org.biojava.nbio.structure.align.gui

Class MultipleAlignmentDisplay

java.lang.Object

org.biojava.nbio.structure.align.gui.MultipleAlignmentDisplay

public class MultipleAlignmentDisplay
extends java.lang.Object

Utility Class that provides methods for the visualization of MultipleAlignments.

Currently supported: Alignment Panel Display, select aligned residues by PDB code, JmolPanel display.

Author:

Aleix Lafita

Constructor Summary

Constructors

Constructor and Description
MultipleAlignmentDisplay()

Method Summary

Methods

Modifier and Type	Method and Description
static MultipleAlignmentJmol	display(MultipleAlignment multAln) Display a MultipleAlignment with a JmolPanel.
static java.util.List<java.lang.String>	getPDBresnum(int structNum, MultipleAlignment multAln, Atom[] ca) Utility method used in the MultipleAlignmentJmol panel, when the aligned residues of a structure in the alignment have to be selected for formatting (coloring and style).
static void	showAlignmentImage(MultipleAlignment multAln, java.lang.String result) Creates a new Frame with the String output representation of the MultipleAlignment.
static void	showMultipleAligmentPanel(MultipleAlignment multAln, AbstractAlignmentJmol jmol, ColorBrewer colorPattelete) Creates a new Frame with the MultipleAlignment Sequence Panel.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MultipleAlignmentDisplay

public MultipleAlignmentDisplay()

Method Detail

getPDBresnum

public static final java.util.List<java.lang.String> getPDBresnum(int structNum,
                                            MultipleAlignment multAln,
                                            Atom[] ca)

Utility method used in the MultipleAlignmentJmol panel, when the aligned residues of a structure in the alignment have to be selected for formatting (coloring and style).

Parameters:

structNum - the structure index (row) of the alignment

multAln - the MultipleAlignment that contains the equivalent positions

ca - the atom array of the structure specified (corresponding to the structure index)

Returns:

List of pdb Strings corresponding to the aligned positions of the molecule.

showMultipleAligmentPanel

public static void showMultipleAligmentPanel(MultipleAlignment multAln,
                             AbstractAlignmentJmol jmol,
                             ColorBrewer colorPattelete)
                                      throws StructureException

Creates a new Frame with the MultipleAlignment Sequence Panel. The panel can communicate with the Jmol 3D visualization by selecting the aligned residues of all structures.

Parameters:

multAln -

jmol -

colors -

Throws:

StructureException

showAlignmentImage

public static void showAlignmentImage(MultipleAlignment multAln,
                      java.lang.String result)

Creates a new Frame with the String output representation of the MultipleAlignment.

Parameters:

multAln -

result - String output

display

public static MultipleAlignmentJmol display(MultipleAlignment multAln)
                                     throws StructureException

Display a MultipleAlignment with a JmolPanel. New structures are downloaded if they were not cached in the alignment and they are entirely transformed here with the cached superposition information.

Parameters:

multAln -

Returns:

MultipleAlignmentJmol instance

Throws:

StructureException