001/* 002 * BioJava development code 003 * 004 * This code may be freely distributed and modified under the 005 * terms of the GNU Lesser General Public Licence. This should 006 * be distributed with the code. If you do not have a copy, 007 * see: 008 * 009 * http://www.gnu.org/copyleft/lesser.html 010 * 011 * Copyright for this code is held jointly by the individual 012 * authors. These should be listed in @author doc comments. 013 * 014 * For more information on the BioJava project and its aims, 015 * or to join the biojava-l mailing list, visit the home page 016 * at: 017 * 018 * http://www.biojava.org/ 019 * 020 */ 021package org.biojava.nbio.structure.symmetry.gui; 022 023import java.awt.event.ActionEvent; 024import java.awt.event.ActionListener; 025 026import org.biojava.nbio.structure.Atom; 027import org.biojava.nbio.structure.StructureTools; 028import org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay; 029import org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol; 030import org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol; 031import org.biojava.nbio.structure.align.util.RotationAxis; 032import org.biojava.nbio.structure.symmetry.internal.CeSymmResult; 033import org.slf4j.Logger; 034import org.slf4j.LoggerFactory; 035 036/** 037 * Action Listener for the symmetry menu. Trigger various internal symmetry 038 * specific analysis. 039 * 040 * @author Aleix Lafita 041 * @since 4.2.0 042 * 043 */ 044public class SymmetryListener implements ActionListener { 045 046 private MultipleAlignmentJmol jmol; 047 private CeSymmResult symm; 048 049 private static final Logger logger = LoggerFactory 050 .getLogger(SymmetryListener.class); 051 052 public SymmetryListener(MultipleAlignmentJmol jmol, CeSymmResult symm) { 053 this.jmol = jmol; 054 this.symm = symm; 055 } 056 057 @Override 058 public void actionPerformed(ActionEvent ae) { 059 String cmd = ae.getActionCommand(); 060 if (cmd.equals("New Symmetry Analysis")) 061 SymmetryGui.getInstance(); 062 063 if (symm == null) 064 logger.error("Currently not displaying a symmetry!"); 065 066 try { 067 if (cmd.equals("Repeats Superposition")) { 068 MultipleAlignmentJmol j = SymmetryDisplay.displayRepeats(symm); 069 String s = SymmetryDisplay.printSymmetryAxes(symm, false); 070 j.evalString(s); 071 072 } else if (cmd.equals("Multiple Structure Alignment")) { 073 MultipleAlignmentJmol j = SymmetryDisplay.displayFull(symm); 074 String s = SymmetryDisplay.printSymmetryAxes(symm); 075 j.evalString(s); 076 077 } else if (cmd.equals("Optimal Self Alignment")) { 078 Atom[] cloned = StructureTools.cloneAtomArray(symm.getAtoms()); 079 AbstractAlignmentJmol jmol = StructureAlignmentDisplay.display( 080 symm.getSelfAlignment(), symm.getAtoms(), cloned); 081 RotationAxis axis = new RotationAxis(symm.getSelfAlignment()); 082 jmol.evalString(axis.getJmolScript(symm.getAtoms())); 083 jmol.setTitle(SymmetryDisplay.getSymmTitle(symm)); 084 085 } else if (cmd.equals("Show Symmetry Group")) { 086 String script = SymmetryDisplay.printSymmetryGroup(symm); 087 jmol.evalString(script); 088 089 } else if (cmd.equals("Show Symmetry Axes")) { 090 String s = SymmetryDisplay.printSymmetryAxes(symm); 091 jmol.evalString(s); 092 } 093 094 } catch (Exception e) { 095 logger.error("Could not complete display option", e); 096 } 097 } 098}