X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FMappingUtilsTest.java;h=87070d73a7605b208be2f8e0f7eadaf6996265f4;hb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;hp=22fe5689bed5a072f79a5a2f065df6fa3376d7b5;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java index 22fe568..87070d7 100644 --- a/test/jalview/util/MappingUtilsTest.java +++ b/test/jalview/util/MappingUtilsTest.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -21,6 +21,7 @@ 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; @@ -32,28 +33,38 @@ import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; -import jalview.datamodel.SearchResults; -import jalview.datamodel.SearchResults.Match; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.SearchResultMatchI; +import jalview.datamodel.SearchResultsI; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.gui.AlignViewport; -import jalview.io.AppletFormatAdapter; +import jalview.gui.JvOptionPane; +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.LinkedHashSet; import java.util.List; -import java.util.Set; +import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; public class MappingUtilsTest { + + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + private AlignViewportI dnaView; private AlignViewportI proteinView; @@ -77,14 +88,15 @@ public class MappingUtilsTest 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 12 maps to codon 5-7, 13 to codon 8-10 */ - SearchResults sr = MappingUtils.buildSearchResults(aseq1, 12, acfList); + SearchResultsI sr = MappingUtils.buildSearchResults(aseq1, 12, acfList); assertEquals(1, sr.getResults().size()); - Match m = sr.getResults().get(0); + SearchResultMatchI m = sr.getResults().get(0); assertEquals(seq1.getDatasetSequence(), m.getSequence()); assertEquals(5, m.getStart()); assertEquals(7, m.getEnd()); @@ -129,14 +141,15 @@ public class MappingUtilsTest 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 8 maps to [6, 8, 9] */ - SearchResults sr = MappingUtils.buildSearchResults(aseq1, 8, acfList); + SearchResultsI sr = MappingUtils.buildSearchResults(aseq1, 8, acfList); assertEquals(2, sr.getResults().size()); - Match m = sr.getResults().get(0); + SearchResultMatchI m = sr.getResults().get(0); assertEquals(seq1.getDatasetSequence(), m.getSequence()); assertEquals(6, m.getStart()); assertEquals(6, m.getEnd()); @@ -197,10 +210,10 @@ 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); @@ -209,7 +222,8 @@ 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); @@ -267,11 +281,11 @@ 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; } @@ -287,49 +301,60 @@ public class MappingUtilsTest setupMappedAlignments(); ColumnSelection colsel = new ColumnSelection(); + HiddenColumns hidden = new HiddenColumns(); /* * 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 */ colsel.addElement(0); - ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, - proteinView, dnaView); + ColumnSelection cs = new ColumnSelection(); + HiddenColumns hs = new HiddenColumns(); + MappingUtils.mapColumnSelection(colsel, hidden, proteinView, dnaView, + cs, hs); assertEquals("[0, 1, 2, 3, 4]", cs.getSelected().toString()); /* * Column 1 in protein picks up Seq1/K which maps to cols 0-3 in dna */ + cs.clear(); colsel.clear(); colsel.addElement(1); - cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView); + MappingUtils.mapColumnSelection(colsel, hidden, proteinView, dnaView, + cs, hs); assertEquals("[0, 1, 2, 3]", cs.getSelected().toString()); /* * Column 2 in protein picks up gaps only - no mapping */ + cs.clear(); colsel.clear(); colsel.addElement(2); - cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView); + MappingUtils.mapColumnSelection(colsel, hidden, proteinView, + dnaView, cs, hs); assertEquals("[]", cs.getSelected().toString()); /* * 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 */ + cs.clear(); colsel.clear(); colsel.addElement(3); - cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView); + MappingUtils.mapColumnSelection(colsel, hidden, proteinView, + dnaView, cs, hs); assertEquals("[5, 6, 7, 8, 9, 10]", cs.getSelected().toString()); /* * Combine selection of columns 1 and 3 to get a discontiguous mapped * selection */ + cs.clear(); colsel.clear(); colsel.addElement(1); colsel.addElement(3); - cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView); + MappingUtils.mapColumnSelection(colsel, hidden, proteinView, + dnaView, cs, hs); assertEquals("[0, 1, 2, 3, 5, 6, 7, 8, 9, 10]", cs.getSelected() .toString()); } @@ -343,16 +368,18 @@ public class MappingUtilsTest 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(">Seq1/10-18\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 @@ -373,7 +400,8 @@ public class MappingUtilsTest 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); @@ -391,14 +419,17 @@ public class MappingUtilsTest setupMappedAlignments(); ColumnSelection colsel = new ColumnSelection(); + HiddenColumns hidden = new HiddenColumns(); /* * Column 0 in dna picks up first bases which map to residue 1, columns 0-1 * in protein. */ + ColumnSelection cs = new ColumnSelection(); + HiddenColumns hs = new HiddenColumns(); colsel.addElement(0); - ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, dnaView, - proteinView); + MappingUtils.mapColumnSelection(colsel, hidden, dnaView, proteinView, + cs, hs); assertEquals("[0, 1]", cs.getSelected().toString()); /* @@ -408,7 +439,9 @@ public class MappingUtilsTest colsel.addElement(3); colsel.addElement(4); colsel.addElement(5); - cs = MappingUtils.mapColumnSelection(colsel, dnaView, proteinView); + cs.clear(); + MappingUtils.mapColumnSelection(colsel, hidden, dnaView, proteinView, + cs, hs); assertEquals("[0, 1, 3]", cs.getSelected().toString()); } @@ -416,8 +449,10 @@ public class MappingUtilsTest public void testMapColumnSelection_null() throws IOException { setupMappedAlignments(); - ColumnSelection cs = MappingUtils.mapColumnSelection(null, dnaView, - proteinView); + ColumnSelection cs = new ColumnSelection(); + HiddenColumns hs = new HiddenColumns(); + MappingUtils.mapColumnSelection(null, null, dnaView, proteinView, cs, + hs); assertTrue("mapped selection not empty", cs.getSelected().isEmpty()); } @@ -442,7 +477,7 @@ 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, @@ -462,10 +497,11 @@ 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); @@ -474,7 +510,8 @@ 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); @@ -544,10 +581,10 @@ 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); @@ -556,7 +593,8 @@ 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); @@ -651,7 +689,7 @@ 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); @@ -697,6 +735,82 @@ public class MappingUtilsTest assertEquals(0, result.size()); } + /** + * just like the one above, but this time, we provide a set of sequences to + * subselect the mapping search + */ + @Test(groups = { "Functional" }) + public void testFindMappingsForSequenceAndOthers() + { + 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, seq3 to seq4 + */ + 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); + AlignedCodonFrame acf4 = new AlignedCodonFrame(); + acf4.addMap(seq3.getDatasetSequence(), seq4.getDatasetSequence(), map); + + List mappings = new ArrayList<>(); + mappings.add(acf1); + mappings.add(acf2); + mappings.add(acf3); + mappings.add(acf4); + + /* + * test for null args + */ + List result = MappingUtils + .findMappingsForSequenceAndOthers(null, mappings, + Arrays.asList(new SequenceI[] { seq1, seq2 })); + assertTrue(result.isEmpty()); + + result = MappingUtils.findMappingsForSequenceAndOthers(seq1, null, + Arrays.asList(new SequenceI[] { seq1, seq2 })); + assertTrue(result.isEmpty()); + + /* + * Seq1 has three mappings, but filter argument will only accept + * those to seq2 + */ + result = MappingUtils.findMappingsForSequenceAndOthers( + seq1, + mappings, + Arrays.asList(new SequenceI[] { seq1, seq2, + seq1.getDatasetSequence() })); + assertEquals(2, result.size()); + assertTrue(result.contains(acf1)); + assertTrue(result.contains(acf2)); + assertFalse("Did not expect to find mapping acf3 - subselect failed", + result.contains(acf3)); + assertFalse( + "Did not expect to find mapping acf4 - doesn't involve sequence", + result.contains(acf4)); + + /* + * and verify the no filter case + */ + result = MappingUtils.findMappingsForSequenceAndOthers(seq1, mappings, + null); + assertEquals(3, result.size()); + assertTrue(result.contains(acf1)); + assertTrue(result.contains(acf2)); + assertTrue(result.contains(acf3)); + } + @Test(groups = { "Functional" }) public void testMapEditCommand() { @@ -707,7 +821,7 @@ public class MappingUtilsTest 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); - Set mappings = new LinkedHashSet(); + List mappings = new ArrayList<>(); mappings.add(acf); AlignmentI prot = new Alignment(new SequenceI[] { protein }); @@ -736,4 +850,392 @@ public class MappingUtilsTest 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(); + HiddenColumns hiddenCols = new HiddenColumns(); + + /* + * 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.hideSelectedColumns(0, hiddenCols); + ColumnSelection dnaSelection = new ColumnSelection(); + HiddenColumns dnaHidden = new HiddenColumns(); + MappingUtils.mapColumnSelection(proteinSelection, hiddenCols, + proteinView, dnaView, dnaSelection, dnaHidden); + assertEquals("[]", dnaSelection.getSelected().toString()); + List hidden = dnaHidden.getHiddenColumnsCopy(); + 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 + */ + dnaSelection = new ColumnSelection(); + dnaHidden = new HiddenColumns(); + hiddenCols.revealAllHiddenColumns(proteinSelection); + // 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.hideSelectedColumns(1, hiddenCols); + MappingUtils.mapColumnSelection(proteinSelection, hiddenCols, + proteinView, dnaView, dnaSelection, dnaHidden); + hidden = dnaHidden.getHiddenColumnsCopy(); + assertEquals(1, hidden.size()); + assertEquals("[0, 3]", Arrays.toString(hidden.get(0))); + + /* + * Column 2 in protein picks up gaps only - no mapping + */ + dnaSelection = new ColumnSelection(); + dnaHidden = new HiddenColumns(); + hiddenCols.revealAllHiddenColumns(proteinSelection); + proteinSelection.clear(); + proteinSelection.hideSelectedColumns(2, hiddenCols); + MappingUtils.mapColumnSelection(proteinSelection, hiddenCols, + proteinView, dnaView, dnaSelection, dnaHidden); + assertTrue(dnaHidden.getHiddenColumnsCopy().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 + */ + dnaSelection = new ColumnSelection(); + dnaHidden = new HiddenColumns(); + hiddenCols.revealAllHiddenColumns(proteinSelection); + proteinSelection.clear(); + proteinSelection.hideSelectedColumns(3, hiddenCols); // 5-10 hidden in dna + proteinSelection.addElement(1); // 0-3 selected in dna + MappingUtils.mapColumnSelection(proteinSelection, hiddenCols, + proteinView, dnaView, dnaSelection, dnaHidden); + assertEquals("[0, 1, 2, 3]", dnaSelection.getSelected().toString()); + hidden = dnaHidden.getHiddenColumnsCopy(); + assertEquals(1, hidden.size()); + assertEquals("[5, 10]", Arrays.toString(hidden.get(0))); + + /* + * Combine hiding columns 1 and 3 to get discontiguous hidden columns + */ + dnaSelection = new ColumnSelection(); + dnaHidden = new HiddenColumns(); + hiddenCols.revealAllHiddenColumns(proteinSelection); + proteinSelection.clear(); + proteinSelection.hideSelectedColumns(1, hiddenCols); + proteinSelection.hideSelectedColumns(3, hiddenCols); + MappingUtils.mapColumnSelection(proteinSelection, hiddenCols, + proteinView, dnaView, dnaSelection, dnaHidden); + hidden = dnaHidden.getHiddenColumnsCopy(); + 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)); + } + + @Test(groups = { "Functional" }) + public void testRangeContains() + { + /* + * both forward ranges + */ + assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] { + 1, 10 })); + assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] { + 2, 10 })); + assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] { + 1, 9 })); + assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] { + 4, 5 })); + assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] { + 0, 9 })); + assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] { + -10, -9 })); + assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] { + 1, 11 })); + assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] { + 11, 12 })); + + /* + * forward range, reverse query + */ + assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] { + 10, 1 })); + assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] { + 9, 1 })); + assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] { + 10, 2 })); + assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] { + 5, 5 })); + assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] { + 11, 1 })); + assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] { + 10, 0 })); + + /* + * reverse range, forward query + */ + assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] { + 1, 10 })); + assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] { + 1, 9 })); + assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] { + 2, 10 })); + assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] { + 6, 6 })); + assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] { + 6, 11 })); + assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] { + 11, 20 })); + assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] { + -3, -2 })); + + /* + * both reverse + */ + assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] { + 10, 1 })); + assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] { + 9, 1 })); + assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] { + 10, 2 })); + assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] { + 3, 3 })); + assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] { + 11, 1 })); + assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] { + 10, 0 })); + assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] { + 12, 11 })); + assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] { + -5, -8 })); + + /* + * bad arguments + */ + assertFalse(MappingUtils.rangeContains(new int[] { 1, 10, 12 }, + new int[] { + 1, 10 })); + assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, + new int[] { 1 })); + assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, null)); + assertFalse(MappingUtils.rangeContains(null, new int[] { 1, 10 })); + } + }