Class MultipleAlignmentJmol

  • All Implemented Interfaces:
    java.awt.event.ActionListener, java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.awt.event.WindowListener, java.util.EventListener

    public class MultipleAlignmentJmol
    extends AbstractAlignmentJmol
    A class that provides a 3D visualization Frame in Jmol for MultipleAlignments.
    Since:
    4.1.0
    Author:
    Aleix Lafita
    • Constructor Detail

      • MultipleAlignmentJmol

        public MultipleAlignmentJmol()
        Default constructor creates an empty JmolPanel window, from where alignments can be made through the align menu.
      • MultipleAlignmentJmol

        public MultipleAlignmentJmol​(MultipleAlignment msa,
                                     java.util.List<Atom[]> rotatedAtoms)
        The constructor displays the Mutltiple Alignment in a new JmolPanel Frame.
        Parameters:
        msa - : contains the aligned residues.
        rotatedAtoms - : contains the transformed Atom coordinates.
    • Method Detail

      • actionPerformed

        public void actionPerformed​(java.awt.event.ActionEvent ae)
        Specified by:
        actionPerformed in interface java.awt.event.ActionListener
        Specified by:
        actionPerformed in class AbstractAlignmentJmol
      • getJmolString

        public static java.lang.String getJmolString​(MultipleAlignment multAln,
                                                     java.util.List<Atom[]> transformedAtoms,
                                                     ColorBrewer colorPalette,
                                                     boolean colorByBlocks)
        Generate a Jmol command String that colors the aligned residues of every structure.
      • getMultiBlockJmolString

        public static java.lang.String getMultiBlockJmolString​(MultipleAlignment multAln,
                                                               java.util.List<Atom[]> transformedAtoms,
                                                               ColorBrewer colorPalette,
                                                               boolean colorByBlocks)
        Colors every Block of the structures with a different color, following the palette. It colors each Block differently, no matter if it is from the same or different BlockSet.
      • setColorByBlocks

        public void setColorByBlocks​(boolean colorByBlocks)
      • getFrame

        public javax.swing.JFrame getFrame()