org.biojava.nbio.structure.align.gui

Class MultipleAlignmentJmolDisplay

java.lang.Object

org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay

public class MultipleAlignmentJmolDisplay
extends Object

Utility Class that provides helper methods for the visualization of MultipleAlignments.

Currently supported: Alignment Panel Display, select aligned residues in Jmol by their PDB name, show a text Frame for any sequence alignment format, basic Jmol display from a MultipleAlignment, generate an artificial PDB structure with a new model for every aligned structure.

Since:

4.2.0

Author:

Aleix Lafita

Constructor Summary

Constructors

Constructor and Description
MultipleAlignmentJmolDisplay()

Method Summary

Modifier and Type	Method and Description
static MultipleAlignmentJmol	display(MultipleAlignment multAln) Display a MultipleAlignment with a JmolPanel.
static Structure	getAlignedStructure(List<Atom[]> atomArrays) Get an artifical Structure containing a different model for every input structure, so that the alignment result can be viewed in Jmol.
static List<String>	getPDBresnum(int structNum, MultipleAlignment multAln, Atom[] ca) Utility method used in the MultipleAlignmentJmol Frame, when the aligned residues of a structure in the alignment have to be selected for formatting them (coloring and style).
static void	showAlignmentImage(MultipleAlignment multAln, String result) Creates a new Frame with the String output representation of the MultipleAlignment.
static void	showMultipleAligmentPanel(MultipleAlignment multAln, AbstractAlignmentJmol jmol) 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

MultipleAlignmentJmolDisplay

public MultipleAlignmentJmolDisplay()

Method Detail

getPDBresnum

public static List<String> getPDBresnum(int structNum,
                                        MultipleAlignment multAln,
                                        Atom[] ca)

Utility method used in the MultipleAlignmentJmol Frame, when the aligned residues of a structure in the alignment have to be selected for formatting them (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 structure.

showMultipleAligmentPanel

public static void showMultipleAligmentPanel(MultipleAlignment multAln,
                                             AbstractAlignmentJmol jmol)
                                      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 every structure.

Parameters:

multAln -

jmol -

Throws:

StructureException

showAlignmentImage

public static void showAlignmentImage(MultipleAlignment multAln,
                                      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 superposition information in the Multiple Alignment.

Parameters:

multAln -

Returns:

MultipleAlignmentJmol instance

Throws:

StructureException

getAlignedStructure

public static final Structure getAlignedStructure(List<Atom[]> atomArrays)
                                           throws StructureException

Get an artifical Structure containing a different model for every input structure, so that the alignment result can be viewed in Jmol. The Atoms have to be rotated beforehand.

Parameters:

atomArrays - an array of Atoms for every aligned structure

Returns:

a structure object containing a set of models, one for each input array of Atoms.

Throws:

StructureException