org.biojava.bio.structure.align.gui.jmol
Class StructureAlignmentJmol

java.lang.Object
  extended by org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
All Implemented Interfaces:
ActionListener, MouseListener, MouseMotionListener, WindowListener, EventListener

public class StructureAlignmentJmol
extends Object
implements MouseMotionListener, MouseListener, WindowListener, ActionListener

A class that provides a simple GUI for Jmol

Since:
1.6
Author:
Andreas Prlic

Field Summary
protected static String COMMAND_LINE_HELP
           
static String DEFAULT_SCRIPT
           
 
Constructor Summary
StructureAlignmentJmol()
           
StructureAlignmentJmol(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
           
 
Method Summary
 void actionPerformed(ActionEvent e)
           
 void destroy()
           
 void evalString(String rasmolScript)
           
 JmolPanel getJmolPanel()
           
static String getJmolScript4Block(AFPChain afpChain, Atom[] ca1, Atom[] ca2, int blockNr)
           
static String getJmolString(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
           
 Structure getStructure()
           
 String getTitle()
           
static void main(String[] args)
           
 void mouseClicked(MouseEvent e)
           
 void mouseDragged(MouseEvent e)
           
 void mouseEntered(MouseEvent e)
           
 void mouseExited(MouseEvent e)
           
 void mouseMoved(MouseEvent e)
           
 void mousePressed(MouseEvent e)
           
 void mouseReleased(MouseEvent e)
           
 void resetDisplay()
           
 void setAtoms(Atom[] atoms)
           
 void setJmolPanel(JmolPanel jmolPanel)
           
 void setStructure(Structure s)
           
 void setTitle(String label)
           
 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 java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

COMMAND_LINE_HELP

protected static final String COMMAND_LINE_HELP
See Also:
Constant Field Values

DEFAULT_SCRIPT

public static final String DEFAULT_SCRIPT
Constructor Detail

StructureAlignmentJmol

public StructureAlignmentJmol()

StructureAlignmentJmol

public StructureAlignmentJmol(AFPChain afpChain,
                              Atom[] ca1,
                              Atom[] ca2)
Method Detail

main

public static void main(String[] args)

destroy

public void destroy()

setAtoms

public void setAtoms(Atom[] atoms)

getJmolPanel

public JmolPanel getJmolPanel()

setJmolPanel

public void setJmolPanel(JmolPanel jmolPanel)

evalString

public void evalString(String rasmolScript)

setStructure

public void setStructure(Structure s)

getStructure

public Structure getStructure()

setTitle

public void setTitle(String label)

getTitle

public String getTitle()

mouseDragged

public void mouseDragged(MouseEvent e)
Specified by:
mouseDragged in interface MouseMotionListener

mouseMoved

public void mouseMoved(MouseEvent e)
Specified by:
mouseMoved in interface MouseMotionListener

mouseClicked

public void mouseClicked(MouseEvent e)
Specified by:
mouseClicked in interface MouseListener

mouseEntered

public void mouseEntered(MouseEvent e)
Specified by:
mouseEntered in interface MouseListener

mouseExited

public void mouseExited(MouseEvent e)
Specified by:
mouseExited in interface MouseListener

mousePressed

public void mousePressed(MouseEvent e)
Specified by:
mousePressed in interface MouseListener

mouseReleased

public void mouseReleased(MouseEvent e)
Specified by:
mouseReleased in interface MouseListener

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

getJmolString

public static String getJmolString(AFPChain afpChain,
                                   Atom[] ca1,
                                   Atom[] ca2)

getJmolScript4Block

public static String getJmolScript4Block(AFPChain afpChain,
                                         Atom[] ca1,
                                         Atom[] ca2,
                                         int blockNr)

resetDisplay

public void resetDisplay()