public class SequenceFragmentationPanel extends JPanel
JPanel.AccessibleJPanel
JComponent.AccessibleJComponent
Container.AccessibleAWTContainer
Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy
listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW
accessibleContext, BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
Constructor and Description |
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SequenceFragmentationPanel()
Empty default constructor
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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.
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SequenceFragmentationPanel(String taggedModifiedSequence,
IonMatch[] aIonMatches,
boolean aHighlightModifications,
ModificationParameters 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(Graphics g)
Paints the SequenceFragmentationPanel.
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void |
setFontColor(Color fontColor)
Set the color for the font of the peptide sequence.
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void |
setIonMatches(IonMatch[] lIonMatches)
Set the ArrayList with FragmentIon matches.
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void |
setPeptideSequenceFont(Font peptideSequenceFont)
Set the font to use for the peptide sequence.
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void |
setSequence(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, 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
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, 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()
public SequenceFragmentationPanel(String aSequence, IonMatch[] aIonMatches, boolean boolModifiedSequence, boolean aHighlightModifications, ModificationParameters modificationProfile, int forwardIon, int rewindIon)
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 fieldsGraphicsEnvironment.isHeadless()
,
JComponent.getDefaultLocale()
public SequenceFragmentationPanel(String taggedModifiedSequence, IonMatch[] aIonMatches, boolean aHighlightModifications, ModificationParameters modificationProfile, int forwardIon, int rewindIon) throws HeadlessException
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 fieldsHeadlessException
- if GraphicsEnvironment.isHeadless()
returns true.GraphicsEnvironment.isHeadless()
,
JComponent.getDefaultLocale()
public void setPeptideSequenceFont(Font peptideSequenceFont)
peptideSequenceFont
- the font to usepublic void setFontColor(Color fontColor)
fontColor
- the font colorpublic void paint(Graphics g)
paint
in class JComponent
g
- the specified Graphics windowComponent.update(java.awt.Graphics)
public void setSequence(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(IonMatch[] lIonMatches)
lIonMatches
- ArrayListCopyright © 2021. All rights reserved.