X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FMappingUtilsTest.java;h=492cbb66dab6f444f9d3be8d0aad629f0cdafbe7;hb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;hp=ad7193aef3ca6952c531cdd44d2aa094bb6052c8;hpb=8f118c154e74caaef6bec19acd0466904ac424d4;p=jalview.git diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java index ad7193a..492cbb66 100644 --- a/test/jalview/util/MappingUtilsTest.java +++ b/test/jalview/util/MappingUtilsTest.java @@ -21,11 +21,16 @@ 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 jalview.api.AlignViewportI; +import jalview.commands.EditCommand; +import jalview.commands.EditCommand.Action; +import jalview.commands.EditCommand.Edit; import jalview.datamodel.AlignedCodonFrame; +import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; import jalview.datamodel.SearchResults; @@ -34,16 +39,16 @@ 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; import java.io.IOException; +import java.util.ArrayList; import java.util.Arrays; -import java.util.Collections; -import java.util.HashSet; import java.util.List; -import java.util.Set; import org.testng.annotations.Test; @@ -59,46 +64,48 @@ public class MappingUtilsTest @Test(groups = { "Functional" }) public void testBuildSearchResults() { - final Sequence seq1 = new Sequence("Seq1", "C-G-TA-GC"); + final Sequence seq1 = new Sequence("Seq1/5-10", "C-G-TA-GC"); seq1.createDatasetSequence(); - final Sequence aseq1 = new Sequence("Seq1", "-P-R"); + final Sequence aseq1 = new Sequence("Seq1/12-13", "-P-R"); aseq1.createDatasetSequence(); /* - * Map dna bases 1-6 to protein residues 1-2 + * Map dna bases 5-10 to protein residues 12-13 */ AlignedCodonFrame acf = new AlignedCodonFrame(); - MapList map = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 }, 3, 1); + MapList map = new MapList(new int[] { 5, 10 }, new int[] { 12, 13 }, 3, + 1); acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map); - Set acfList = Collections.singleton(acf); + List acfList = Arrays.asList(new AlignedCodonFrame[] + { acf }); /* - * Check protein residue 1 maps to codon 1-3, 2 to codon 4-6 + * Check protein residue 12 maps to codon 5-7, 13 to codon 8-10 */ - SearchResults sr = MappingUtils.buildSearchResults(aseq1, 1, acfList); + SearchResults sr = MappingUtils.buildSearchResults(aseq1, 12, acfList); assertEquals(1, sr.getResults().size()); Match m = sr.getResults().get(0); assertEquals(seq1.getDatasetSequence(), m.getSequence()); - assertEquals(1, m.getStart()); - assertEquals(3, m.getEnd()); - sr = MappingUtils.buildSearchResults(aseq1, 2, acfList); + assertEquals(5, m.getStart()); + assertEquals(7, m.getEnd()); + sr = MappingUtils.buildSearchResults(aseq1, 13, acfList); assertEquals(1, sr.getResults().size()); m = sr.getResults().get(0); assertEquals(seq1.getDatasetSequence(), m.getSequence()); - assertEquals(4, m.getStart()); - assertEquals(6, m.getEnd()); + assertEquals(8, m.getStart()); + assertEquals(10, m.getEnd()); /* - * Check inverse mappings, from codons 1-3, 4-6 to protein 1, 2 + * Check inverse mappings, from codons 5-7, 8-10 to protein 12, 13 */ - for (int i = 1; i < 7; i++) + for (int i = 5; i < 11; i++) { sr = MappingUtils.buildSearchResults(seq1, i, acfList); assertEquals(1, sr.getResults().size()); m = sr.getResults().get(0); assertEquals(aseq1.getDatasetSequence(), m.getSequence()); - int residue = i > 3 ? 2 : 1; + int residue = i > 7 ? 13 : 12; assertEquals(residue, m.getStart()); assertEquals(residue, m.getEnd()); } @@ -110,61 +117,62 @@ public class MappingUtilsTest @Test(groups = { "Functional" }) public void testBuildSearchResults_withIntron() { - final Sequence seq1 = new Sequence("Seq1", "C-G-TAGA-GCAGCTT"); + final Sequence seq1 = new Sequence("Seq1/5-17", "c-G-tAGa-GcAgCtt"); seq1.createDatasetSequence(); - final Sequence aseq1 = new Sequence("Seq1", "-P-R"); + final Sequence aseq1 = new Sequence("Seq1/8-9", "-E-D"); aseq1.createDatasetSequence(); /* - * Map dna bases [2, 4, 5], [7, 9, 11] to protein residues 1 and 2 + * Map dna bases [6, 8, 9], [11, 13, 115] to protein residues 8 and 9 */ AlignedCodonFrame acf = new AlignedCodonFrame(); - MapList map = new MapList(new int[] { 2, 2, 4, 5, 7, 7, 9, 9, 11, 11 }, - new int[] { 1, 2 }, 3, 1); + MapList map = new MapList(new int[] { 6, 6, 8, 9, 11, 11, 13, 13, 15, + 15 }, new int[] { 8, 9 }, 3, 1); acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map); - Set acfList = Collections.singleton(acf); + List acfList = Arrays.asList(new AlignedCodonFrame[] + { acf }); /* - * Check protein residue 1 maps to [2, 4, 5] + * Check protein residue 8 maps to [6, 8, 9] */ - SearchResults sr = MappingUtils.buildSearchResults(aseq1, 1, acfList); + SearchResults sr = MappingUtils.buildSearchResults(aseq1, 8, acfList); assertEquals(2, sr.getResults().size()); Match m = sr.getResults().get(0); assertEquals(seq1.getDatasetSequence(), m.getSequence()); - assertEquals(2, m.getStart()); - assertEquals(2, m.getEnd()); + assertEquals(6, m.getStart()); + assertEquals(6, m.getEnd()); m = sr.getResults().get(1); assertEquals(seq1.getDatasetSequence(), m.getSequence()); - assertEquals(4, m.getStart()); - assertEquals(5, m.getEnd()); + assertEquals(8, m.getStart()); + assertEquals(9, m.getEnd()); /* - * Check protein residue 2 maps to [7, 9, 11] + * Check protein residue 9 maps to [11, 13, 15] */ - sr = MappingUtils.buildSearchResults(aseq1, 2, acfList); + sr = MappingUtils.buildSearchResults(aseq1, 9, acfList); assertEquals(3, sr.getResults().size()); m = sr.getResults().get(0); assertEquals(seq1.getDatasetSequence(), m.getSequence()); - assertEquals(7, m.getStart()); - assertEquals(7, m.getEnd()); + assertEquals(11, m.getStart()); + assertEquals(11, m.getEnd()); m = sr.getResults().get(1); assertEquals(seq1.getDatasetSequence(), m.getSequence()); - assertEquals(9, m.getStart()); - assertEquals(9, m.getEnd()); + assertEquals(13, m.getStart()); + assertEquals(13, m.getEnd()); m = sr.getResults().get(2); assertEquals(seq1.getDatasetSequence(), m.getSequence()); - assertEquals(11, m.getStart()); - assertEquals(11, m.getEnd()); + assertEquals(15, m.getStart()); + assertEquals(15, m.getEnd()); /* * Check inverse mappings, from codons to protein */ - for (int i = 1; i < 14; i++) + for (int i = 5; i < 18; i++) { sr = MappingUtils.buildSearchResults(seq1, i, acfList); - int residue = (i == 2 || i == 4 || i == 5) ? 1 : (i == 7 || i == 9 - || i == 11 ? 2 : 0); + int residue = (i == 6 || i == 8 || i == 9) ? 8 : (i == 11 || i == 13 + || i == 15 ? 9 : 0); if (residue == 0) { assertEquals(0, sr.getResults().size()); @@ -191,10 +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); @@ -203,7 +211,8 @@ public class MappingUtilsTest acf.addMap(cdna.getSequenceAt(seq).getDatasetSequence(), protein .getSequenceAt(seq).getDatasetSequence(), map); } - Set acfList = Collections.singleton(acf); + List acfList = Arrays.asList(new AlignedCodonFrame[] + { acf }); AlignViewportI dnaView = new AlignViewport(cdna); AlignViewportI proteinView = new AlignViewport(protein); @@ -261,11 +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; } @@ -329,34 +338,48 @@ public class MappingUtilsTest } /** + * Set up mappings for tests from 3 dna to 3 protein sequences. Sequences have + * offset start positions for a more general test case. + * * @throws IOException */ protected void setupMappedAlignments() throws IOException { /* - * Set up dna and protein Seq1/2/3 with mappings (held on the protein - * viewport). Lower case for introns. + * Map (upper-case = coding): + * Seq1/10-18 AC-GctGtC-T to Seq1/40 -K-P + * Seq2/20-27 Tc-GA-G-T-T to Seq2/20-27 L--Q + * Seq3/30-38 TtTT-AaCGg- to Seq3/60-61\nG--S */ - AlignmentI cdna = loadAlignment(">Seq1\nAC-GctGtC-T\n" - + ">Seq2\nTc-GA-G-T-Tc\n" + ">Seq3\nTtTT-AaCGg-\n", "FASTA"); + 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", + FileFormat.Fasta); cdna.setDataset(null); AlignmentI protein = loadAlignment( - ">Seq1\n-K-P\n>Seq2\nL--Q\n>Seq3\nG--S\n", "FASTA"); + ">Seq1/40-41\n-K-P\n>Seq2/50-51\nL--Q\n>Seq3/60-61\nG--S\n", + FileFormat.Fasta); protein.setDataset(null); + + // map first dna to first protein seq AlignedCodonFrame acf = new AlignedCodonFrame(); - MapList map = new MapList(new int[] { 1, 3, 6, 6, 8, 9 }, new int[] { - 1, 2 }, 3, 1); + MapList map = new MapList(new int[] { 10, 12, 15, 15, 17, 18 }, + new int[] { 40, 41 }, 3, 1); acf.addMap(cdna.getSequenceAt(0).getDatasetSequence(), protein .getSequenceAt(0).getDatasetSequence(), map); - map = new MapList(new int[] { 1, 1, 3, 4, 5, 7 }, new int[] { 1, 2 }, - 3, 1); + + // map second dna to second protein seq + map = new MapList(new int[] { 20, 20, 22, 23, 24, 26 }, new int[] { 50, + 51 }, 3, 1); acf.addMap(cdna.getSequenceAt(1).getDatasetSequence(), protein .getSequenceAt(1).getDatasetSequence(), map); - map = new MapList(new int[] { 1, 1, 3, 4, 5, 5, 7, 8 }, new int[] { 1, - 2 }, 3, 1); + + // map third dna to third protein seq + map = new MapList(new int[] { 30, 30, 32, 34, 36, 37 }, new int[] { 60, + 61 }, 3, 1); acf.addMap(cdna.getSequenceAt(2).getDatasetSequence(), protein .getSequenceAt(2).getDatasetSequence(), map); - Set acfList = Collections.singleton(acf); + List acfList = Arrays.asList(new AlignedCodonFrame[] + { acf }); dnaView = new AlignViewport(cdna); proteinView = new AlignViewport(protein); @@ -425,7 +448,7 @@ public class MappingUtilsTest "[1, 2, 3, 4, 7, 8, 9, 12]", Arrays.toString(MappingUtils.flattenRanges(new int[] { 1, 4, 7, 9, 12, 12 }))); - // unpaired start position is ignored: + // trailing unpaired start position is ignored: assertEquals( "[1, 2, 3, 4, 7, 8, 9, 12]", Arrays.toString(MappingUtils.flattenRanges(new int[] { 1, 4, 7, @@ -445,10 +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); @@ -457,7 +481,8 @@ public class MappingUtilsTest acf.addMap(cdna.getSequenceAt(seq).getDatasetSequence(), protein .getSequenceAt(seq).getDatasetSequence(), map); } - Set acfList = Collections.singleton(acf); + List acfList = Arrays.asList(new AlignedCodonFrame[] + { acf }); AlignViewportI dnaView = new AlignViewport(cdna); AlignViewportI proteinView = new AlignViewport(protein); @@ -527,10 +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); @@ -539,7 +564,8 @@ public class MappingUtilsTest acf.addMap(cdna.getSequenceAt(seq).getDatasetSequence(), protein .getSequenceAt(seq).getDatasetSequence(), map); } - Set acfList = Collections.singleton(acf); + List acfList = Arrays.asList(new AlignedCodonFrame[] + { acf }); AlignViewportI dnaView = new AlignViewport(cdna); AlignViewportI proteinView = new AlignViewport(protein); @@ -634,7 +660,7 @@ public class MappingUtilsTest AlignedCodonFrame acf3 = new AlignedCodonFrame(); acf3.addMap(seq3.getDatasetSequence(), seq1.getDatasetSequence(), map); - Set mappings = new HashSet(); + List mappings = new ArrayList(); mappings.add(acf1); mappings.add(acf2); mappings.add(acf3); @@ -679,4 +705,328 @@ public class MappingUtilsTest result = MappingUtils.findMappingsForSequence(null, null); assertEquals(0, result.size()); } + + @Test(groups = { "Functional" }) + public void testMapEditCommand() + { + SequenceI dna = new Sequence("Seq1", "---ACG---GCATCA", 8, 16); + SequenceI protein = new Sequence("Seq2", "-T-AS", 5, 7); + dna.createDatasetSequence(); + protein.createDatasetSequence(); + AlignedCodonFrame acf = new AlignedCodonFrame(); + MapList map = new MapList(new int[] { 8, 16 }, new int[] { 5, 7 }, 3, 1); + acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map); + List mappings = new ArrayList(); + mappings.add(acf); + + AlignmentI prot = new Alignment(new SequenceI[] { protein }); + prot.setCodonFrames(mappings); + AlignmentI nuc = new Alignment(new SequenceI[] { dna }); + + /* + * construct and perform the edit command to turn "-T-AS" in to "-T-A--S" + * i.e. insert two gaps at column 4 + */ + EditCommand ec = new EditCommand(); + final Edit edit = ec.new Edit(Action.INSERT_GAP, + new SequenceI[] { protein }, 4, 2, '-'); + ec.appendEdit(edit, prot, true, null); + + /* + * the mapped edit command should be to insert 6 gaps before base 4 in the + * nucleotide sequence, which corresponds to aligned column 12 in the dna + */ + EditCommand mappedEdit = MappingUtils.mapEditCommand(ec, false, nuc, + '-', mappings); + assertEquals(1, mappedEdit.getEdits().size()); + Edit e = mappedEdit.getEdits().get(0); + assertEquals(1, e.getSequences().length); + assertEquals(dna, e.getSequences()[0]); + assertEquals(12, e.getPosition()); + assertEquals(6, e.getNumber()); + } + + /** + * Tests for the method that converts a series of [start, end] ranges to + * single positions, where the mapping is to a reverse strand i.e. start is + * greater than end point mapped to + */ + @Test(groups = { "Functional" }) + public void testFlattenRanges_reverseStrand() + { + assertEquals("[4, 3, 2, 1]", + Arrays.toString(MappingUtils.flattenRanges(new int[] { 4, 1 }))); + assertEquals( + "[4, 3, 2, 1]", + Arrays.toString(MappingUtils.flattenRanges(new int[] { 4, 3, 2, + 1 }))); + assertEquals( + "[4, 3, 2, 1]", + Arrays.toString(MappingUtils.flattenRanges(new int[] { 4, 4, 3, + 3, 2, 2, 1, 1 }))); + assertEquals( + "[12, 9, 8, 7, 4, 3, 2, 1]", + Arrays.toString(MappingUtils.flattenRanges(new int[] { 12, 12, + 9, 7, 4, 1 }))); + // forwards and backwards anyone? + assertEquals( + "[4, 5, 6, 3, 2, 1]", + Arrays.toString(MappingUtils.flattenRanges(new int[] { 4, 6, 3, + 1 }))); + // backwards and forwards + assertEquals( + "[3, 2, 1, 4, 5, 6]", + Arrays.toString(MappingUtils.flattenRanges(new int[] { 3, 1, 4, + 6 }))); + // trailing unpaired start position is ignored: + assertEquals( + "[12, 9, 8, 7, 4, 3, 2]", + Arrays.toString(MappingUtils.flattenRanges(new int[] { 12, 12, + 9, 7, 4, 2, 1 }))); + } + + /** + * Test mapping a column selection including hidden columns + * + * @throws IOException + */ + @Test(groups = { "Functional" }) + public void testMapColumnSelection_hiddenColumns() throws IOException + { + setupMappedAlignments(); + + ColumnSelection proteinSelection = new ColumnSelection(); + + /* + * Column 0 in protein picks up Seq2/L, Seq3/G which map to cols 0-4 and 0-3 + * in dna respectively, overall 0-4 + */ + proteinSelection.hideColumns(0); + ColumnSelection dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, + proteinView, dnaView); + assertEquals("[]", dnaSelection.getSelected().toString()); + List hidden = dnaSelection.getHiddenColumns(); + assertEquals(1, hidden.size()); + assertEquals("[0, 4]", Arrays.toString(hidden.get(0))); + + /* + * Column 1 in protein picks up Seq1/K which maps to cols 0-3 in dna + */ + proteinSelection.revealAllHiddenColumns(); + // the unhidden columns are now marked selected! + assertEquals("[0]", proteinSelection.getSelected().toString()); + // deselect these or hideColumns will be expanded to include 0 + proteinSelection.clear(); + proteinSelection.hideColumns(1); + dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView); + hidden = dnaSelection.getHiddenColumns(); + assertEquals(1, hidden.size()); + assertEquals("[0, 3]", Arrays.toString(hidden.get(0))); + + /* + * Column 2 in protein picks up gaps only - no mapping + */ + proteinSelection.revealAllHiddenColumns(); + proteinSelection.clear(); + proteinSelection.hideColumns(2); + dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView); + assertTrue(dnaSelection.getHiddenColumns().isEmpty()); + + /* + * Column 3 in protein picks up Seq1/P, Seq2/Q, Seq3/S which map to columns + * 6-9, 6-10, 5-8 respectively, overall to 5-10 + */ + proteinSelection.revealAllHiddenColumns(); + proteinSelection.clear(); + proteinSelection.hideColumns(3); // 5-10 hidden in dna + proteinSelection.addElement(1); // 0-3 selected in dna + dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView); + assertEquals("[0, 1, 2, 3]", dnaSelection.getSelected().toString()); + hidden = dnaSelection.getHiddenColumns(); + assertEquals(1, hidden.size()); + assertEquals("[5, 10]", Arrays.toString(hidden.get(0))); + + /* + * Combine hiding columns 1 and 3 to get discontiguous hidden columns + */ + proteinSelection.revealAllHiddenColumns(); + proteinSelection.clear(); + proteinSelection.hideColumns(1); + proteinSelection.hideColumns(3); + dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView); + hidden = dnaSelection.getHiddenColumns(); + assertEquals(2, hidden.size()); + assertEquals("[0, 3]", Arrays.toString(hidden.get(0))); + assertEquals("[5, 10]", Arrays.toString(hidden.get(1))); + } + + @Test(groups = { "Functional" }) + public void testGetLength() + { + assertEquals(0, MappingUtils.getLength(null)); + + /* + * [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)); + + /* + * [start, end, start, end...] ranges + */ + ranges.clear(); + 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)); + } + + @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, 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)); + } + }