public class SequenceFragmentationPanel
extends javax.swing.JPanel
javax.swing.JPanel.AccessibleJPanel
javax.swing.JComponent.AccessibleJComponent
accessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW
Constructor and Description |
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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.
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Modifier and Type | Method and Description |
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void |
paint(java.awt.Graphics g)
Paints the SequenceFragmentationPanel.
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void |
setIonMatches(java.util.ArrayList lIonMatches)
Set the ArrayList with FragmentIon matches.
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void |
setSequence(java.lang.String lSequence,
boolean boolModifiedSequence)
Set the Sequence for the SequenceFragmentationPanel.
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getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI
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, 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
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
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, transferFocusBackward, transferFocusUpCycle
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 profilejava.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 fieldsjava.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 fieldsjava.awt.HeadlessException
- if GraphicsEnvironment.isHeadless()
returns true.GraphicsEnvironment.isHeadless()
,
JComponent.getDefaultLocale()
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
- ArrayListCopyright © 2013. All Rights Reserved.