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();
}