code: 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);
  	}
docs: 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