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

Class MultipleAlignmentJmol

java.lang.Object

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

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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.awt.event.WindowListener, java.util.EventListener

public class MultipleAlignmentJmol
extends AbstractAlignmentJmol

A class that provides 3D visualization in Jmol for MultipleAlignments.

Author:

Aleix Lafita

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, LIGAND_DISPLAY_SCRIPT, nrOpenWindows, status, structure, text

Constructor Summary

Constructors

Constructor and Description
MultipleAlignmentJmol() Default constructor creates an empty JmolPanel window, from where alignments can be made through the align menu.
MultipleAlignmentJmol(MultipleAlignment msa, java.util.List<Atom[]> rotatedAtoms) The constructor displays the Mutltiple Alignment in a JmolPanel window.

Method Summary

Methods

Modifier and Type	Method and Description
void	actionPerformed(java.awt.event.ActionEvent e)
void	destroy() Set all the member variables to null.
java.util.List<Matrix>	getDistanceMatrices() Returns a List of internal Distance Matrices, one for each structure in the alignment.
protected void	initCoords() Display the structures in its initial coordinates.
void	resetDisplay() Return to the initial state of the alignment visualization.

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

MultipleAlignmentJmol

public MultipleAlignmentJmol()

Default constructor creates an empty JmolPanel window, from where alignments can be made through the align menu.

MultipleAlignmentJmol

public MultipleAlignmentJmol(MultipleAlignment msa,
                     java.util.List<Atom[]> rotatedAtoms)

The constructor displays the Mutltiple Alignment in a JmolPanel window.

Parameters:

multAln: - contains the aligned residues.

atomArrays: - contains the atom coordinates to display, already rotated.

Method Detail

initCoords

protected void initCoords()

Description copied from class: AbstractAlignmentJmol

Display the structures in its initial coordinates.

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(java.awt.event.ActionEvent e)

Specified by:

actionPerformed in interface java.awt.event.ActionListener

Specified by:

actionPerformed in class AbstractAlignmentJmol

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 java.util.List<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