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
Modifier and Type | Field and Description |
---|---|
protected 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 and Description |
---|
AbstractAlignmentJmol() |
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.
|
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) |
protected Structure structure
protected ColorBrewer colorPalette
protected JmolPanel jmolPanel
protected javax.swing.JFrame frame
protected javax.swing.JTextField text
protected javax.swing.JTextField status
protected static final java.lang.String COMMAND_LINE_HELP
protected static final int DEFAULT_HEIGHT
protected static final int DEFAULT_WIDTH
protected static final java.lang.String DEFAULT_SCRIPT
protected static int nrOpenWindows
protected abstract void initCoords()
public void destroy()
public abstract void resetDisplay()
public void setAtoms(Atom[] atoms)
atoms
- public ColorBrewer getColorPalette()
public JmolPanel getJmolPanel()
public void setJmolPanel(JmolPanel jmolPanel)
jmolPanel
- public void evalString(java.lang.String rasmolScript)
rasmolScript
- public void setStructure(Structure s)
s
- public Structure getStructure()
public abstract java.util.List<Matrix> getDistanceMatrices()
public void setTitle(java.lang.String title)
label
- public java.lang.String getTitle()
public void mouseDragged(java.awt.event.MouseEvent e)
mouseDragged
in interface java.awt.event.MouseMotionListener
public void mouseMoved(java.awt.event.MouseEvent e)
mouseMoved
in interface java.awt.event.MouseMotionListener
public void mouseClicked(java.awt.event.MouseEvent e)
mouseClicked
in interface java.awt.event.MouseListener
public void mouseEntered(java.awt.event.MouseEvent e)
mouseEntered
in interface java.awt.event.MouseListener
public void mouseExited(java.awt.event.MouseEvent e)
mouseExited
in interface java.awt.event.MouseListener
public void mousePressed(java.awt.event.MouseEvent e)
mousePressed
in interface java.awt.event.MouseListener
public void mouseReleased(java.awt.event.MouseEvent e)
mouseReleased
in interface java.awt.event.MouseListener
public void windowActivated(java.awt.event.WindowEvent e)
windowActivated
in interface java.awt.event.WindowListener
public void windowClosed(java.awt.event.WindowEvent e)
windowClosed
in interface java.awt.event.WindowListener
public void windowClosing(java.awt.event.WindowEvent e)
windowClosing
in interface java.awt.event.WindowListener
public void windowDeactivated(java.awt.event.WindowEvent e)
windowDeactivated
in interface java.awt.event.WindowListener
public void windowDeiconified(java.awt.event.WindowEvent e)
windowDeiconified
in interface java.awt.event.WindowListener
public void windowIconified(java.awt.event.WindowEvent e)
windowIconified
in interface java.awt.event.WindowListener
public void windowOpened(java.awt.event.WindowEvent e)
windowOpened
in interface java.awt.event.WindowListener
public abstract void actionPerformed(java.awt.event.ActionEvent e)
actionPerformed
in interface java.awt.event.ActionListener