import static org.testng.AssertJUnit.assertTrue;
import java.util.BitSet;
+import java.util.List;
import org.junit.Assert;
import org.testng.annotations.BeforeClass;
int marked = 0;
SequenceI seq1 = new Sequence("", "abcdefghijklm");
SequenceI seq2 = new Sequence("", "abcdefghijklm");
- SequenceGroup s1g=new SequenceGroup(), s2g=new SequenceGroup(), sallg=new SequenceGroup();
+ SequenceGroup s1g = new SequenceGroup(), s2g = new SequenceGroup(),
+ sallg = new SequenceGroup();
s1g.addSequence(seq1, false);
s2g.addSequence(seq2, false);
sallg.addSequence(seq1, false);
sallg.addSequence(seq2, false);
-
+
SearchResultsI sr = new SearchResults();
BitSet bs = new BitSet();
-
+
SearchResultMatchI srm = null;
srm = sr.addResult(seq1, 1, 1);
Assert.assertNotNull("addResult didn't return Match", srm);
assertEquals("Sequence reference not set", seq2, srm.getSequence());
assertEquals("match start incorrect", 1, srm.getStart());
assertEquals("match end incorrect", 2, srm.getEnd());
-
+
// set start/end range for groups to cover matches
s1g.setStartRes(0);
assertTrue("Didn't mark expected position", bs.get(0));
// now check return value for marking the same again
assertEquals(
- "Didn't count number of bits marked for existing marked set",
- 0,
+ "Didn't count number of bits marked for existing marked set", 0,
sr.markColumns(s1g, bs));
bs.clear();
-
+
/*
* just seq2
*/
assertEquals("Didn't return count of number of bits marked", 2, marked);
assertTrue("Didn't mark expected position (1)", bs.get(0));
assertTrue("Didn't mark expected position (2)", bs.get(1));
-
+
/*
* both seq1 and seq2
* should be same as seq2
s2g.setEndRes(1);
sallg.setEndRes(0);
BitSet tbs = new BitSet();
- assertEquals("Group start/end didn't select columns to mark",1, sr.markColumns(s2g, tbs));
- assertEquals("Group start/end didn't select columns to mark", 1, sr.markColumns(sallg, tbs));
+ assertEquals("Group start/end didn't select columns to mark", 1,
+ sr.markColumns(s2g, tbs));
+ assertEquals("Group start/end didn't select columns to mark", 1,
+ sr.markColumns(sallg, tbs));
assertEquals(
"Didn't set expected number of columns in total for two successive marks",
2, tbs.cardinality());
SequenceI seq1 = new Sequence("", "abcdefghijklm");
SearchResultsI sr = new SearchResults();
sr.addResult(seq1, 3, 5);
- assertEquals(1, sr.getSize());
+ assertEquals(1, sr.getCount());
sr.addResult(seq1, 3, 5);
- assertEquals(1, sr.getSize());
+ assertEquals(1, sr.getCount());
sr.addResult(seq1, 3, 6);
- assertEquals(2, sr.getSize());
+ assertEquals(2, sr.getCount());
}
/**
sr.addResult(cds2, 7, 9); // start-end overlap
assertTrue(sr.involvesSequence(cds2));
}
+
+ /**
+ * Test extraction of Sequence objects for matched ranges on a sequence
+ */
+ @Test(groups = { "Functional" })
+ public void testGetSequences()
+ {
+ SequenceI seq1 = new Sequence("", "abcdefghijklm");
+ SequenceI seq2 = new Sequence("", "nopqrstuvwxyz");
+ seq2.setStart(23);
+ seq2.setEnd(35);
+ List<SequenceI> seqres = null;
+
+ SearchResultsI sr = new SearchResults();
+ seqres = sr.getMatchingSubSequences();
+ assertEquals(0, seqres.size());
+
+ sr.addResult(seq1, 3, 5);
+ seqres = sr.getMatchingSubSequences();
+
+ assertEquals(1, seqres.size());
+ assertEquals("cde", seqres.get(0).getSequenceAsString());
+ assertEquals(3, seqres.get(0).getStart());
+ assertEquals(seq1, seqres.get(0).getDatasetSequence());
+
+ sr.addResult(seq1, 3, 6);
+ seqres = sr.getMatchingSubSequences();
+
+ assertEquals(2, seqres.size());
+ assertEquals("cdef", seqres.get(1).getSequenceAsString());
+ assertEquals(3, seqres.get(1).getStart());
+
+ // this is a quirk - match on 26-29 yields subsequence 27-30
+ sr.addResult(seq2, 26, 29);
+ seqres = sr.getMatchingSubSequences();
+ assertEquals(3, seqres.size());
+ assertEquals("qrst", seqres.get(2).getSequenceAsString());
+ assertEquals(26, seqres.get(2).getStart());
+ }
+
}