org.biojava.nbio.structure.align.gui.aligpanel.MultipleAligPanel

All Implemented Interfaces:: ActionListener, WindowListener, ImageObserver, MenuContainer, Printable, Serializable, EventListener, Accessible, AlignmentPositionListener

public class MultipleAligPanel extends JPrintPanel implements AlignmentPositionListener, WindowListener

A JPanel that can display the sequence alignment of a MultipleAlignment 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

Nested Class Summary

Nested classes/interfaces inherited from class javax.swing.JPanel
JPanel.AccessibleJPanel

Nested classes/interfaces inherited from class javax.swing.JComponent
JComponent.AccessibleJComponent

Nested classes/interfaces inherited from class java.awt.Container
Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component
Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy
Field Summary

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

Fields inherited from class java.awt.Component
accessibleContext, BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Fields inherited from interface java.awt.print.Printable
NO_SUCH_PAGE, PAGE_EXISTS
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.
Method Summary

Modifier and Type

Method

Description

void

actionPerformed(ActionEvent e)

void

addAlignmentPositionListener(AlignmentPositionListener li)

void

destroy()

List<String>

getAlnSequences()

List<Atom[]>

getAtomArrays()

MultipleAlignmentCoordManager

getCoordManager()

List<Integer>

getMapSeqToStruct()

MultipleAlignment

getMultipleAlignment()

void

mouseOverPosition(AlignedPosition p)

void

paintComponent(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(WindowEvent e)

void

windowClosed(WindowEvent e)

void

windowClosing(WindowEvent e)

void

windowDeactivated(WindowEvent e)

void

windowDeiconified(WindowEvent e)

void

windowIconified(WindowEvent e)

void

windowOpened(WindowEvent e)

Methods inherited from class org.biojava.nbio.structure.align.gui.JPrintPanel
print

Methods inherited from class javax.swing.JPanel
getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI

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

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

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

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details
- MultipleAligPanel
  
  public MultipleAligPanel()
  
  Default constructor. Empty MultipleAligPanel instance.
- 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
- MultipleAligPanel
  
  public MultipleAligPanel(MultipleAlignment msa, AbstractAlignmentJmol jm)
  
  Constructor using a MultipleAlignment.
  
  Parameters:
  
  multAln -
  
  colors -
Method Details
- getCoordManager
  
  public MultipleAlignmentCoordManager getCoordManager()
- addAlignmentPositionListener
  
  public void addAlignmentPositionListener(AlignmentPositionListener li)
- destroy
  
  public void destroy()
- paintComponent
  
  public void paintComponent(Graphics g)
  
  Overrides:
  
  paintComponent in class JComponent
- mouseOverPosition
  
  public void mouseOverPosition(AlignedPosition p)
  
  Specified by:
  
  mouseOverPosition in interface AlignmentPositionListener
- positionSelected
  
  public void positionSelected(AlignedPosition p)
  
  Specified by:
  
  positionSelected in interface AlignmentPositionListener
- rangeSelected
  
  public void rangeSelected(AlignedPosition start, AlignedPosition end)
  
  Specified by:
  
  rangeSelected in interface AlignmentPositionListener
- selectionLocked
  
  public void selectionLocked()
  
  Specified by:
  
  selectionLocked in interface AlignmentPositionListener
- selectionUnlocked
  
  public void selectionUnlocked()
  
  Specified by:
  
  selectionUnlocked in interface AlignmentPositionListener
- toggleSelection
  
  public void toggleSelection(AlignedPosition p)
  
  Specified by:
  
  toggleSelection in interface AlignmentPositionListener
- setStructureAlignmentJmol
  
  public void setStructureAlignmentJmol(AbstractAlignmentJmol jmol)
- windowActivated
  
  public void windowActivated(WindowEvent e)
  
  Specified by:
  
  windowActivated in interface WindowListener
- windowClosed
  
  public void windowClosed(WindowEvent e)
  
  Specified by:
  
  windowClosed in interface WindowListener
- windowClosing
  
  public void windowClosing(WindowEvent e)
  
  Specified by:
  
  windowClosing in interface WindowListener
- windowDeactivated
  
  public void windowDeactivated(WindowEvent e)
  
  Specified by:
  
  windowDeactivated in interface WindowListener
- windowDeiconified
  
  public void windowDeiconified(WindowEvent e)
  
  Specified by:
  
  windowDeiconified in interface WindowListener
- windowIconified
  
  public void windowIconified(WindowEvent e)
  
  Specified by:
  
  windowIconified in interface WindowListener
- windowOpened
  
  public void windowOpened(WindowEvent e)
  
  Specified by:
  
  windowOpened in interface WindowListener
- actionPerformed
  
  public void actionPerformed(ActionEvent e)
  
  Specified by:
  
  actionPerformed in interface ActionListener
  
  Overrides:
  
  actionPerformed in class JPrintPanel
- getAtomArrays
  
  public List<Atom[]> getAtomArrays()
- getMultipleAlignment
  
  public MultipleAlignment getMultipleAlignment()
- getAlnSequences
  
  public List<String> getAlnSequences()
- getMapSeqToStruct
  
  public List<Integer> getMapSeqToStruct()

Class MultipleAligPanel

Nested Class Summary

Nested classes/interfaces inherited from class javax.swing.JPanel

Nested classes/interfaces inherited from class javax.swing.JComponent

Nested classes/interfaces inherited from class java.awt.Container

Nested classes/interfaces inherited from class java.awt.Component

Field Summary

Fields inherited from class javax.swing.JComponent

Fields inherited from class java.awt.Component

Fields inherited from interface java.awt.image.ImageObserver

Fields inherited from interface java.awt.print.Printable

Constructor Summary

Method Summary

Methods inherited from class org.biojava.nbio.structure.align.gui.JPrintPanel

Methods inherited from class javax.swing.JPanel

Methods inherited from class javax.swing.JComponent

Methods inherited from class java.awt.Container

Methods inherited from class java.awt.Component

Methods inherited from class java.lang.Object

Constructor Details

MultipleAligPanel

MultipleAligPanel

MultipleAligPanel

Method Details

getCoordManager

addAlignmentPositionListener

destroy

paintComponent

mouseOverPosition

positionSelected

rangeSelected

selectionLocked

selectionUnlocked

toggleSelection

setStructureAlignmentJmol

windowActivated

windowClosed

windowClosing

windowDeactivated

windowDeiconified

windowIconified

windowOpened

actionPerformed

getAtomArrays

getMultipleAlignment

getAlnSequences

getMapSeqToStruct