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

Class AbstractAlignmentJmol

java.lang.Object

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

All Implemented Interfaces:

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

Direct Known Subclasses:

MultipleAlignmentJmol, StructureAlignmentJmol

public abstract class AbstractAlignmentJmol
extends java.lang.Object
implements java.awt.event.MouseMotionListener, java.awt.event.MouseListener, java.awt.event.WindowListener, java.awt.event.ActionListener

An Abstract Class to generalize the visualization of AFP and MultipleAlignment structure alignments in Jmol.

Author:

Aleix Lafita

Field Summary

Fields

Modifier and Type	Field and Description
protected org.jcolorbrewer.ColorBrewer	colorPalette
protected static java.lang.String	COMMAND_LINE_HELP
protected static int	DEFAULT_HEIGHT
protected static java.lang.String	DEFAULT_SCRIPT
protected static int	DEFAULT_WIDTH
protected javax.swing.JFrame	frame
protected JmolPanel	jmolPanel
protected static int	nrOpenWindows
protected javax.swing.JTextField	status
protected Structure	structure
protected javax.swing.JTextField	text

Constructor Summary

Constructors

Constructor and Description
AbstractAlignmentJmol()

Method Summary

Modifier and Type	Method and Description
abstract void	actionPerformed(java.awt.event.ActionEvent e)
void	destroy() Set all the member variables to null.
void	evalString(java.lang.String rasmolScript) Execute a command String in the current Jmol panel.
org.jcolorbrewer.ColorBrewer	getColorPalette() Return the color pattelete of the AlignmentJmol instance.
abstract java.util.List<Matrix>	getDistanceMatrices() Returns a List of internal Distance Matrices, one for each structure in the alignment.
JmolPanel	getJmolPanel() Return the jmolPanel instance of the AlignmentJmol.
Structure	getStructure() Return the current Structure in the AlignmentJmol instance.
java.lang.String	getTitle() Return the title of the AlignmentJmol window.
protected abstract void	initCoords() Display the structures after the variable initialization in the constructor.
void	mouseClicked(java.awt.event.MouseEvent e)
void	mouseDragged(java.awt.event.MouseEvent e)
void	mouseEntered(java.awt.event.MouseEvent e)
void	mouseExited(java.awt.event.MouseEvent e)
void	mouseMoved(java.awt.event.MouseEvent e)
void	mousePressed(java.awt.event.MouseEvent e)
void	mouseReleased(java.awt.event.MouseEvent e)
abstract void	resetDisplay() Return to the initial state of the alignment visualization.
void	setAtoms(Atom[] atoms) Create and set a new structure from a given atom array.
void	setJmolPanel(JmolPanel jmolPanel) Set the jmolPanel of the AlignmentJmol instance.
void	setStructure(Structure s) Set a new Structure to visualize in the AlignmentJmol window.
void	setTitle(java.lang.String title) Set the title of the AlignmentJmol window.
void	windowActivated(java.awt.event.WindowEvent e)
void	windowClosed(java.awt.event.WindowEvent e)
void	windowClosing(java.awt.event.WindowEvent e)
void	windowDeactivated(java.awt.event.WindowEvent e)
void	windowDeiconified(java.awt.event.WindowEvent e)
void	windowIconified(java.awt.event.WindowEvent e)
void	windowOpened(java.awt.event.WindowEvent e)

Methods inherited from class java.lang.Object

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

Field Detail

structure

protected Structure structure

colorPalette

protected org.jcolorbrewer.ColorBrewer colorPalette

jmolPanel

protected JmolPanel jmolPanel

frame

protected javax.swing.JFrame frame

text

protected javax.swing.JTextField text

status

protected javax.swing.JTextField status

COMMAND_LINE_HELP

protected static final java.lang.String COMMAND_LINE_HELP

See Also:

Constant Field Values

DEFAULT_HEIGHT

protected static final int DEFAULT_HEIGHT

See Also:

Constant Field Values

DEFAULT_WIDTH

protected static final int DEFAULT_WIDTH

See Also:

Constant Field Values

DEFAULT_SCRIPT

protected static final java.lang.String DEFAULT_SCRIPT

nrOpenWindows

protected static int nrOpenWindows

Constructor Detail

AbstractAlignmentJmol

public AbstractAlignmentJmol()

Method Detail

initCoords

protected abstract void initCoords()

Display the structures after the variable initialization in the constructor.

destroy

public void destroy()

Set all the member variables to null.

resetDisplay

public abstract void resetDisplay()

Return to the initial state of the alignment visualization.

setAtoms

public void setAtoms(Atom[] atoms)

Create and set a new structure from a given atom array.

Parameters:

atoms -

getColorPalette

public org.jcolorbrewer.ColorBrewer getColorPalette()

Return the color pattelete of the AlignmentJmol instance.

getJmolPanel

public JmolPanel getJmolPanel()

Return the jmolPanel instance of the AlignmentJmol.

setJmolPanel

public void setJmolPanel(JmolPanel jmolPanel)

Set the jmolPanel of the AlignmentJmol instance.

Parameters:

jmolPanel -

evalString

public void evalString(java.lang.String rasmolScript)

Execute a command String in the current Jmol panel.

Parameters:

rasmolScript -

setStructure

public void setStructure(Structure s)

Set a new Structure to visualize in the AlignmentJmol window.

Parameters:

s -

getStructure

public Structure getStructure()

Return the current Structure in the AlignmentJmol instance.

getDistanceMatrices

public abstract java.util.List<Matrix> getDistanceMatrices()

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

setTitle

public void setTitle(java.lang.String title)

Set the title of the AlignmentJmol window.

Parameters:

label -

getTitle

public java.lang.String getTitle()

Return the title of the AlignmentJmol window.

mouseDragged

public void mouseDragged(java.awt.event.MouseEvent e)

Specified by:

mouseDragged in interface java.awt.event.MouseMotionListener

mouseMoved

public void mouseMoved(java.awt.event.MouseEvent e)

Specified by:

mouseMoved in interface java.awt.event.MouseMotionListener

mouseClicked

public void mouseClicked(java.awt.event.MouseEvent e)

Specified by:

mouseClicked in interface java.awt.event.MouseListener

mouseEntered

public void mouseEntered(java.awt.event.MouseEvent e)

Specified by:

mouseEntered in interface java.awt.event.MouseListener

mouseExited

public void mouseExited(java.awt.event.MouseEvent e)

Specified by:

mouseExited in interface java.awt.event.MouseListener

mousePressed

public void mousePressed(java.awt.event.MouseEvent e)

Specified by:

mousePressed in interface java.awt.event.MouseListener

mouseReleased

public void mouseReleased(java.awt.event.MouseEvent e)

Specified by:

mouseReleased in interface java.awt.event.MouseListener

windowActivated

public void windowActivated(java.awt.event.WindowEvent e)

Specified by:

windowActivated in interface java.awt.event.WindowListener

windowClosed

public void windowClosed(java.awt.event.WindowEvent e)

Specified by:

windowClosed in interface java.awt.event.WindowListener

windowClosing

public void windowClosing(java.awt.event.WindowEvent e)

Specified by:

windowClosing in interface java.awt.event.WindowListener

windowDeactivated

public void windowDeactivated(java.awt.event.WindowEvent e)

Specified by:

windowDeactivated in interface java.awt.event.WindowListener

windowDeiconified

public void windowDeiconified(java.awt.event.WindowEvent e)

Specified by:

windowDeiconified in interface java.awt.event.WindowListener

windowIconified

public void windowIconified(java.awt.event.WindowEvent e)

Specified by:

windowIconified in interface java.awt.event.WindowListener

windowOpened

public void windowOpened(java.awt.event.WindowEvent e)

Specified by:

windowOpened in interface java.awt.event.WindowListener

actionPerformed

public abstract void actionPerformed(java.awt.event.ActionEvent e)

Specified by:

actionPerformed in interface java.awt.event.ActionListener