/**
  * 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);
 }
Beispiel #2
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  @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]);
    }
  }