java.lang.Object

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

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

All Implemented Interfaces:: ActionListener, MouseListener, MouseMotionListener, WindowListener, EventListener

public class StructureAlignmentJmol extends AbstractAlignmentJmol

A class that provides a simple GUI for Jmol

Since:: 1.6
Author:: Andreas Prlic

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

StructureAlignmentJmol()

StructureAlignmentJmol(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
Method Summary

Modifier and Type

Method

Description

void

actionPerformed(ActionEvent e)

void

destroy()

Set all the member variables to null.

List<Matrix>

getDistanceMatrices()

Returns a List of internal Distance Matrices, one for each structure in the alignment.

static String

getJmolScript4Block(AFPChain afpChain, Atom[] ca1, Atom[] ca2, int blockNr)

static String

getJmolString(AFPChain afpChain, Atom[] ca1, Atom[] ca2)

protected void

initCoords()

Display the structures after the variable initialization in the constructor.

static void

main(String[] args)

void

resetDisplay()

Return to the initial state of the alignment visualization.

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 Details
- StructureAlignmentJmol
  
  public StructureAlignmentJmol()
- StructureAlignmentJmol
  
  public StructureAlignmentJmol(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
Method Details
- main
  
  public static void main(String[] args)
- 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 e)
  
  Specified by:
  
  actionPerformed in interface ActionListener
  
  Specified by:
  
  actionPerformed in class AbstractAlignmentJmol
- getJmolString
  
  public static String getJmolString(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
- getJmolScript4Block
  
  public static String getJmolScript4Block(AFPChain afpChain, Atom[] ca1, Atom[] ca2, int blockNr)
- 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<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

Class StructureAlignmentJmol

Field Summary

Fields inherited from class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol

Constructor Summary

Method Summary

Methods inherited from class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol

Methods inherited from class java.lang.Object

Constructor Details

StructureAlignmentJmol

StructureAlignmentJmol

Method Details

main

initCoords

destroy

actionPerformed

getJmolString

getJmolScript4Block

resetDisplay

getDistanceMatrices