+ private List<TestRetrieveObject> toRetrieve = Arrays.asList(
+ new TestRetrieveObject("1QIP", 4),
+ new TestRetrieveObject("4IM2", 1));
+
+ private void testRetrieveProteinSeqFromPDB() throws Exception
+ {
+ List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
+ for (TestRetrieveObject str : toRetrieve)
+ {
+ AlignmentI response = sps.get(0).getSequenceRecords(str.id);
+ assertTrue("No aligment for " + str.id, response != null);
+ assertEquals(response.getHeight(), str.expectedHeight,
+ "Number of chains for " + str.id);
+ for (SequenceI sq : response.getSequences())
+ {
+ assertTrue("No annotation transfered to sequence " + sq.getName(),
+ sq.getAnnotation().length > 0);
+ assertTrue("No PDBEntry on sequence " + sq.getName(),
+ sq.getAllPDBEntries().size() > 0);
+ org.testng.Assert.assertEquals(sq.getEnd() - sq.getStart() + 1,
+ sq.getLength(),
+ "Sequence start/end doesn't match number of residues in sequence for "
+ + sq.getName());
+ }
+ }
+ }