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());