org.biojava.nbio.structure.align.gui.jmol

Class StructureAlignmentJmol

java.lang.Object

org.biojava.nbio.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

Fields

Modifier and Type	Field and Description
protected static String	COMMAND_LINE_HELP
static String	DEFAULT_SCRIPT

Constructor Summary

Constructors

Constructor and Description
StructureAlignmentJmol()
StructureAlignmentJmol(AFPChain afpChain, Atom[] ca1, Atom[] ca2)

Method Summary

Methods

Modifier and Type	Method and Description
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()