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

Class StructureAlignmentJmol

java.lang.Object

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

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

All Implemented Interfaces:

ActionListener, MouseListener, MouseMotionListener, WindowListener, EventListener, ChangeListener

public class StructureAlignmentJmol
extends AbstractAlignmentJmol
implements ChangeListener

A class that provides a simple GUI for Jmol

Since:

1.6

Author:

Andreas Prlic

Field Summary

Fields inherited from class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol

colorPalette, COMMAND_LINE_HELP, DEFAULT_HEIGHT, DEFAULT_SCRIPT, DEFAULT_WIDTH, frame, jmolPanel, nrOpenWindows, status, structure, text

Constructor Summary

Constructors

Constructor	Description
StructureAlignmentJmol()
StructureAlignmentJmol(org.biojava.nbio.structure.align.model.AFPChain afpChain, org.biojava.nbio.structure.Atom[] ca1, org.biojava.nbio.structure.Atom[] ca2)

Method Summary

Modifier and Type	Method	Description
void	actionPerformed(ActionEvent e)
void	destroy()	Set all the member variables to null.
List<org.biojava.nbio.structure.jama.Matrix>	getDistanceMatrices()	Returns a List of internal Distance Matrices, one for each structure in the alignment.
static String	getJmolScript4Block(org.biojava.nbio.structure.align.model.AFPChain afpChain, org.biojava.nbio.structure.Atom[] ca1, org.biojava.nbio.structure.Atom[] ca2, int blockNr)
static String	getJmolString(org.biojava.nbio.structure.align.model.AFPChain afpChain, org.biojava.nbio.structure.Atom[] ca1, org.biojava.nbio.structure.Atom[] ca2)
protected void	initCoords()	Display the structures after the variable initialization in the constructor.
static void	main(String[] args)
void	resetDisplay()	Return to the initial state of the alignment visualization.
void	stateChanged(ChangeEvent e)

Methods inherited from class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol

evalString, getColorPalette, getJmolPanel, getStructure, getTitle, mouseClicked, mouseDragged, mouseEntered, mouseExited, mouseMoved, mousePressed, mouseReleased, setAtoms, setJmolPanel, setStructure, setTitle, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

StructureAlignmentJmol

public StructureAlignmentJmol()

StructureAlignmentJmol

public StructureAlignmentJmol(org.biojava.nbio.structure.align.model.AFPChain afpChain,
                              org.biojava.nbio.structure.Atom[] ca1,
                              org.biojava.nbio.structure.Atom[] ca2)

Method Detail

main

public static void main(String[] args)

initCoords

protected void initCoords()

Description copied from class: AbstractAlignmentJmol

Display the structures after the variable initialization in the constructor.

Specified by:

initCoords in class AbstractAlignmentJmol

destroy

public void destroy()

Description copied from class: AbstractAlignmentJmol

Set all the member variables to null.

Overrides:

destroy in class AbstractAlignmentJmol

actionPerformed

public void actionPerformed(ActionEvent e)

Specified by:

actionPerformed in interface ActionListener

Specified by:

actionPerformed in class AbstractAlignmentJmol

getJmolString

public static String getJmolString(org.biojava.nbio.structure.align.model.AFPChain afpChain,
                                   org.biojava.nbio.structure.Atom[] ca1,
                                   org.biojava.nbio.structure.Atom[] ca2)

getJmolScript4Block

public static String getJmolScript4Block(org.biojava.nbio.structure.align.model.AFPChain afpChain,
                                         org.biojava.nbio.structure.Atom[] ca1,
                                         org.biojava.nbio.structure.Atom[] ca2,
                                         int blockNr)

resetDisplay

public void resetDisplay()

Description copied from class: AbstractAlignmentJmol

Return to the initial state of the alignment visualization.

Specified by:

resetDisplay in class AbstractAlignmentJmol

getDistanceMatrices

public List<org.biojava.nbio.structure.jama.Matrix> getDistanceMatrices()

Description copied from class: AbstractAlignmentJmol

Returns a List of internal Distance Matrices, one for each structure in the alignment. Returns null if no alignment is being displayed.

Specified by:

getDistanceMatrices in class AbstractAlignmentJmol

stateChanged

public void stateChanged(ChangeEvent e)

Specified by:

stateChanged in interface ChangeListener