public void actionPerformed(ActionEvent e) {
String cmd = e.getActionCommand();
// print is handled by superclass
if (cmd.equals(MenuCreator.PRINT)) {
super.actionPerformed(e);
} else if (cmd.equals(MenuCreator.TEXT_ONLY)) {
String result = AfpChainWriter.toWebSiteDisplay(afpChain, ca1, ca2);
DisplayAFP.showAlignmentImage(afpChain, result);
} else if (cmd.equals(MenuCreator.PAIRS_ONLY)) {
String result = AfpChainWriter.toAlignedPairs(afpChain, ca1, ca2);
DisplayAFP.showAlignmentImage(afpChain, result);
} else if (cmd.equals(MenuCreator.FATCAT_TEXT)) {
String result = afpChain.toFatcat(ca1, ca2);
result += AFPChain.newline;
result += afpChain.toRotMat();
DisplayAFP.showAlignmentImage(afpChain, result);
} else if (cmd.equals(MenuCreator.SELECT_EQR)) {
selectEQR();
} else if (cmd.equals(MenuCreator.SIMILARITY_COLOR)) {
colorBySimilarity(true);
} else if (cmd.equals(MenuCreator.EQR_COLOR)) {
colorBySimilarity(false);
} else if (cmd.equals(MenuCreator.FATCAT_BLOCK)) {
colorByAlignmentBlock();
} else {
System.err.println("Unknown command:" + cmd);
}
}
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();
}
}