Class MultipleAlignmentJmolDisplay


  • public class MultipleAlignmentJmolDisplay
    extends java.lang.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 Detail

      • MultipleAlignmentJmolDisplay

        public MultipleAlignmentJmolDisplay()
    • Method Detail

      • getPDBresnum

        public static java.util.List<java.lang.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,
                                              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 superposition information in the Multiple Alignment.
        Parameters:
        multAln -
        Returns:
        MultipleAlignmentJmol instance
        Throws:
        StructureException