*/
assertEquals(aa.getSequenceAt(1), acf.findAlignedSequence(cdna
.getSequenceAt(0).getDatasetSequence(), aa));
+ // can also find this from the dna aligned sequence
+ assertEquals(aa.getSequenceAt(1),
+ acf.findAlignedSequence(cdna.getSequenceAt(0), aa));
assertEquals(cdna.getSequenceAt(0), acf.findAlignedSequence(aa
.getSequenceAt(1).getDatasetSequence(), cdna));
assertArrayEquals(new int[] { 2, 2 },
acf.getMappedRegion(seq2, seq1, 6));
}
+
+ /**
+ * Tests for addMap. See also tests for MapList.addMapList
+ */
+ @Test(groups = { "Functional" })
+ public void testAddMap()
+ {
+ final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T");
+ seq1.createDatasetSequence();
+ final Sequence aseq1 = new Sequence("Seq1", "-V-L");
+ aseq1.createDatasetSequence();
+
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 }, new int[] {
+ 1, 2 }, 3, 1);
+ acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
+ assertEquals(1, acf.getMappingsFromSequence(seq1).size());
+ Mapping before = acf.getMappingsFromSequence(seq1).get(0);
+
+ /*
+ * add the same map again, verify it doesn't get duplicated
+ */
+ acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
+ assertEquals(1, acf.getMappingsFromSequence(seq1).size());
+ assertSame(before, acf.getMappingsFromSequence(seq1).get(0));
+ }
}