X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FMappingUtilsTest.java;fp=test%2Fjalview%2Futil%2FMappingUtilsTest.java;h=c86259b78824f8b4049bd1ecfeed63fff20f8193;hb=de358652f0fe9b535353c8018509d52c2b5e96d5;hp=f32e7ffe49e6688b8d9167b63b29ce164f77f8fc;hpb=5baa6110829dabd15c3333007042e06ea6449242;p=jalview.git diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java index f32e7ff..c86259b 100644 --- a/test/jalview/util/MappingUtilsTest.java +++ b/test/jalview/util/MappingUtilsTest.java @@ -3,7 +3,17 @@ package jalview.util; import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertSame; import static org.junit.Assert.assertTrue; -import static org.junit.Assert.fail; + +import java.awt.Color; +import java.io.IOException; +import java.util.Arrays; +import java.util.Collections; +import java.util.HashSet; +import java.util.List; +import java.util.Set; + +import org.junit.Test; + import jalview.api.AlignViewportI; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; @@ -13,18 +23,11 @@ import jalview.datamodel.SearchResults; import jalview.datamodel.SearchResults.Match; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; import jalview.gui.AlignViewport; import jalview.io.AppletFormatAdapter; import jalview.io.FormatAdapter; -import java.awt.Color; -import java.io.IOException; -import java.util.Arrays; -import java.util.Collections; -import java.util.Set; - -import org.junit.Test; - public class MappingUtilsTest { private AlignViewportI dnaView; @@ -87,7 +90,7 @@ public class MappingUtilsTest * Simple test of mapping with introns involved. */ @Test - public void testBuildSearchResults_withIntro() + public void testBuildSearchResults_withIntron() { final Sequence seq1 = new Sequence("Seq1", "C-G-TAGA-GCAGCTT"); seq1.createDatasetSequence(); @@ -159,12 +162,12 @@ public class MappingUtilsTest } /** - * Test mapping a sequence group. + * Test mapping a sequence group made of entire sequences. * * @throws IOException */ @Test - public void testMapSequenceGroup() throws IOException + public void testMapSequenceGroup_sequences() throws IOException { /* * Set up dna and protein Seq1/2/3 with mappings (held on the protein @@ -192,7 +195,7 @@ public class MappingUtilsTest protein.setCodonFrames(acfList); /* - * Select Seq1 and Seq3 in the protein + * Select Seq1 and Seq3 in the protein (startRes=endRes=0) */ SequenceGroup sg = new SequenceGroup(); sg.setColourText(true); @@ -211,6 +214,8 @@ public class MappingUtilsTest assertEquals(2, mappedGroup.getSequences().size()); assertSame(cdna.getSequenceAt(0), mappedGroup.getSequences().get(0)); assertSame(cdna.getSequenceAt(2), mappedGroup.getSequences().get(1)); + assertEquals(0, mappedGroup.getStartRes()); + assertEquals(2, mappedGroup.getEndRes()); /* * Verify mapping sequence group from dna to protein @@ -218,6 +223,8 @@ public class MappingUtilsTest sg.clear(); sg.addSequence(cdna.getSequenceAt(1), false); sg.addSequence(cdna.getSequenceAt(0), false); + sg.setStartRes(0); + sg.setEndRes(2); mappedGroup = MappingUtils.mapSequenceGroup(sg, dnaView, proteinView); assertTrue(mappedGroup.getColourText()); assertSame(sg.getIdColour(), mappedGroup.getIdColour()); @@ -225,6 +232,8 @@ public class MappingUtilsTest assertEquals(2, mappedGroup.getSequences().size()); assertSame(protein.getSequenceAt(1), mappedGroup.getSequences().get(0)); assertSame(protein.getSequenceAt(0), mappedGroup.getSequences().get(1)); + assertEquals(0, mappedGroup.getStartRes()); + assertEquals(0, mappedGroup.getEndRes()); } /** @@ -399,4 +408,257 @@ public class MappingUtilsTest Arrays.toString(MappingUtils.flattenRanges(new int[] { 1, 4, 7, 9, 12, 12, 15 }))); } + + /** + * Test mapping a sequence group made of entire columns. + * + * @throws IOException + */ + @Test + public void testMapSequenceGroup_columns() throws IOException + { + /* + * Set up dna and protein Seq1/2/3 with mappings (held on the protein + * viewport). + */ + AlignmentI cdna = loadAlignment( + ">Seq1\nACGGCA\n>Seq2\nTGACAG\n>Seq3\nTACGTA\n", + "FASTA"); + cdna.setDataset(null); + AlignmentI protein = loadAlignment(">Seq1\nKA\n>Seq2\nLQ\n>Seq3\nQV\n", + "FASTA"); + protein.setDataset(null); + AlignedCodonFrame acf = new AlignedCodonFrame(); + MapList map = new MapList(new int[] + { 1, 6 }, new int[] + { 1, 2 }, 3, 1); + for (int seq = 0; seq < 3; seq++) + { + acf.addMap(cdna.getSequenceAt(seq).getDatasetSequence(), protein + .getSequenceAt(seq).getDatasetSequence(), map); + } + Set acfList = Collections.singleton(acf); + + AlignViewportI dnaView = new AlignViewport(cdna); + AlignViewportI proteinView = new AlignViewport(protein); + protein.setCodonFrames(acfList); + + /* + * Select all sequences, column 2 in the protein + */ + SequenceGroup sg = new SequenceGroup(); + sg.setColourText(true); + sg.setIdColour(Color.GREEN); + sg.setOutlineColour(Color.LIGHT_GRAY); + sg.addSequence(protein.getSequenceAt(0), false); + sg.addSequence(protein.getSequenceAt(1), false); + sg.addSequence(protein.getSequenceAt(2), false); + sg.setStartRes(1); + sg.setEndRes(1); + + /* + * Verify the mapped sequence group in dna + */ + SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, proteinView, dnaView); + assertTrue(mappedGroup.getColourText()); + assertSame(sg.getIdColour(), mappedGroup.getIdColour()); + assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour()); + assertEquals(3, mappedGroup.getSequences().size()); + assertSame(cdna.getSequenceAt(0), mappedGroup.getSequences().get(0)); + assertSame(cdna.getSequenceAt(1), mappedGroup.getSequences().get(1)); + assertSame(cdna.getSequenceAt(2), mappedGroup.getSequences().get(2)); + assertEquals(3, mappedGroup.getStartRes()); + assertEquals(5, mappedGroup.getEndRes()); + + /* + * Verify mapping sequence group from dna to protein + */ + sg.clear(); + sg.addSequence(cdna.getSequenceAt(0), false); + sg.addSequence(cdna.getSequenceAt(1), false); + sg.addSequence(cdna.getSequenceAt(2), false); + // select columns 2 and 3 in DNA which span protein columns 0 and 1 + sg.setStartRes(2); + sg.setEndRes(3); + mappedGroup = MappingUtils.mapSequenceGroup(sg, dnaView, proteinView); + assertTrue(mappedGroup.getColourText()); + assertSame(sg.getIdColour(), mappedGroup.getIdColour()); + assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour()); + assertEquals(3, mappedGroup.getSequences().size()); + assertSame(protein.getSequenceAt(0), mappedGroup.getSequences().get(0)); + assertSame(protein.getSequenceAt(1), mappedGroup.getSequences().get(1)); + assertSame(protein.getSequenceAt(2), mappedGroup.getSequences().get(2)); + assertEquals(0, mappedGroup.getStartRes()); + assertEquals(1, mappedGroup.getEndRes()); + } + + /** + * Test mapping a sequence group made of a sequences/columns region. + * + * @throws IOException + */ + @Test + public void testMapSequenceGroup_region() throws IOException + { + /* + * Set up gapped dna and protein Seq1/2/3 with mappings (held on the protein + * viewport). + */ + AlignmentI cdna = loadAlignment( + ">Seq1\nA-CG-GC--AT-CA\n>Seq2\n-TG-AC-AG-T-AT\n>Seq3\n-T--ACG-TAAT-G\n", + "FASTA"); + cdna.setDataset(null); + AlignmentI protein = loadAlignment( + ">Seq1\n-KA-S\n>Seq2\n--L-QY\n>Seq3\nQ-V-M\n", "FASTA"); + protein.setDataset(null); + AlignedCodonFrame acf = new AlignedCodonFrame(); + MapList map = new MapList(new int[] + { 1, 9 }, new int[] + { 1, 3 }, 3, 1); + for (int seq = 0; seq < 3; seq++) + { + acf.addMap(cdna.getSequenceAt(seq).getDatasetSequence(), protein + .getSequenceAt(seq).getDatasetSequence(), map); + } + Set acfList = Collections.singleton(acf); + + AlignViewportI dnaView = new AlignViewport(cdna); + AlignViewportI proteinView = new AlignViewport(protein); + protein.setCodonFrames(acfList); + + /* + * Select Seq1 and Seq2 in the protein, column 1 (K/-). Expect mapped + * sequence group to cover Seq1, columns 0-3 (ACG). Because the selection + * only includes a gap in Seq2 there is no mappable selection region in the + * corresponding DNA. + */ + SequenceGroup sg = new SequenceGroup(); + sg.setColourText(true); + sg.setIdColour(Color.GREEN); + sg.setOutlineColour(Color.LIGHT_GRAY); + sg.addSequence(protein.getSequenceAt(0), false); + sg.addSequence(protein.getSequenceAt(1), false); + sg.setStartRes(1); + sg.setEndRes(1); + + /* + * Verify the mapped sequence group in dna + */ + SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, proteinView, dnaView); + assertTrue(mappedGroup.getColourText()); + assertSame(sg.getIdColour(), mappedGroup.getIdColour()); + assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour()); + assertEquals(1, mappedGroup.getSequences().size()); + assertSame(cdna.getSequenceAt(0), mappedGroup.getSequences().get(0)); + // Seq2 in protein has a gap in column 1 - ignored + // Seq1 has K which should map to columns 0-3 in Seq1 + assertEquals(0, mappedGroup.getStartRes()); + assertEquals(3, mappedGroup.getEndRes()); + + /* + * Now select cols 2-4 in protein. These cover Seq1:AS Seq2:LQ Seq3:VM which + * extend over DNA columns 3-12, 1-7, 6-13 respectively, or 1-13 overall. + */ + sg.setStartRes(2); + sg.setEndRes(4); + mappedGroup = MappingUtils.mapSequenceGroup(sg, proteinView, dnaView); + assertEquals(1, mappedGroup.getStartRes()); + assertEquals(13, mappedGroup.getEndRes()); + + /* + * Verify mapping sequence group from dna to protein + */ + sg.clear(); + sg.addSequence(cdna.getSequenceAt(0), false); + + // select columns 4,5 - includes Seq1:codon2 (A) only + sg.setStartRes(4); + sg.setEndRes(5); + mappedGroup = MappingUtils.mapSequenceGroup(sg, dnaView, proteinView); + assertEquals(2, mappedGroup.getStartRes()); + assertEquals(2, mappedGroup.getEndRes()); + + // add Seq2 to dna selection cols 4-5 include codons 1 and 2 (LQ) + sg.addSequence(cdna.getSequenceAt(1), false); + mappedGroup = MappingUtils.mapSequenceGroup(sg, dnaView, proteinView); + assertEquals(2, mappedGroup.getStartRes()); + assertEquals(4, mappedGroup.getEndRes()); + + // add Seq3 to dna selection cols 4-5 include codon 1 (Q) + sg.addSequence(cdna.getSequenceAt(2), false); + mappedGroup = MappingUtils.mapSequenceGroup(sg, dnaView, proteinView); + assertEquals(0, mappedGroup.getStartRes()); + assertEquals(4, mappedGroup.getEndRes()); + } + + @Test + public void testFindMappingsForSequence() + { + SequenceI seq1 = new Sequence("Seq1", "ABC"); + SequenceI seq2 = new Sequence("Seq2", "ABC"); + SequenceI seq3 = new Sequence("Seq3", "ABC"); + SequenceI seq4 = new Sequence("Seq4", "ABC"); + seq1.createDatasetSequence(); + seq2.createDatasetSequence(); + seq3.createDatasetSequence(); + seq4.createDatasetSequence(); + + /* + * Create mappings from seq1 to seq2, seq2 to seq1, seq3 to seq1 + */ + AlignedCodonFrame acf1 = new AlignedCodonFrame(); + MapList map = new MapList(new int[] + { 1, 3 }, new int[] + { 1, 3 },1, 1); + acf1.addMap(seq1.getDatasetSequence(), seq2.getDatasetSequence(), map); + AlignedCodonFrame acf2 = new AlignedCodonFrame(); + acf2.addMap(seq2.getDatasetSequence(), seq1.getDatasetSequence(), map); + AlignedCodonFrame acf3 = new AlignedCodonFrame(); + acf3.addMap(seq3.getDatasetSequence(), seq1.getDatasetSequence(), map); + + Set mappings = new HashSet(); + mappings.add(acf1); + mappings.add(acf2); + mappings.add(acf3); + + /* + * Seq1 has three mappings + */ + List result = MappingUtils.findMappingsForSequence( + seq1, mappings); + assertEquals(3, result.size()); + assertTrue(result.contains(acf1)); + assertTrue(result.contains(acf2)); + assertTrue(result.contains(acf3)); + + /* + * Seq2 has two mappings + */ + result = MappingUtils.findMappingsForSequence(seq2, mappings); + assertEquals(2, result.size()); + assertTrue(result.contains(acf1)); + assertTrue(result.contains(acf2)); + + /* + * Seq3 has one mapping + */ + result = MappingUtils.findMappingsForSequence(seq3, mappings); + assertEquals(1, result.size()); + assertTrue(result.contains(acf3)); + + /* + * Seq4 has no mappings + */ + result = MappingUtils.findMappingsForSequence(seq4, mappings); + assertEquals(0, result.size()); + + result = MappingUtils.findMappingsForSequence(null, mappings); + assertEquals(0, result.size()); + + result = MappingUtils.findMappingsForSequence(seq1, null); + assertEquals(0, result.size()); + + result = MappingUtils.findMappingsForSequence(null, null); + assertEquals(0, result.size()); +} }