+
+ /**
+ * 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);
+
+ /*
+ * acf now has two mappings one from Seq1 to Seq2, one from Seq1 to Seq2a
+ */
+ assertEquals(2, acf.getdnaSeqs().length);
+ assertSame(seq1proxy, acf.getdnaSeqs()[0]);
+ assertSame(seq1proxy, acf.getdnaSeqs()[1]);
+ assertEquals(2, acf.getProtMappings().length);
+
+ // 'realise' these mappings with the compatible sequence seq1
+ // two mappings should be updated:
+ assertEquals(2, acf.realiseWith(seq1));
+ assertSame(seq1.getDatasetSequence(), acf.getdnaSeqs()[0]);
+ assertSame(seq1.getDatasetSequence(), acf.getdnaSeqs()[1]);
+ }
+
+ /**
+ * 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));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetCoveringMapping()
+ {
+ SequenceI dna = new Sequence("dna", "acttcaATGGCGGACtaattt");
+ SequenceI cds = new Sequence("cds/7-15", "ATGGCGGAC");
+ cds.setDatasetSequence(dna);
+ SequenceI pep = new Sequence("pep", "MAD");
+
+ /*
+ * with null argument or no mappings
+ */
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ assertNull(acf.getCoveringMapping(null, null));
+ assertNull(acf.getCoveringMapping(dna, null));
+ assertNull(acf.getCoveringMapping(null, pep));
+ assertNull(acf.getCoveringMapping(dna, pep));
+
+ /*
+ * with a non-covering mapping e.g. overlapping exon
+ */
+ MapList map = new MapList(new int[] { 7, 9 }, new int[] { 1, 1 }, 3, 1);
+ acf.addMap(dna, pep, map);
+ assertNull(acf.getCoveringMapping(dna, pep));
+
+ acf = new AlignedCodonFrame();
+ MapList map2 = new MapList(new int[] { 13, 18 }, new int[] { 2, 2 }, 3,
+ 1);
+ acf.addMap(dna, pep, map2);
+ assertNull(acf.getCoveringMapping(dna, pep));
+
+ /*
+ * with a covering mapping from CDS (dataset) to protein
+ */
+ acf = new AlignedCodonFrame();
+ MapList map3 = new MapList(new int[] { 7, 15 }, new int[] { 1, 3 }, 3,
+ 1);
+ acf.addMap(dna, pep, map3);
+ assertNull(acf.getCoveringMapping(dna, pep));
+ SequenceToSequenceMapping mapping = acf.getCoveringMapping(cds, pep);
+ assertNotNull(mapping);
+
+ /*
+ * with a mapping that extends to stop codon
+ */
+ acf = new AlignedCodonFrame();
+ MapList map4 = new MapList(new int[] { 7, 18 }, new int[] { 1, 3 }, 3,
+ 1);
+ acf.addMap(dna, pep, map4);
+ assertNull(acf.getCoveringMapping(dna, pep));
+ assertNull(acf.getCoveringMapping(cds, pep));
+ SequenceI cds2 = new Sequence("cds/7-18", "ATGGCGGACtaa");
+ cds2.setDatasetSequence(dna);
+ mapping = acf.getCoveringMapping(cds2, pep);
+ assertNotNull(mapping);
+ }
+
+ /**
+ * Test the method that adds mapped positions to SearchResults
+ */
+ @Test(groups = { "Functional" })
+ public void testMarkMappedRegion()
+ {
+ // introns lower case, exons upper case
+ final Sequence dna1 = new Sequence("Seq1/10-18", "c-G-TA-gC-gT-T");
+ dna1.createDatasetSequence();
+ final Sequence dna2 = new Sequence("Seq2/20-28", "-TA-gG-Gg-CG-a");
+ dna2.createDatasetSequence();
+
+ final Sequence pep1 = new Sequence("Seq1/3-4", "-P-R");
+ pep1.createDatasetSequence();
+ final Sequence pep2 = new Sequence("Seq2/7-9", "-LY-Q");
+ pep2.createDatasetSequence();
+
+ /*
+ * First with no mappings
+ */
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ SearchResults sr = new SearchResults();
+ acf.markMappedRegion(dna1, 12, sr);
+ assertTrue(sr.isEmpty());
+
+ /*
+ * Set up the mappings for the exons (upper-case bases)
+ * Note residue Q is unmapped
+ */
+ MapList map1 = new MapList(new int[] { 11, 13, 15, 15, 17, 18 },
+ new int[]
+ { 3, 4 }, 3, 1);
+ acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map1);
+ MapList map2 = new MapList(new int[] { 20, 21, 23, 24, 26, 27 },
+ new int[]
+ { 7, 8 }, 3, 1);
+ acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map2);
+
+ /*
+ * intron bases are not mapped
+ */
+ acf.markMappedRegion(dna1, 10, sr);
+ assertTrue(sr.isEmpty());
+
+ /*
+ * Q is not mapped
+ */
+ acf.markMappedRegion(pep2, 9, sr);
+ assertTrue(sr.isEmpty());
+
+ /*
+ * mark peptide position for exon position (of aligned sequence)
+ */
+ acf.markMappedRegion(dna1, 11, sr);
+ SearchResults expected = new SearchResults();
+ expected.addResult(pep1.getDatasetSequence(), 3, 3);
+ assertEquals(sr, expected);
+
+ /*
+ * mark peptide position for exon position of dataset sequence - same result
+ */
+ sr = new SearchResults();
+ acf.markMappedRegion(dna1.getDatasetSequence(), 11, sr);
+ assertEquals(sr, expected);
+
+ /*
+ * marking the same position a second time should not create a duplicate match
+ */
+ acf.markMappedRegion(dna1.getDatasetSequence(), 12, sr);
+ assertEquals(sr, expected);
+
+ /*
+ * mark exon positions for peptide position (of aligned sequence)
+ */
+ sr = new SearchResults();
+ acf.markMappedRegion(pep2, 7, sr); // codon positions 20, 21, 23
+ expected = new SearchResults();
+ expected.addResult(dna2.getDatasetSequence(), 20, 21);
+ expected.addResult(dna2.getDatasetSequence(), 23, 23);
+ assertEquals(sr, expected);
+
+ /*
+ * add another codon to the same SearchResults
+ */
+ acf.markMappedRegion(pep1.getDatasetSequence(), 4, sr); // codon positions
+ // 15, 17, 18
+ expected.addResult(dna1.getDatasetSequence(), 15, 15);
+ expected.addResult(dna1.getDatasetSequence(), 17, 18);
+ assertEquals(sr, expected);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetCoveringCodonMapping()
+ {
+ SequenceI dna = new Sequence("dna/10-30", "acttcaATGGCGGACtaattt");
+ // CDS sequence with its own dataset sequence (JAL-3763)
+ SequenceI cds = new Sequence("cds/1-9", "-A--TGGC-GGAC");
+ cds.createDatasetSequence();
+ SequenceI pep = new Sequence("pep/1-3", "MAD");
+
+ /*
+ * with null argument or no mappings
+ */
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ assertNull(acf.getCoveringCodonMapping(null));
+ assertNull(acf.getCoveringCodonMapping(dna));
+ assertNull(acf.getCoveringCodonMapping(pep));
+
+ /*
+ * with a non-covering mapping e.g. overlapping exon
+ */
+ MapList map = new MapList(new int[] { 16, 18 }, new int[] { 1, 1 }, 3,
+ 1);
+ acf.addMap(dna, pep, map);
+ assertNull(acf.getCoveringCodonMapping(dna));
+ assertNull(acf.getCoveringCodonMapping(pep));
+
+ acf = new AlignedCodonFrame();
+ MapList map2 = new MapList(new int[] { 13, 18 }, new int[] { 2, 2 }, 3,
+ 1);
+ acf.addMap(dna, pep, map2);
+ assertNull(acf.getCoveringCodonMapping(dna));
+ assertNull(acf.getCoveringCodonMapping(pep));
+
+ /*
+ * with a covering mapping from CDS (dataset) to protein
+ */
+ acf = new AlignedCodonFrame();
+ MapList map3 = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3,
+ 1);
+ acf.addMap(cds.getDatasetSequence(), pep, map3);
+ assertNull(acf.getCoveringCodonMapping(dna));
+ SequenceToSequenceMapping mapping = acf.getCoveringCodonMapping(pep);
+ assertNotNull(mapping);
+ SequenceToSequenceMapping mapping2 = acf
+ .getCoveringCodonMapping(cds.getDatasetSequence());
+ assertSame(mapping, mapping2);
+
+ /*
+ * with a mapping that extends to stop codon
+ * (EMBL CDS location often includes the stop codon)
+ * - getCoveringCodonMapping is lenient (doesn't require exact length match)
+ */
+ SequenceI cds2 = new Sequence("cds/1-12", "-A--TGGC-GGACTAA");
+ cds2.createDatasetSequence();
+ acf = new AlignedCodonFrame();
+ MapList map4 = new MapList(new int[] { 1, 12 }, new int[] { 1, 3 }, 3,
+ 1);
+ acf.addMap(cds2, pep, map4);
+ mapping = acf.getCoveringCodonMapping(cds2.getDatasetSequence());
+ assertNotNull(mapping);
+ mapping2 = acf.getCoveringCodonMapping(pep);
+ assertSame(mapping, mapping2);
+ }