+ acf.addMap(seq2.getDatasetSequence(), aseq1.getDatasetSequence(), map);
+
+ assertEquals(2, acf.getMappedCodons(aseq1.getDatasetSequence(), 1)
+ .size());
+ List<char[]> codonsForV = acf.getMappedCodons(
+ aseq1.getDatasetSequence(), 1);
+ assertEquals("[G, T, A]", Arrays.toString(codonsForV.get(0)));
+ assertEquals("[G, T, T]", Arrays.toString(codonsForV.get(1)));
+ List<char[]> codonsForL = acf.getMappedCodons(
+ aseq1.getDatasetSequence(), 2);
+ assertEquals("[C, T, T]", Arrays.toString(codonsForL.get(0)));
+ assertEquals("[T, T, A]", Arrays.toString(codonsForL.get(1)));
+ }
+
+ /**
+ * Test for the case where sequences have start > 1
+ */
+ @Test(groups = { "Functional" })
+ public void testGetMappedCodons_forSubSequences()
+ {
+ final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T", 27, 35);
+ seq1.createDatasetSequence();
+
+ final Sequence aseq1 = new Sequence("Seq1", "-V-L", 12, 13);
+ aseq1.createDatasetSequence();
+
+ /*
+ * Set up the mappings for the exons (upper-case bases)
+ */
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ MapList map = new MapList(new int[] { 28, 30, 32, 32, 34, 35 },
+ new int[] { 12, 13 }, 3, 1);
+ acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
+
+ assertEquals(
+ "[G, T, A]",
+ Arrays.toString(acf.getMappedCodons(aseq1.getDatasetSequence(),
+ 12).get(0)));
+ assertEquals(
+ "[C, T, T]",
+ Arrays.toString(acf.getMappedCodons(aseq1.getDatasetSequence(),
+ 13).get(0)));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testCouldReplaceSequence()
+ {
+ SequenceI seq1 = new Sequence("Seq1/10-21", "aaacccgggttt");
+ SequenceI seq1proxy = new SequenceDummy("Seq1");
+
+ // map to region within sequence is ok
+ assertTrue(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 12,
+ 17));
+ // map to region overlapping sequence is ok
+ assertTrue(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 5,
+ 10));
+ assertTrue(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 21,
+ 26));
+ // map to region before sequence is not ok
+ assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 4,
+ 9));
+ // map to region after sequence is not ok
+ assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 22,
+ 27));
+
+ /*
+ * test should fail if name doesn't match
+ */
+ seq1proxy.setName("Seq1a");
+ assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 12,
+ 17));
+ seq1proxy.setName("Seq1");
+ seq1.setName("Seq1a");
+ assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 12,
+ 17));
+
+ /*
+ * a dummy sequence can't replace a real one
+ */
+ assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1, seq1proxy, 12,
+ 17));
+
+ /*
+ * a dummy sequence can't replace a dummy sequence
+ */
+ SequenceI seq1proxy2 = new SequenceDummy("Seq1");
+ assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1proxy,
+ seq1proxy2, 12, 17));
+
+ /*
+ * a real sequence can't replace a real one
+ */
+ SequenceI seq1a = new Sequence("Seq1/10-21", "aaacccgggttt");
+ assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1, seq1a, 12, 17));
+ }
+
+ /**
+ * Tests for the method that tests whether any mapping to a dummy sequence can
+ * be 'realised' to a given real sequence
+ */
+ @Test(groups = { "Functional" })
+ public void testIsRealisableWith()
+ {
+ SequenceI seq1 = new Sequence("Seq1", "tttaaaCCCGGGtttaaa");
+ SequenceI seq2 = new Sequence("Seq2", "PG");
+ SequenceI seq1proxy = new SequenceDummy("Seq1");
+ seq1.createDatasetSequence();
+ seq2.createDatasetSequence();
+ MapList mapList = new MapList(new int[] { 7, 12 }, new int[] { 2, 3 },
+ 3, 1);
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ acf.addMap(seq1proxy, seq2, mapList);
+
+ /*
+ * Seq2 is mapped to SequenceDummy seq1proxy bases 4-9
+ * This is 'realisable' from real sequence Seq1
+ */
+ assertTrue(acf.isRealisableWith(seq1));
+
+ /*
+ * test should fail if name doesn't match
+ */
+ seq1proxy.setName("Seq1a");
+ assertFalse(acf.isRealisableWith(seq1));
+ seq1proxy.setName("Seq1");
+
+ SequenceI seq1ds = seq1.getDatasetSequence();
+ seq1ds.setName("Seq1a");
+ assertFalse(acf.isRealisableWith(seq1));
+ seq1ds.setName("Seq1");
+
+ /*
+ * test should fail if no sequence overlap with mapping of bases 7-12
+ * use artificial start/end values to test this
+ */
+ seq1ds.setStart(1);
+ seq1ds.setEnd(6);
+ // seq1 precedes mapped region:
+ assertFalse(acf.isRealisableWith(seq1));
+ seq1ds.setEnd(7);
+ // seq1 includes first mapped base:
+ assertTrue(acf.isRealisableWith(seq1));
+ seq1ds.setStart(13);
+ seq1ds.setEnd(18);
+ // seq1 follows mapped region:
+ assertFalse(acf.isRealisableWith(seq1));
+ seq1ds.setStart(12);
+ // seq1 includes last mapped base:
+ assertTrue(acf.isRealisableWith(seq1));
+ }
+
+ /**
+ * Tests for the method that converts mappings to a dummy sequence to mappings
+ * to a compatible real sequence
+ */
+ @Test(groups = { "Functional" })
+ public void testRealiseWith()
+ {
+ SequenceI seq1 = new Sequence("Seq1", "tttCAACCCGGGtttaaa");
+ SequenceI seq2 = new Sequence("Seq2", "QPG");
+ SequenceI seq2a = new Sequence("Seq2a", "QPG");
+ SequenceI seq1proxy = new SequenceDummy("Seq1");
+ seq1.createDatasetSequence();
+ seq2.createDatasetSequence();
+ seq2a.createDatasetSequence();
+
+ /*
+ * Make mappings from Seq2 and Seq2a peptides to dummy sequence Seq1
+ */
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+
+ // map PG to codons 7-12 (CCCGGG)
+ MapList mapping1 = new MapList(new int[] { 7, 12 }, new int[] { 2, 3 },
+ 3, 1);
+ acf.addMap(seq1proxy, seq2, mapping1);
+ acf.addMap(seq1proxy, seq2a, mapping1);
+
+ // map QP to codons 4-9 (CAACCC)
+ MapList mapping2 = new MapList(new int[] { 4, 9 }, new int[] { 1, 2 },
+ 3, 1);
+ acf.addMap(seq1proxy, seq2, mapping2);
+ acf.addMap(seq1proxy, seq2a, mapping2);