public void setUp() { cache = new AtomCache(); // Delete files which were cached in previous tests String cacheDir = cache.getPath(); String[] uncacheIDs = new String[] {"1cmw", "1hhb", "4hhb"}; ArrayList<String> extensions = new ArrayList<String>(); extensions.add(".ent"); extensions.add(".pdb"); extensions.add(".ent.gz"); extensions.add(".pdb.gz"); extensions.add(".ent.Z"); extensions.add(".pdb.Z"); for (String pdbId : uncacheIDs) { String middle = pdbId.substring(1, 3).toLowerCase(); String fpath = cacheDir + lineSplit + middle + lineSplit + pdbId; String ppath = cacheDir + lineSplit + middle + lineSplit + "pdb" + pdbId; String[] paths = new String[] {fpath, ppath}; for (int p = 0; p < paths.length; p++) { String testpath = paths[p]; // System.out.println(testpath); for (int i = 0; i < extensions.size(); i++) { String ex = (String) extensions.get(i); // System.out.println("PDBFileReader testing: "+testpath+ex); File f = new File(testpath + ex); if (f.exists()) { System.out.println("Deleting " + testpath + ex); assertTrue("Error deleting " + testpath + ex + " during setup.", f.delete()); } } } } }
public static void main(String[] args) { // ScopDatabase berkeley = new BerkeleyScopInstallation(); // ScopFactory.setScopDatabase(berkeley); AtomCache cache = new AtomCache(); // whenever you want to get access to SCOP now request it like this: ScopDatabase scop = ScopFactory.getSCOP("1.75"); ScopFactory.setScopDatabase(scop); System.out.println(cache.getPath()); System.out.println(cache.getCachePath()); // ... and do something with it // eg. you can run all the demos that work for the UK - SCOP (currently at version 1.75) // this demo no automatically picks up the Berkeley version (currently 1.75A) DemoSCOP scopDemo = new DemoSCOP(); scopDemo.getCategories(); scopDemo.printDomainsForPDB(); scopDemo.traverseHierarchy(); scopDemo.alignSuperfamily(); }