set the font to use for the peptide sequence.

Parameters:

peptideSequenceFont - the font to use

setFontColor

public void setFontColor(Color fontColor)

Set the color for the font of the peptide sequence.

Parameters:

fontColor - the font color

paint

public void paint(Graphics g)

Paints the SequenceFragmentationPanel. Based on the given ModifiedSequence Components and Fragmentions, a visualization (inspired by X!Tandem) is drawn on a Graphics object. Next to every possible fragmentation site of the peptide a bar is drawn whether b or y ions were found originating from this fragmentation side.

Overrides:

paint in class JComponent

Parameters:

g - the specified Graphics window

See Also:

• Component.update(java.awt.Graphics)

setSequence

public void setSequence(String lSequence,
 boolean boolModifiedSequence)

Set the Sequence for the SequenceFragmentationPanel.

Parameters:

lSequence - String with peptide sequence.

boolModifiedSequence - Boolean whether lSequence is a Modified Sequence "NH2-K<Ace>ENNY-COOH" or a Flat Sequence "KENNY".

setIonMatches

public void setIonMatches(IonMatch[] lIonMatches)

Set the ArrayList with FragmentIon matches. The double[] indexing b and y ion intensities will be recalculated.

Parameters:

lIonMatches - ArrayList