X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FMappingUtilsTest.java;h=492cbb66dab6f444f9d3be8d0aad629f0cdafbe7;hb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;hp=095ab1b5facef1b16a47afd05bbd35a3ae354fc8;hpb=a7e367109fb4cc5dbc5dfb0b3838c9b12bf86343;p=jalview.git diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java index 095ab1b..492cbb66 100644 --- a/test/jalview/util/MappingUtilsTest.java +++ b/test/jalview/util/MappingUtilsTest.java @@ -21,9 +21,9 @@ package jalview.util; import static org.testng.AssertJUnit.assertEquals; +import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertSame; import static org.testng.AssertJUnit.assertTrue; -import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals; import jalview.api.AlignViewportI; import jalview.commands.EditCommand; @@ -39,7 +39,9 @@ import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.gui.AlignViewport; -import jalview.io.AppletFormatAdapter; +import jalview.io.DataSourceType; +import jalview.io.FileFormat; +import jalview.io.FileFormatI; import jalview.io.FormatAdapter; import java.awt.Color; @@ -197,10 +199,10 @@ public class MappingUtilsTest * viewport). */ AlignmentI cdna = loadAlignment(">Seq1\nACG\n>Seq2\nTGA\n>Seq3\nTAC\n", - "FASTA"); + FileFormat.Fasta); cdna.setDataset(null); AlignmentI protein = loadAlignment(">Seq1\nK\n>Seq2\nL\n>Seq3\nQ\n", - "FASTA"); + FileFormat.Fasta); protein.setDataset(null); AlignedCodonFrame acf = new AlignedCodonFrame(); MapList map = new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 3, 1); @@ -268,11 +270,11 @@ public class MappingUtilsTest * @return * @throws IOException */ - protected AlignmentI loadAlignment(final String data, String format) + protected AlignmentI loadAlignment(final String data, FileFormatI format) throws IOException { AlignmentI a = new FormatAdapter().readFile(data, - AppletFormatAdapter.PASTE, format); + DataSourceType.PASTE, format); a.setDataset(null); return a; } @@ -351,11 +353,11 @@ public class MappingUtilsTest */ AlignmentI cdna = loadAlignment(">Seq1/10-18\nAC-GctGtC-T\n" + ">Seq2/20-27\nTc-GA-G-T-Tc\n" + ">Seq3/30-38\nTtTT-AaCGg-\n", - "FASTA"); + FileFormat.Fasta); cdna.setDataset(null); AlignmentI protein = loadAlignment( ">Seq1/40-41\n-K-P\n>Seq2/50-51\nL--Q\n>Seq3/60-61\nG--S\n", - "FASTA"); + FileFormat.Fasta); protein.setDataset(null); // map first dna to first protein seq @@ -466,10 +468,11 @@ public class MappingUtilsTest * viewport). */ AlignmentI cdna = loadAlignment( - ">Seq1\nACGGCA\n>Seq2\nTGACAG\n>Seq3\nTACGTA\n", "FASTA"); + ">Seq1\nACGGCA\n>Seq2\nTGACAG\n>Seq3\nTACGTA\n", + FileFormat.Fasta); cdna.setDataset(null); AlignmentI protein = loadAlignment(">Seq1\nKA\n>Seq2\nLQ\n>Seq3\nQV\n", - "FASTA"); + FileFormat.Fasta); protein.setDataset(null); AlignedCodonFrame acf = new AlignedCodonFrame(); MapList map = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 }, 3, 1); @@ -549,10 +552,10 @@ public class MappingUtilsTest */ 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"); + FileFormat.Fasta); cdna.setDataset(null); AlignmentI protein = loadAlignment( - ">Seq1\n-KA-S\n>Seq2\n--L-QY\n>Seq3\nQ-V-M\n", "FASTA"); + ">Seq1\n-KA-S\n>Seq2\n--L-QY\n>Seq3\nQ-V-M\n", FileFormat.Fasta); protein.setDataset(null); AlignedCodonFrame acf = new AlignedCodonFrame(); MapList map = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3, 1); @@ -857,58 +860,173 @@ public class MappingUtilsTest assertEquals("[5, 10]", Arrays.toString(hidden.get(1))); } - /** - * Tests for the method that removes the trailing stop codon from a mapping - * range i.e. the last 3 positions (whether split or not) - */ @Test(groups = { "Functional" }) - public void testUnmapStopCodon() + public void testGetLength() { - List ranges = new ArrayList(); + assertEquals(0, MappingUtils.getLength(null)); - // simple case, forward strand: - ranges.add(new int[] { 1, 3 }); - ranges.add(new int[] { 9, 14 }); - MappingUtils.unmapStopCodon(ranges, 9); - assertEquals(2, ranges.size()); - assertArrayEquals(new int[] { 1, 3 }, ranges.get(0)); - assertArrayEquals(new int[] { 9, 11 }, ranges.get(1)); + /* + * [start, end] ranges + */ + List ranges = new ArrayList(); + assertEquals(0, MappingUtils.getLength(ranges)); + ranges.add(new int[] { 1, 1 }); + assertEquals(1, MappingUtils.getLength(ranges)); + ranges.add(new int[] { 2, 10 }); + assertEquals(10, MappingUtils.getLength(ranges)); + ranges.add(new int[] { 20, 10 }); + assertEquals(21, MappingUtils.getLength(ranges)); - // split stop codon, forward strand: + /* + * [start, end, start, end...] ranges + */ ranges.clear(); - ranges.add(new int[] { 1, 8 }); - ranges.add(new int[] { 10, 10 }); - MappingUtils.unmapStopCodon(ranges, 9); - assertEquals(1, ranges.size()); - assertArrayEquals(new int[] { 1, 6 }, ranges.get(0)); + ranges.add(new int[] { 1, 5, 8, 4 }); + ranges.add(new int[] { 8, 2 }); + ranges.add(new int[] { 12, 12 }); + assertEquals(18, MappingUtils.getLength(ranges)); + } - // very split stop codon, forward strand: - ranges.clear(); - ranges.add(new int[] { 1, 1 }); - ranges.add(new int[] { 3, 4 }); + @Test(groups = { "Functional" }) + public void testContains() + { + assertFalse(MappingUtils.contains(null, 1)); + List ranges = new ArrayList(); + assertFalse(MappingUtils.contains(ranges, 1)); + + ranges.add(new int[] { 1, 4 }); ranges.add(new int[] { 6, 6 }); - ranges.add(new int[] { 8, 8 }); - ranges.add(new int[] { 10, 10 }); - MappingUtils.unmapStopCodon(ranges, 6); - assertEquals(2, ranges.size()); - assertArrayEquals(new int[] { 1, 1 }, ranges.get(0)); - assertArrayEquals(new int[] { 3, 4 }, ranges.get(1)); - - // simple case, reverse strand: - ranges.clear(); - ranges.add(new int[] { 12, 10 }); - ranges.add(new int[] { 6, 1 }); - MappingUtils.unmapStopCodon(ranges, 9); - assertEquals(2, ranges.size()); - assertArrayEquals(new int[] { 12, 10 }, ranges.get(0)); - assertArrayEquals(new int[] { 6, 4 }, ranges.get(1)); - - // split stop codon, reverse strand: - ranges.clear(); - ranges.add(new int[] { 12, 6 }); - ranges.add(new int[] { 4, 3 }); - MappingUtils.unmapStopCodon(ranges, 9); - assertEquals(1, ranges.size()); - assertArrayEquals(new int[] { 12, 7 }, ranges.get(0)); + ranges.add(new int[] { 8, 10 }); + ranges.add(new int[] { 30, 20 }); + ranges.add(new int[] { -16, -44 }); + + assertFalse(MappingUtils.contains(ranges, 0)); + assertTrue(MappingUtils.contains(ranges, 1)); + assertTrue(MappingUtils.contains(ranges, 2)); + assertTrue(MappingUtils.contains(ranges, 3)); + assertTrue(MappingUtils.contains(ranges, 4)); + assertFalse(MappingUtils.contains(ranges, 5)); + + assertTrue(MappingUtils.contains(ranges, 6)); + assertFalse(MappingUtils.contains(ranges, 7)); + + assertTrue(MappingUtils.contains(ranges, 8)); + assertTrue(MappingUtils.contains(ranges, 9)); + assertTrue(MappingUtils.contains(ranges, 10)); + + assertFalse(MappingUtils.contains(ranges, 31)); + assertTrue(MappingUtils.contains(ranges, 30)); + assertTrue(MappingUtils.contains(ranges, 29)); + assertTrue(MappingUtils.contains(ranges, 20)); + assertFalse(MappingUtils.contains(ranges, 19)); + + assertFalse(MappingUtils.contains(ranges, -15)); + assertTrue(MappingUtils.contains(ranges, -16)); + assertTrue(MappingUtils.contains(ranges, -44)); + assertFalse(MappingUtils.contains(ranges, -45)); } + + /** + * Test the method that drops positions from the start of a mapped range + */ + @Test(groups = "Functional") + public void testRemoveStartPositions() + { + int[] ranges = new int[] { 1, 10 }; + int[] adjusted = MappingUtils.removeStartPositions(0, ranges); + assertEquals("[1, 10]", Arrays.toString(adjusted)); + + adjusted = MappingUtils.removeStartPositions(1, ranges); + assertEquals("[2, 10]", Arrays.toString(adjusted)); + assertEquals("[1, 10]", Arrays.toString(ranges)); + + ranges = adjusted; + adjusted = MappingUtils.removeStartPositions(1, ranges); + assertEquals("[3, 10]", Arrays.toString(adjusted)); + assertEquals("[2, 10]", Arrays.toString(ranges)); + + ranges = new int[] { 2, 3, 10, 12 }; + adjusted = MappingUtils.removeStartPositions(1, ranges); + assertEquals("[3, 3, 10, 12]", Arrays.toString(adjusted)); + assertEquals("[2, 3, 10, 12]", Arrays.toString(ranges)); + + ranges = new int[] { 2, 2, 8, 12 }; + adjusted = MappingUtils.removeStartPositions(1, ranges); + assertEquals("[8, 12]", Arrays.toString(adjusted)); + assertEquals("[2, 2, 8, 12]", Arrays.toString(ranges)); + + ranges = new int[] { 2, 2, 8, 12 }; + adjusted = MappingUtils.removeStartPositions(2, ranges); + assertEquals("[9, 12]", Arrays.toString(adjusted)); + assertEquals("[2, 2, 8, 12]", Arrays.toString(ranges)); + + ranges = new int[] { 2, 2, 4, 4, 9, 12 }; + adjusted = MappingUtils.removeStartPositions(1, ranges); + assertEquals("[4, 4, 9, 12]", Arrays.toString(adjusted)); + assertEquals("[2, 2, 4, 4, 9, 12]", Arrays.toString(ranges)); + + ranges = new int[] { 2, 2, 4, 4, 9, 12 }; + adjusted = MappingUtils.removeStartPositions(2, ranges); + assertEquals("[9, 12]", Arrays.toString(adjusted)); + assertEquals("[2, 2, 4, 4, 9, 12]", Arrays.toString(ranges)); + + ranges = new int[] { 2, 3, 9, 12 }; + adjusted = MappingUtils.removeStartPositions(3, ranges); + assertEquals("[10, 12]", Arrays.toString(adjusted)); + assertEquals("[2, 3, 9, 12]", Arrays.toString(ranges)); + } + + /** + * Test the method that drops positions from the start of a mapped range, on + * the reverse strand + */ + @Test(groups = "Functional") + public void testRemoveStartPositions_reverseStrand() + { + int[] ranges = new int[] { 10, 1 }; + int[] adjusted = MappingUtils.removeStartPositions(0, ranges); + assertEquals("[10, 1]", Arrays.toString(adjusted)); + assertEquals("[10, 1]", Arrays.toString(ranges)); + + ranges = adjusted; + adjusted = MappingUtils.removeStartPositions(1, ranges); + assertEquals("[9, 1]", Arrays.toString(adjusted)); + assertEquals("[10, 1]", Arrays.toString(ranges)); + + ranges = adjusted; + adjusted = MappingUtils.removeStartPositions(1, ranges); + assertEquals("[8, 1]", Arrays.toString(adjusted)); + assertEquals("[9, 1]", Arrays.toString(ranges)); + + ranges = new int[] { 12, 11, 9, 6 }; + adjusted = MappingUtils.removeStartPositions(1, ranges); + assertEquals("[11, 11, 9, 6]", Arrays.toString(adjusted)); + assertEquals("[12, 11, 9, 6]", Arrays.toString(ranges)); + + ranges = new int[] { 12, 12, 8, 4 }; + adjusted = MappingUtils.removeStartPositions(1, ranges); + assertEquals("[8, 4]", Arrays.toString(adjusted)); + assertEquals("[12, 12, 8, 4]", Arrays.toString(ranges)); + + ranges = new int[] { 12, 12, 8, 4 }; + adjusted = MappingUtils.removeStartPositions(2, ranges); + assertEquals("[7, 4]", Arrays.toString(adjusted)); + assertEquals("[12, 12, 8, 4]", Arrays.toString(ranges)); + + ranges = new int[] { 12, 12, 10, 10, 8, 4 }; + adjusted = MappingUtils.removeStartPositions(1, ranges); + assertEquals("[10, 10, 8, 4]", Arrays.toString(adjusted)); + assertEquals("[12, 12, 10, 10, 8, 4]", Arrays.toString(ranges)); + + ranges = new int[] { 12, 12, 10, 10, 8, 4 }; + adjusted = MappingUtils.removeStartPositions(2, ranges); + assertEquals("[8, 4]", Arrays.toString(adjusted)); + assertEquals("[12, 12, 10, 10, 8, 4]", Arrays.toString(ranges)); + + ranges = new int[] { 12, 11, 8, 4 }; + adjusted = MappingUtils.removeStartPositions(3, ranges); + assertEquals("[7, 4]", Arrays.toString(adjusted)); + assertEquals("[12, 11, 8, 4]", Arrays.toString(ranges)); + } + }