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

Class AbstractAlignmentJmol

java.lang.Object

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

All Implemented Interfaces:

ActionListener, MouseListener, MouseMotionListener, WindowListener, EventListener

Direct Known Subclasses:

MultipleAlignmentJmol, StructureAlignmentJmol

public abstract class AbstractAlignmentJmol
extends Object
implements MouseMotionListener, MouseListener, WindowListener, 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	Description
protected org.jcolorbrewer.ColorBrewer	colorPalette
protected static final String	COMMAND_LINE_HELP
protected static final int	DEFAULT_HEIGHT
protected static final String	DEFAULT_SCRIPT
protected static final int	DEFAULT_WIDTH
protected JFrame	frame
protected JmolPanel	jmolPanel
protected static int	nrOpenWindows
protected JTextField	status
protected Structure	structure
protected JTextField	text

Constructor Summary

Constructors

Constructor	Description
AbstractAlignmentJmol()

Method Summary

Modifier and Type	Method	Description
abstract void	actionPerformed(ActionEvent e)
void	destroy()	Set all the member variables to null.
void	evalString(String rasmolScript)	Execute a command String in the current Jmol panel.
org.jcolorbrewer.ColorBrewer	getColorPalette()	Return the color pattelete of the AlignmentJmol instance.
abstract 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.
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(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)
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(String title)	Set the title of the AlignmentJmol window.
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 Details

structure

protected Structure structure

colorPalette

protected org.jcolorbrewer.ColorBrewer colorPalette

jmolPanel

protected JmolPanel jmolPanel

frame

protected JFrame frame

text

protected JTextField text

status

protected JTextField status

COMMAND_LINE_HELP

protected static final 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 String DEFAULT_SCRIPT

nrOpenWindows

protected static int nrOpenWindows

Constructor Details

AbstractAlignmentJmol

public AbstractAlignmentJmol()

Method Details

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(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 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(String title)

Set the title of the AlignmentJmol window.

Parameters:

title -

getTitle

public String getTitle()

Return the title of the AlignmentJmol window.

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 abstract void actionPerformed(ActionEvent e)

Specified by:

actionPerformed in interface ActionListener