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
- See Also:
- Serialized Form
Constructor Summary |
SequenceFragmentationPanel(String aSequence,
ArrayList<IonMatch> aIonMatches,
boolean boolModifiedSequence,
boolean aHighlightModifications,
ModificationProfile modificationProfile)
Deprecated. use the panel with ion selection instead |
SequenceFragmentationPanel(String aSequence,
ArrayList<IonMatch> aIonMatches,
boolean boolModifiedSequence,
boolean aHighlightModifications,
ModificationProfile modificationProfile,
int forwardIon,
int rewindIon)
Creates a new SequenceFragmentationPanel working with B and Y ions. |
SequenceFragmentationPanel(String taggedModifiedSequence,
ArrayList<IonMatch> aIonMatches,
boolean aHighlightModifications,
ModificationProfile modificationProfile,
int forwardIon,
int rewindIon)
Creates a new SequenceFragmentationPanel working with B and Y ions. |
Method Summary |
void |
paint(Graphics g)
Paints the SequenceFragmentationPanel. |
void |
setIonMatches(ArrayList lIonMatches)
Set the ArrayList with FragmentIon matches. |
void |
setSequence(String lSequence,
boolean boolModifiedSequence)
Set the Sequence for the SequenceFragmentationPanel. |
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, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, 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, transferFocusBackward, 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, hide, 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, transferFocusUpCycle |
SequenceFragmentationPanel
public SequenceFragmentationPanel(String aSequence,
ArrayList<IonMatch> aIonMatches,
boolean boolModifiedSequence,
boolean aHighlightModifications,
ModificationProfile modificationProfile)
throws HeadlessException
- Deprecated. use the panel with ion selection instead
- Creates a new SequenceFragmentationPanel.
- Parameters:
aSequence
- String with the Modified Sequence of an peptide
identification.aIonMatches
- ArrayList with Fragmentation 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 profile
- Throws:
HeadlessException
- if GraphicsEnvironment.isHeadless()
returns true.- See Also:
GraphicsEnvironment.isHeadless()
,
JComponent.getDefaultLocale()
SequenceFragmentationPanel
public SequenceFragmentationPanel(String aSequence,
ArrayList<IonMatch> aIonMatches,
boolean boolModifiedSequence,
boolean aHighlightModifications,
ModificationProfile modificationProfile,
int forwardIon,
int rewindIon)
throws HeadlessException
- Creates a new SequenceFragmentationPanel working with B and Y ions.
- Parameters:
aSequence
- String with the Modified Sequence of an peptide
identification.aIonMatches
- ArrayList with Fragmentation 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
- Throws:
HeadlessException
- if GraphicsEnvironment.isHeadless()
returns true.- See Also:
GraphicsEnvironment.isHeadless()
,
JComponent.getDefaultLocale()
SequenceFragmentationPanel
public SequenceFragmentationPanel(String taggedModifiedSequence,
ArrayList<IonMatch> aIonMatches,
boolean aHighlightModifications,
ModificationProfile modificationProfile,
int forwardIon,
int rewindIon)
throws HeadlessException
- Creates a new SequenceFragmentationPanel working with B and Y ions.
- Parameters:
taggedModifiedSequence
- the tagged modified peptide sequenceaIonMatches
- ArrayList with Fragmentation 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()
paint
public void paint(Graphics g)
- Paints the SequenceFragmentationPanel.
Based on the given ModifiedSequence Components and Fragmentions, a
visualisation (inspired by X!Tandem) is drawn on a Graphics object. Next
to every possible fragmentation site of the peptide a bar is drawn wether
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(ArrayList lIonMatches)
- Set the ArrayList with FragmentIon matches. The double[] indexing b and y
ion intensities will be recalculated.
- Parameters:
lIonMatches
- ArrayList
Copyright © 2013. All Rights Reserved.