public static void buildDefault(File censusFile, int[] sunIds) {
try {
int maxThreads = Runtime.getRuntime().availableProcessors() - 1;
ScopDescriptionCensus census = new ScopDescriptionCensus(maxThreads, sunIds);
census.setOutputWriter(censusFile);
AtomCache cache = new AtomCache();
cache.setFetchFileEvenIfObsolete(true);
census.setCache(cache);
census.run();
System.out.println(census);
} catch (RuntimeException e) {
logger.fatal(e.getMessage(), e);
}
}
public void testFetchObsolete() throws IOException, StructureException {
cache.setUseMmCif(false); // TODO Remove after implementing obsolete mmcif fetching
cache.setAutoFetch(true);
cache.setFetchCurrent(false);
cache.setFetchFileEvenIfObsolete(true);
Structure s;
// OBSOLETE PDB; should throw an exception
s = cache.getStructure("1CMW");
assertEquals("Failed to get OBSOLETE file 1CMW.", "1CMW", s.getPDBCode());
s = cache.getStructure("1HHB");
assertEquals("Failed to get OBSOLETE file 1HHB.", "1HHB", s.getPDBCode());
System.err.println(
"Please ignore the previous four errors. They are expected for this ancient PDB.");
}
public void testFetchCurrent() throws IOException, StructureException {
cache.setUseMmCif(false); // TODO Remove after implementing obsolete mmcif fetching
cache.setAutoFetch(true);
cache.setFetchCurrent(true);
cache.setFetchFileEvenIfObsolete(false);
Structure s;
try {
// OBSOLETE PDB; should throw an exception
s = cache.getStructure("1CMW");
fail("1CMW has no current structure. Should have thrown an error");
} catch (IOException e) {
// expected
System.err.println("Please ignore previous exceptions. They are expected.");
} catch (StructureException e) {
// expected
System.err.println("Please ignore previous exceptions. They are expected.");
}
s = cache.getStructure("1HHB");
assertEquals("Failed to get the current ID for 1HHB.", "4HHB", s.getPDBCode());
}