Class MultipleAligPanel
- java.lang.Object
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- java.awt.Component
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- java.awt.Container
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- javax.swing.JComponent
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- javax.swing.JPanel
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- org.biojava.nbio.structure.align.gui.JPrintPanel
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- org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel
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- All Implemented Interfaces:
java.awt.event.ActionListener
,java.awt.event.WindowListener
,java.awt.image.ImageObserver
,java.awt.MenuContainer
,java.awt.print.Printable
,java.io.Serializable
,java.util.EventListener
,javax.accessibility.Accessible
,AlignmentPositionListener
public class MultipleAligPanel extends JPrintPanel implements AlignmentPositionListener, java.awt.event.WindowListener
A JPanel that can display the sequence alignment of aMultipleAlignment
in a nice way and interact with Jmol by selecting the aligned atoms of the sequence selection.Coloring options include: sequence similarity, by Block or by Structure. Colors are connected with the JmolPanel using the same pattelete.
The positions can be selected individually or in ranges and they will be translated to jmol commands.
- Since:
- 4.1.0
- Author:
- Aleix Lafita
- See Also:
- Serialized Form
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Nested Class Summary
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Nested classes/interfaces inherited from class javax.swing.JPanel
javax.swing.JPanel.AccessibleJPanel
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Nested classes/interfaces inherited from class javax.swing.JComponent
javax.swing.JComponent.AccessibleJComponent
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Field Summary
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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
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Fields inherited from class java.awt.Component
accessibleContext, BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT
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Constructor Summary
Constructors Constructor Description MultipleAligPanel()
Default constructor.MultipleAligPanel(AFPChain afpChain, Atom[] ca1, Atom[] ca2, AbstractAlignmentJmol jmol)
Constructor using an afpChain and the atom arrays for pairwise alignments.MultipleAligPanel(MultipleAlignment msa, AbstractAlignmentJmol jm)
Constructor using a MultipleAlignment.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
actionPerformed(java.awt.event.ActionEvent e)
void
addAlignmentPositionListener(AlignmentPositionListener li)
void
destroy()
java.util.List<java.lang.String>
getAlnSequences()
java.util.List<Atom[]>
getAtomArrays()
MultipleAlignmentCoordManager
getCoordManager()
java.util.List<java.lang.Integer>
getMapSeqToStruct()
MultipleAlignment
getMultipleAlignment()
void
mouseOverPosition(AlignedPosition p)
void
paintComponent(java.awt.Graphics g)
void
positionSelected(AlignedPosition p)
void
rangeSelected(AlignedPosition start, AlignedPosition end)
void
selectionLocked()
void
selectionUnlocked()
void
setStructureAlignmentJmol(AbstractAlignmentJmol jmol)
void
toggleSelection(AlignedPosition p)
void
windowActivated(java.awt.event.WindowEvent e)
void
windowClosed(java.awt.event.WindowEvent e)
void
windowClosing(java.awt.event.WindowEvent e)
void
windowDeactivated(java.awt.event.WindowEvent e)
void
windowDeiconified(java.awt.event.WindowEvent e)
void
windowIconified(java.awt.event.WindowEvent e)
void
windowOpened(java.awt.event.WindowEvent e)
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Methods inherited from class org.biojava.nbio.structure.align.gui.JPrintPanel
print
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Methods inherited from class javax.swing.JPanel
getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI
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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, paint, paintBorder, paintChildren, 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
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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
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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 Detail
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MultipleAligPanel
public MultipleAligPanel()
Default constructor. Empty MultipleAligPanel instance.
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MultipleAligPanel
public MultipleAligPanel(AFPChain afpChain, Atom[] ca1, Atom[] ca2, AbstractAlignmentJmol jmol) throws StructureException
Constructor using an afpChain and the atom arrays for pairwise alignments. The AFPChain is converted into a MultipleAlignment.- Parameters:
afpChain
-ca1
-ca2
-- Throws:
StructureException
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MultipleAligPanel
public MultipleAligPanel(MultipleAlignment msa, AbstractAlignmentJmol jm)
Constructor using a MultipleAlignment.- Parameters:
multAln
-colors
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Method Detail
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getCoordManager
public MultipleAlignmentCoordManager getCoordManager()
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addAlignmentPositionListener
public void addAlignmentPositionListener(AlignmentPositionListener li)
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destroy
public void destroy()
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paintComponent
public void paintComponent(java.awt.Graphics g)
- Overrides:
paintComponent
in classjavax.swing.JComponent
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mouseOverPosition
public void mouseOverPosition(AlignedPosition p)
- Specified by:
mouseOverPosition
in interfaceAlignmentPositionListener
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positionSelected
public void positionSelected(AlignedPosition p)
- Specified by:
positionSelected
in interfaceAlignmentPositionListener
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rangeSelected
public void rangeSelected(AlignedPosition start, AlignedPosition end)
- Specified by:
rangeSelected
in interfaceAlignmentPositionListener
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selectionLocked
public void selectionLocked()
- Specified by:
selectionLocked
in interfaceAlignmentPositionListener
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selectionUnlocked
public void selectionUnlocked()
- Specified by:
selectionUnlocked
in interfaceAlignmentPositionListener
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toggleSelection
public void toggleSelection(AlignedPosition p)
- Specified by:
toggleSelection
in interfaceAlignmentPositionListener
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setStructureAlignmentJmol
public void setStructureAlignmentJmol(AbstractAlignmentJmol jmol)
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windowActivated
public void windowActivated(java.awt.event.WindowEvent e)
- Specified by:
windowActivated
in interfacejava.awt.event.WindowListener
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windowClosed
public void windowClosed(java.awt.event.WindowEvent e)
- Specified by:
windowClosed
in interfacejava.awt.event.WindowListener
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windowClosing
public void windowClosing(java.awt.event.WindowEvent e)
- Specified by:
windowClosing
in interfacejava.awt.event.WindowListener
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windowDeactivated
public void windowDeactivated(java.awt.event.WindowEvent e)
- Specified by:
windowDeactivated
in interfacejava.awt.event.WindowListener
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windowDeiconified
public void windowDeiconified(java.awt.event.WindowEvent e)
- Specified by:
windowDeiconified
in interfacejava.awt.event.WindowListener
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windowIconified
public void windowIconified(java.awt.event.WindowEvent e)
- Specified by:
windowIconified
in interfacejava.awt.event.WindowListener
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windowOpened
public void windowOpened(java.awt.event.WindowEvent e)
- Specified by:
windowOpened
in interfacejava.awt.event.WindowListener
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actionPerformed
public void actionPerformed(java.awt.event.ActionEvent e)
- Specified by:
actionPerformed
in interfacejava.awt.event.ActionListener
- Overrides:
actionPerformed
in classJPrintPanel
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getAtomArrays
public java.util.List<Atom[]> getAtomArrays()
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getMultipleAlignment
public MultipleAlignment getMultipleAlignment()
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getAlnSequences
public java.util.List<java.lang.String> getAlnSequences()
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getMapSeqToStruct
public java.util.List<java.lang.Integer> getMapSeqToStruct()
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