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

Class MultipleAligPanel

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

javax.swing.JPanel

org.biojava.nbio.structure.align.gui.JPrintPanel

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

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 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

javax.swing.JPanel.AccessibleJPanel

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

javax.swing.JComponent.AccessibleJComponent

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

java.awt.Container.AccessibleAWTContainer

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

java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.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(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)

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 Detail

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 Detail

getCoordManager

public MultipleAlignmentCoordManager getCoordManager()

addAlignmentPositionListener

public void addAlignmentPositionListener(AlignmentPositionListener li)

destroy

public void destroy()

paintComponent

public void paintComponent(java.awt.Graphics g)

Overrides:

paintComponent in class javax.swing.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(java.awt.event.WindowEvent e)

Specified by:

windowActivated in interface java.awt.event.WindowListener

windowClosed

public void windowClosed(java.awt.event.WindowEvent e)

Specified by:

windowClosed in interface java.awt.event.WindowListener

windowClosing

public void windowClosing(java.awt.event.WindowEvent e)

Specified by:

windowClosing in interface java.awt.event.WindowListener

windowDeactivated

public void windowDeactivated(java.awt.event.WindowEvent e)

Specified by:

windowDeactivated in interface java.awt.event.WindowListener

windowDeiconified

public void windowDeiconified(java.awt.event.WindowEvent e)

Specified by:

windowDeiconified in interface java.awt.event.WindowListener

windowIconified

public void windowIconified(java.awt.event.WindowEvent e)

Specified by:

windowIconified in interface java.awt.event.WindowListener

windowOpened

public void windowOpened(java.awt.event.WindowEvent e)

Specified by:

windowOpened in interface java.awt.event.WindowListener

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent e)

Specified by:

actionPerformed in interface java.awt.event.ActionListener

Overrides:

actionPerformed in class JPrintPanel

getAtomArrays

public java.util.List<Atom[]> getAtomArrays()

getMultipleAlignment

public MultipleAlignment getMultipleAlignment()

getAlnSequences

public java.util.List<java.lang.String> getAlnSequences()

getMapSeqToStruct

public java.util.List<java.lang.Integer> getMapSeqToStruct()