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 String`	`COMMAND_LINE_HELP`
`protected static int`	`DEFAULT_HEIGHT`
`protected static String`	`DEFAULT_SCRIPT`
`protected static 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

All Methods Instance Methods Abstract Methods Concrete Methods
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 Detail
  - 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 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(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:
    
    label -
  - 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

Class AbstractAlignmentJmol

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

structure

colorPalette

jmolPanel

frame

text

status

COMMAND_LINE_HELP

DEFAULT_HEIGHT

DEFAULT_WIDTH

DEFAULT_SCRIPT

nrOpenWindows

Constructor Detail

AbstractAlignmentJmol

Method Detail

initCoords

destroy

resetDisplay

setAtoms

getColorPalette

getJmolPanel

setJmolPanel

evalString

setStructure

getStructure

getDistanceMatrices

setTitle

getTitle

mouseDragged

mouseMoved

mouseClicked

mouseEntered

mouseExited

mousePressed

mouseReleased

windowActivated

windowClosed

windowClosing

windowDeactivated

windowDeiconified

windowIconified

windowOpened

actionPerformed