+
+ /**
+ * Test the method that locates the mapped codon for a protein position.
+ */
+ @Test(groups = { "Functional" })
+ public void testGetMappedRegion_eitherWay()
+ {
+ final Sequence seq1 = new Sequence("Seq1", "AAACCCGGGTTT");
+ seq1.createDatasetSequence();
+ final Sequence seq2 = new Sequence("Seq2", "KPGF");
+ seq2.createDatasetSequence();
+ final Sequence seq3 = new Sequence("Seq3", "QYKPGFSW");
+ seq3.createDatasetSequence();
+
+ /*
+ * map Seq1 to all of Seq2 and part of Seq3
+ */
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1);
+ acf.addMap(seq1.getDatasetSequence(), seq2.getDatasetSequence(), map);
+ map = new MapList(new int[] { 1, 12 }, new int[] { 3, 6 }, 3, 1);
+ acf.addMap(seq1.getDatasetSequence(), seq3.getDatasetSequence(), map);
+
+ /*
+ * map part of Seq3 to Seq2
+ */
+ map = new MapList(new int[] { 3, 6 }, new int[] { 1, 4 }, 1, 1);
+ acf.addMap(seq3.getDatasetSequence(), seq2.getDatasetSequence(), map);
+
+ /*
+ * original case - locate mapped codon for protein position
+ */
+ assertArrayEquals(new int[] { 4, 6 },
+ acf.getMappedRegion(seq1, seq2, 2));
+ assertArrayEquals(new int[] { 7, 9 },
+ acf.getMappedRegion(seq1, seq3, 5));
+ assertNull(acf.getMappedRegion(seq1, seq3, 1));
+
+ /*
+ * locate mapped protein for protein position
+ */
+ assertArrayEquals(new int[] { 4, 4 },
+ acf.getMappedRegion(seq3, seq2, 2));
+
+ /*
+ * reverse location protein-to-protein
+ */
+ assertArrayEquals(new int[] { 2, 2 },
+ acf.getMappedRegion(seq2, seq3, 4));
+
+ /*
+ * reverse location protein-from-nucleotide
+ * any of codon [4, 5, 6] positions map to seq2/2
+ */
+ assertArrayEquals(new int[] { 2, 2 },
+ acf.getMappedRegion(seq2, seq1, 4));
+ assertArrayEquals(new int[] { 2, 2 },
+ acf.getMappedRegion(seq2, seq1, 5));
+ 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));
+ }