java.lang.Object

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

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

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

public class MultipleAlignmentJmol extends AbstractAlignmentJmol

A class that provides a 3D visualization Frame in Jmol for MultipleAlignments.

Since:: 4.1.0
Author:: Aleix Lafita

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

MultipleAlignmentJmol()

Default constructor creates an empty JmolPanel window, from where alignments can be made through the align menu.

MultipleAlignmentJmol(MultipleAlignment msa, List<Atom[]> rotatedAtoms)

The constructor displays the Mutltiple Alignment in a new JmolPanel Frame.
Method Summary

Modifier and Type

Method

Description

void

actionPerformed(ActionEvent ae)

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.

JFrame

getFrame()

static String

getJmolString(MultipleAlignment multAln, List<Atom[]> transformedAtoms, ColorBrewer colorPalette, boolean colorByBlocks)

Generate a Jmol command String that colors the aligned residues of every structure.

static String

getMultiBlockJmolString(MultipleAlignment multAln, List<Atom[]> transformedAtoms, ColorBrewer colorPalette, boolean colorByBlocks)

Colors every Block of the structures with a different color, following the palette.

MultipleAlignment

getMultipleAlignment()

protected void

initCoords()

Display the structures after the variable initialization in the constructor.

void

resetDisplay()

Return to the initial state of the alignment visualization.

void

setColorByBlocks(boolean colorByBlocks)

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
- MultipleAlignmentJmol
  
  public MultipleAlignmentJmol()
  
  Default constructor creates an empty JmolPanel window, from where alignments can be made through the align menu.
- MultipleAlignmentJmol
  
  public MultipleAlignmentJmol(MultipleAlignment msa, List<Atom[]> rotatedAtoms)
  
  The constructor displays the Mutltiple Alignment in a new JmolPanel Frame.
  
  Parameters:
  
  msa - : contains the aligned residues.
  
  rotatedAtoms - : contains the transformed Atom coordinates.
Method Details
- 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 ae)
  
  Specified by:
  
  actionPerformed in interface ActionListener
  
  Specified by:
  
  actionPerformed in class AbstractAlignmentJmol
- getJmolString
  
  public static String getJmolString(MultipleAlignment multAln, List<Atom[]> transformedAtoms, ColorBrewer colorPalette, boolean colorByBlocks)
  
  Generate a Jmol command String that colors the aligned residues of every structure.
- getMultiBlockJmolString
  
  public static String getMultiBlockJmolString(MultipleAlignment multAln, List<Atom[]> transformedAtoms, ColorBrewer colorPalette, boolean colorByBlocks)
  
  Colors every Block of the structures with a different color, following the palette. It colors each Block differently, no matter if it is from the same or different BlockSet.
- 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
- setColorByBlocks
  
  public void setColorByBlocks(boolean colorByBlocks)
- getFrame
  
  public JFrame getFrame()
- getMultipleAlignment
  
  public MultipleAlignment getMultipleAlignment()

Class MultipleAlignmentJmol

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

MultipleAlignmentJmol

MultipleAlignmentJmol

Method Details

initCoords

destroy

actionPerformed

getJmolString

getMultiBlockJmolString

resetDisplay

getDistanceMatrices

setColorByBlocks

getFrame

getMultipleAlignment