X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FAlignedCodonFrameTest.java;fp=test%2Fjalview%2Fdatamodel%2FAlignedCodonFrameTest.java;h=337ac1a8bbc0463ae66100f7ac72da1016ea7fcf;hb=39b4859e1a1b011af5d06058461db4d075acb578;hp=fb4073a0713e52f6a21c73b13142f623b9a3ab15;hpb=f3dcb2f8f602117ac390799b1f310dcaa9918592;p=jalview.git diff --git a/test/jalview/datamodel/AlignedCodonFrameTest.java b/test/jalview/datamodel/AlignedCodonFrameTest.java index fb4073a..337ac1a 100644 --- a/test/jalview/datamodel/AlignedCodonFrameTest.java +++ b/test/jalview/datamodel/AlignedCodonFrameTest.java @@ -22,20 +22,22 @@ package jalview.datamodel; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertFalse; +import static org.testng.AssertJUnit.assertNotNull; import static org.testng.AssertJUnit.assertNull; import static org.testng.AssertJUnit.assertSame; import static org.testng.AssertJUnit.assertTrue; import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals; -import jalview.gui.JvOptionPane; -import jalview.util.MapList; - import java.util.Arrays; import java.util.List; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; +import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping; +import jalview.gui.JvOptionPane; +import jalview.util.MapList; + public class AlignedCodonFrameTest { @@ -98,52 +100,67 @@ public class AlignedCodonFrameTest public void testGetMappedRegion() { // introns lower case, exons upper case - final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T"); - seq1.createDatasetSequence(); - final Sequence seq2 = new Sequence("Seq2", "-TA-gG-Gg-CG-a"); - seq2.createDatasetSequence(); + 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 aseq1 = new Sequence("Seq1", "-P-R"); - aseq1.createDatasetSequence(); - final Sequence aseq2 = new Sequence("Seq2", "-LY-Q"); - aseq2.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(); - assertNull(acf.getMappedRegion(seq1, aseq1, 1)); + assertNull(acf.getMappedRegion(dna1, pep1, 3)); /* * Set up the mappings for the exons (upper-case bases) * Note residue Q is unmapped */ - 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); - map = new MapList(new int[] { 1, 2, 4, 5, 7, 8 }, new int[] { 1, 2 }, + 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, 9 }, 3, 1); - acf.addMap(seq2.getDatasetSequence(), aseq2.getDatasetSequence(), map); + acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map2); - assertArrayEquals(new int[] { 2, 4 }, - acf.getMappedRegion(seq1, aseq1, 1)); - assertArrayEquals(new int[] { 6, 6, 8, 9 }, - acf.getMappedRegion(seq1, aseq1, 2)); - assertArrayEquals(new int[] { 1, 2, 4, 4 }, - acf.getMappedRegion(seq2, aseq2, 1)); - assertArrayEquals(new int[] { 5, 5, 7, 8 }, - acf.getMappedRegion(seq2, aseq2, 2)); + /* + * get codon positions for peptide position + */ + assertArrayEquals(new int[] { 11, 13 }, + acf.getMappedRegion(dna1, pep1, 3)); + assertArrayEquals(new int[] { 15, 15, 17, 18 }, + acf.getMappedRegion(dna1, pep1, 4)); + assertArrayEquals(new int[] { 20, 21, 23, 23 }, + acf.getMappedRegion(dna2, pep2, 7)); + assertArrayEquals(new int[] { 24, 24, 26, 27 }, + acf.getMappedRegion(dna2, pep2, 8)); /* - * No mapping from seq2 to Q + * No mapping from dna2 to Q */ - assertNull(acf.getMappedRegion(seq2, aseq2, 3)); + assertNull(acf.getMappedRegion(dna2, pep2, 9)); /* - * No mapping from sequence 1 to sequence 2 + * No mapping from dna1 to pep2 */ - assertNull(acf.getMappedRegion(seq1, aseq2, 1)); + assertNull(acf.getMappedRegion(dna1, pep2, 7)); + + /* + * get peptide position for codon position + */ + assertArrayEquals(new int[] { 3, 3 }, + acf.getMappedRegion(pep1, dna1, 11)); + assertArrayEquals(new int[] { 3, 3 }, + acf.getMappedRegion(pep1, dna1, 12)); + assertArrayEquals(new int[] { 3, 3 }, + acf.getMappedRegion(pep1, dna1, 13)); + assertNull(acf.getMappedRegion(pep1, dna1, 14)); // intron base, not mapped + } @Test(groups = { "Functional" }) @@ -486,4 +503,212 @@ public class AlignedCodonFrameTest 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); + } }