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();
}