public static void main(String[] args) { String file = "/Users/ap3/tmp/4hhb.ce"; try { BufferedReader in = new BufferedReader(new FileReader(file)); StringBuffer xml = new StringBuffer(); String str; while ((str = in.readLine()) != null) { xml.append(str); } in.close(); AFPChain[] afps = AFPChainXMLParser.parseMultiXML(xml.toString()); AFPChain afpChain = afps[0]; UserConfiguration config = WebStartMain.getWebStartConfig(); AtomCache cache = new AtomCache(config.getPdbFilePath(), config.isSplit()); Atom[] ca1 = cache.getAtoms(afpChain.getName1()); Atom[] ca2 = cache.getAtoms(afpChain.getName2()); AFPChainXMLParser.rebuildAFPChain(afpChain, ca1, ca2); // StructureAlignment algorithm = // StructureAlignmentFactory.getAlgorithm(afpChain.getAlgorithmName()); StructureAlignmentJmol jmol = StructureAlignmentDisplay.display(afpChain, ca1, ca2); DisplayAFP.showAlignmentImage(afpChain, ca1, ca2, jmol); } catch (Exception e) { e.printStackTrace(); } }
/** make sure all paths are initialized correctly */ public static void checkPath() { UserConfiguration config = new UserConfiguration(); path = config.getCacheFilePath(); }