Class 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.

    Aleix Lafita
    • Method Detail

      • getPDBresnum

        public static List<StringgetPDBresnum​(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).
        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)
        List of pdb Strings corresponding to the aligned positions of the structure.
      • 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.
        multAln -
        MultipleAlignmentJmol instance