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java.lang.Objectjava.awt.Component
java.awt.Container
javax.swing.JComponent
javax.swing.JPanel
com.compomics.util.gui.spectrum.SequenceFragmentationPanel
public class SequenceFragmentationPanel
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.
Nested Class Summary |
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Nested classes/interfaces inherited from class javax.swing.JPanel |
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javax.swing.JPanel.AccessibleJPanel |
Nested classes/interfaces inherited from class javax.swing.JComponent |
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javax.swing.JComponent.AccessibleJComponent |
Nested classes/interfaces inherited from class java.awt.Container |
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java.awt.Container.AccessibleAWTContainer |
Nested classes/interfaces inherited from class java.awt.Component |
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java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy |
Field Summary |
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Fields inherited from class javax.swing.JComponent |
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accessibleContext, 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 |
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BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT |
Fields inherited from interface java.awt.image.ImageObserver |
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ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH |
Constructor Summary | |
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SequenceFragmentationPanel(java.lang.String aSequence,
java.util.ArrayList<IonMatch> aIonMatches,
boolean boolModifiedSequence,
boolean aHighlightModifications,
ModificationProfile modificationProfile)
Deprecated. use the panel with ion selection instead |
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SequenceFragmentationPanel(java.lang.String aSequence,
java.util.ArrayList<IonMatch> aIonMatches,
boolean boolModifiedSequence,
boolean aHighlightModifications,
ModificationProfile modificationProfile,
int forwardIon,
int rewindIon)
Creates a new SequenceFragmentationPanel working with B and Y ions. |
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SequenceFragmentationPanel(java.lang.String taggedModifiedSequence,
java.util.ArrayList<IonMatch> aIonMatches,
boolean aHighlightModifications,
ModificationProfile modificationProfile,
int forwardIon,
int rewindIon)
Creates a new SequenceFragmentationPanel working with B and Y ions. |
Method Summary | |
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void |
paint(java.awt.Graphics g)
Paints the SequenceFragmentationPanel. |
void |
setIonMatches(java.util.ArrayList lIonMatches)
Set the ArrayList with FragmentIon matches. |
void |
setSequence(java.lang.String lSequence,
boolean boolModifiedSequence)
Set the Sequence for the SequenceFragmentationPanel. |
Methods inherited from class javax.swing.JPanel |
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getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI |
Methods inherited from class javax.swing.JComponent |
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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 |
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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 |
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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 |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public SequenceFragmentationPanel(java.lang.String aSequence, java.util.ArrayList<IonMatch> aIonMatches, boolean boolModifiedSequence, boolean aHighlightModifications, ModificationProfile modificationProfile) throws java.awt.HeadlessException
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
java.awt.HeadlessException
- if GraphicsEnvironment.isHeadless()
returns true.GraphicsEnvironment.isHeadless()
,
JComponent.getDefaultLocale()
public SequenceFragmentationPanel(java.lang.String aSequence, java.util.ArrayList<IonMatch> aIonMatches, boolean boolModifiedSequence, boolean aHighlightModifications, ModificationProfile modificationProfile, int forwardIon, int rewindIon) throws java.awt.HeadlessException
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
java.awt.HeadlessException
- if GraphicsEnvironment.isHeadless()
returns true.GraphicsEnvironment.isHeadless()
,
JComponent.getDefaultLocale()
public SequenceFragmentationPanel(java.lang.String taggedModifiedSequence, java.util.ArrayList<IonMatch> aIonMatches, boolean aHighlightModifications, ModificationProfile modificationProfile, int forwardIon, int rewindIon) throws java.awt.HeadlessException
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
java.awt.HeadlessException
- if GraphicsEnvironment.isHeadless()
returns true.GraphicsEnvironment.isHeadless()
,
JComponent.getDefaultLocale()
Method Detail |
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public void paint(java.awt.Graphics g)
paint
in class javax.swing.JComponent
g
- the specified Graphics windowComponent.update(java.awt.Graphics)
public void setSequence(java.lang.String lSequence, boolean boolModifiedSequence)
lSequence
- String with peptide sequence.boolModifiedSequence
- Boolean whether lSequence is a Modified
Sequence "NH2-K<Ace>ENNY-COOH" or a Flat Sequence "KENNY".public void setIonMatches(java.util.ArrayList lIonMatches)
lIonMatches
- ArrayList
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