Package 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 Details

    • MultipleAlignmentJmolDisplay

      public MultipleAlignmentJmolDisplay()

  • Method Details

    • 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