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
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Nested Class Summary
Nested classes/interfaces inherited from class javax.swing.JComponent
JComponent.AccessibleJComponent
Nested classes/interfaces inherited from class java.awt.Component
Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy
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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
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Constructor Summary
Constructors Constructor Description SequenceFragmentationPanel()
Empty default constructorSequenceFragmentationPanel(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
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Constructor Details
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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 namemodificationProfile
- the modification profileforwardIon
- the forward ion type (for instance B ion) as indexed by the PeptideFragmentIon static fieldsrewindIon
- the rewind ion type (for instance Y ion) as indexed by the PeptideFragmentIon static fields- See Also:
GraphicsEnvironment.isHeadless()
,JComponent.getDefaultLocale()
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SequenceFragmentationPanel
public SequenceFragmentationPanel(String taggedModifiedSequence, IonMatch[] aIonMatches, boolean aHighlightModifications, ModificationParameters modificationProfile, int forwardIon, int rewindIon) throws HeadlessExceptionCreates a new SequenceFragmentationPanel working with B and Y ions.- Parameters:
taggedModifiedSequence
- the tagged modified peptide sequenceaIonMatches
- 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 namemodificationProfile
- the modification profileforwardIon
- the forward ion type (for instance B ion) as indexed by the PeptideFragmentIon static fieldsrewindIon
- 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()
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Method Details
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setPeptideSequenceFont
Set the font to use for the peptide sequence.- Parameters:
peptideSequenceFont
- the font to use
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setFontColor
Set the color for the font of the peptide sequence.- Parameters:
fontColor
- the font color
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paint
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 classJComponent
- Parameters:
g
- the specified Graphics window- See Also:
Component.update(java.awt.Graphics)
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setSequence
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".
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setIonMatches
Set the ArrayList with FragmentIon matches. The double[] indexing b and y ion intensities will be recalculated.- Parameters:
lIonMatches
- ArrayList
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