assertEquals("EMBL", ref.getSource());
assertEquals("1.2", ref.getVersion());
assertEquals("a7890", ref.getAccessionId());
- assertNull(seq.getAllPDBEntries());
+ assertTrue(seq.getAllPDBEntries().isEmpty());
}
/**
ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
1 }, 1, 1)));
- DBRefEntry[] matches = DBRefUtils.searchRefs(new DBRefEntry[] { ref1,
- ref2, ref3, ref4, ref5 }, "A1234");
+ DBRefEntry[] dbrefs = new DBRefEntry[] { ref1,
+ ref2, ref3, ref4, ref5 };
+ DBRefEntry[] matches = DBRefUtils.searchRefs(dbrefs, "A1234");
assertEquals(3, matches.length);
assertSame(ref1, matches[0]);
assertSame(ref2, matches[1]);
assertSame(ref5, matches[2]);
}
+
+ /**
+ * Test the method that searches for matches references - case when we are
+ * matching a reference with null (any) accession id
+ */
+ @Test(groups = { "Functional" })
+ public void testSearchRefs_wildcardAccessionid()
+ {
+ DBRefEntry target = new DBRefEntry("EMBL", "2", null);
+
+ DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
+ // constructor changes embl to EMBL
+ DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1235"); // matches
+ // constructor does not upper-case accession id
+ DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "A1236"); // matches
+ DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1234"); // no match
+ // ref5 matches although it has a mapping - ignored
+ DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1237");
+ ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
+ 1 }, 1, 1)));
+
+ DBRefEntry[] matches = DBRefUtils.searchRefs(new DBRefEntry[] { ref1,
+ ref2, ref3, ref4, ref5 }, target);
+ assertEquals(4, matches.length);
+ assertSame(ref1, matches[0]);
+ assertSame(ref2, matches[1]);
+ assertSame(ref3, matches[2]);
+ assertSame(ref5, matches[3]);
+ }
}