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(); } }