@Test
public void testIndependence() throws IOException, StructureException {
String[] names = new String[] {"1hiv.A", "4i4q", "1n0r.A"};
int[] orders = new int[] {2, 3, 4};
for (int i = 0; i < names.length; i++) {
Structure s = StructureTools.getStructure(names[i]);
Atom[] atoms = StructureTools.getRepresentativeAtomArray(s);
CeSymmResult result = CeSymm.analyze(atoms);
assertTrue(result.isSignificant());
assertEquals(result.getSymmOrder(), orders[i]);
}
}
@Override
public void actionPerformed(ActionEvent ae) {
String cmd = ae.getActionCommand();
if (cmd.equals("New Symmetry Analysis")) SymmetryGui.getInstance();
if (symm == null) logger.error("Currently not displaying a symmetry!");
try {
if (cmd.equals("Repeats Superposition")) {
MultipleAlignmentJmol j = SymmetryDisplay.displayRepeats(symm);
String s = SymmetryDisplay.printSymmetryAxes(symm);
j.evalString(s);
} else if (cmd.equals("Multiple Structure Alignment")) {
MultipleAlignmentJmol j = SymmetryDisplay.displayFull(symm);
String s = SymmetryDisplay.printSymmetryAxes(symm);
j.evalString(s);
} else if (cmd.equals("Optimal Self Alignment")) {
Atom[] cloned = StructureTools.cloneAtomArray(symm.getAtoms());
AbstractAlignmentJmol jmol =
StructureAlignmentDisplay.display(symm.getSelfAlignment(), symm.getAtoms(), cloned);
RotationAxis axis = new RotationAxis(symm.getSelfAlignment());
jmol.evalString(axis.getJmolScript(symm.getAtoms()));
jmol.setTitle(SymmetryDisplay.getSymmTitle(symm));
} else if (cmd.equals("Show Symmetry Group")) {
String script = SymmetryDisplay.printSymmetryGroup(symm);
jmol.evalString(script);
} else if (cmd.equals("Show Symmetry Axes")) {
String s = SymmetryDisplay.printSymmetryAxes(symm);
jmol.evalString(s);
}
} catch (Exception e) {
logger.error("Could not complete display option", e);
}
}