/**
* Prints out the XML representation of an AFPChain from a file containing exactly two FASTA
* sequences.
*
* @param args A String array of fasta-file structure-1-name structure-2-name
* @throws StructureException
* @throws IOException
*/
public static void main(String[] args) throws StructureException, IOException {
if (args.length != 3) {
System.err.println(
"Usage: FastaAFPChainConverter fasta-file structure-1-name structure-2-name");
return;
}
File fasta = new File(args[0]);
Structure structure1 = StructureTools.getStructure(args[1]);
Structure structure2 = StructureTools.getStructure(args[2]);
if (structure1 == null)
throw new IllegalArgumentException("No structure for " + args[1] + " was found");
if (structure2 == null)
throw new IllegalArgumentException("No structure for " + args[2] + " was found");
AFPChain afpChain = fastaFileToAfpChain(fasta, structure1, structure2);
String xml = AFPChainXMLConverter.toXML(afpChain);
System.out.println(xml);
}
@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]);
}
}
