org.biojava.bio.structure.align.gui.aligpanel
Class AligPanel

java.lang.Object
  extended by java.awt.Component
      extended by java.awt.Container
          extended by javax.swing.JComponent
              extended by javax.swing.JPanel
                  extended by org.biojava.bio.structure.align.gui.JPrintPanel
                      extended by org.biojava.bio.structure.align.gui.aligpanel.AligPanel
All Implemented Interfaces:
ActionListener, WindowListener, ImageObserver, MenuContainer, Printable, Serializable, EventListener, Accessible, AlignmentPositionListener

public class AligPanel
extends JPrintPanel
implements AlignmentPositionListener, WindowListener, ActionListener

A JPanel that can display an AFPChain in a nice way and interact with Jmol.

Author:
Andreas Prlic
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
accessibleContext, 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
BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT
 
Fields inherited from interface java.awt.print.Printable
NO_SUCH_PAGE, PAGE_EXISTS
 
Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
 
Constructor Summary
AligPanel()
           
 
Method Summary
 void actionPerformed(ActionEvent e)
           
 void addAlignmentPositionListener(AlignmentPositionListener li)
           
 void destroy()
           
 AFPChain getAFPChain()
           
 Atom[] getCa1()
           
 Atom[] getCa2()
           
 AFPChainCoordManager getCoordManager()
           
static void main(String[] args)
           
 void mouseOverPosition(AlignedPosition p)
           
 void paintComponent(Graphics g)
           
 void positionSelected(AlignedPosition p)
           
 void rangeSelected(AlignedPosition start, AlignedPosition end)
           
 void selectionLocked()
           
 void selectionUnlocked()
           
 void setAFPChain(AFPChain afpChain)
           
 void setCa1(Atom[] ca1)
           
 void setCa2(Atom[] ca2)
           
 void setStructureAlignmentJmol(StructureAlignmentJmol 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.bio.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, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, 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, 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
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

AligPanel

public AligPanel()
Method Detail

main

public static void main(String[] args)

getCoordManager

public AFPChainCoordManager getCoordManager()

addAlignmentPositionListener

public void addAlignmentPositionListener(AlignmentPositionListener li)

destroy

public void destroy()

getAFPChain

public AFPChain getAFPChain()

setAFPChain

public void setAFPChain(AFPChain afpChain)

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(StructureAlignmentJmol 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

getCa1

public Atom[] getCa1()

setCa1

public void setCa1(Atom[] ca1)

getCa2

public Atom[] getCa2()

setCa2

public void setCa2(Atom[] ca2)