Package 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:

ActionListener, MouseListener, MouseMotionListener, WindowListener, EventListener

public class MultipleAlignmentJmol
extends AbstractAlignmentJmol

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

Since:

4.1.0

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, nrOpenWindows, status, structure, text

Constructor Summary

Constructors

Constructor	Description
MultipleAlignmentJmol()	Default constructor creates an empty JmolPanel window, from where alignments can be made through the align menu.
MultipleAlignmentJmol(org.biojava.nbio.structure.align.multiple.MultipleAlignment msa, List<org.biojava.nbio.structure.Atom[]> rotatedAtoms)	The constructor displays the Mutltiple Alignment in a new JmolPanel Frame.

Method Summary

Modifier and Type	Method	Description
void	actionPerformed(ActionEvent ae)
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.
JFrame	getFrame()
static String	getJmolString(org.biojava.nbio.structure.align.multiple.MultipleAlignment multAln, List<org.biojava.nbio.structure.Atom[]> transformedAtoms, org.jcolorbrewer.ColorBrewer colorPalette, boolean colorByBlocks)	Generate a Jmol command String that colors the aligned residues of every structure.
static String	getMultiBlockJmolString(org.biojava.nbio.structure.align.multiple.MultipleAlignment multAln, List<org.biojava.nbio.structure.Atom[]> transformedAtoms, org.jcolorbrewer.ColorBrewer colorPalette, boolean colorByBlocks)	Colors every Block of the structures with a different color, following the palette.
org.biojava.nbio.structure.align.multiple.MultipleAlignment	getMultipleAlignment()
protected void	initCoords()	Display the structures after the variable initialization in the constructor.
void	resetDisplay()	Return to the initial state of the alignment visualization.
void	setColorByBlocks(boolean colorByBlocks)

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(org.biojava.nbio.structure.align.multiple.MultipleAlignment msa,
                             List<org.biojava.nbio.structure.Atom[]> rotatedAtoms)

The constructor displays the Mutltiple Alignment in a new JmolPanel Frame.

Parameters:

msa - : contains the aligned residues.

rotatedAtoms - : contains the transformed Atom coordinates.

Method Detail

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 ae)

Specified by:

actionPerformed in interface ActionListener

Specified by:

actionPerformed in class AbstractAlignmentJmol

getJmolString

public static String getJmolString(org.biojava.nbio.structure.align.multiple.MultipleAlignment multAln,
                                   List<org.biojava.nbio.structure.Atom[]> transformedAtoms,
                                   org.jcolorbrewer.ColorBrewer colorPalette,
                                   boolean colorByBlocks)

Generate a Jmol command String that colors the aligned residues of every structure.

getMultiBlockJmolString

public static String getMultiBlockJmolString(org.biojava.nbio.structure.align.multiple.MultipleAlignment multAln,
                                             List<org.biojava.nbio.structure.Atom[]> transformedAtoms,
                                             org.jcolorbrewer.ColorBrewer colorPalette,
                                             boolean colorByBlocks)

Colors every Block of the structures with a different color, following the palette. It colors each Block differently, no matter if it is from the same or different BlockSet.

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

setColorByBlocks

public void setColorByBlocks(boolean colorByBlocks)

getFrame

public JFrame getFrame()

getMultipleAlignment

public org.biojava.nbio.structure.align.multiple.MultipleAlignment getMultipleAlignment()