X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FMappingUtilsTest.java;h=87070d73a7605b208be2f8e0f7eadaf6996265f4;hb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;hp=492cbb66dab6f444f9d3be8d0aad629f0cdafbe7;hpb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;p=jalview.git diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java index 492cbb66..87070d7 100644 --- a/test/jalview/util/MappingUtilsTest.java +++ b/test/jalview/util/MappingUtilsTest.java @@ -33,12 +33,14 @@ 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.gui.JvOptionPane; import jalview.io.DataSourceType; import jalview.io.FileFormat; import jalview.io.FileFormatI; @@ -50,10 +52,19 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.List; +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; @@ -83,9 +94,9 @@ public class MappingUtilsTest /* * 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()); @@ -136,9 +147,9 @@ public class MappingUtilsTest /* * 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()); @@ -290,49 +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()); } @@ -397,14 +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()); /* @@ -414,7 +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()); } @@ -422,8 +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()); } @@ -660,7 +689,7 @@ public class MappingUtilsTest AlignedCodonFrame acf3 = new AlignedCodonFrame(); acf3.addMap(seq3.getDatasetSequence(), seq1.getDatasetSequence(), map); - List mappings = new ArrayList(); + List mappings = new ArrayList<>(); mappings.add(acf1); mappings.add(acf2); mappings.add(acf3); @@ -706,6 +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() { @@ -716,7 +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); - List mappings = new ArrayList(); + List mappings = new ArrayList<>(); mappings.add(acf); AlignmentI prot = new Alignment(new SequenceI[] { protein }); @@ -794,67 +899,82 @@ public class MappingUtilsTest 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.hideColumns(0); - ColumnSelection dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, - proteinView, dnaView); + 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 = dnaSelection.getHiddenColumns(); + 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 */ - proteinSelection.revealAllHiddenColumns(); + 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.hideColumns(1); - dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView); - hidden = dnaSelection.getHiddenColumns(); + 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 */ - proteinSelection.revealAllHiddenColumns(); + dnaSelection = new ColumnSelection(); + dnaHidden = new HiddenColumns(); + hiddenCols.revealAllHiddenColumns(proteinSelection); proteinSelection.clear(); - proteinSelection.hideColumns(2); - dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView); - assertTrue(dnaSelection.getHiddenColumns().isEmpty()); + 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 */ - proteinSelection.revealAllHiddenColumns(); + dnaSelection = new ColumnSelection(); + dnaHidden = new HiddenColumns(); + hiddenCols.revealAllHiddenColumns(proteinSelection); proteinSelection.clear(); - proteinSelection.hideColumns(3); // 5-10 hidden in dna + proteinSelection.hideSelectedColumns(3, hiddenCols); // 5-10 hidden in dna proteinSelection.addElement(1); // 0-3 selected in dna - dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView); + MappingUtils.mapColumnSelection(proteinSelection, hiddenCols, + proteinView, dnaView, dnaSelection, dnaHidden); assertEquals("[0, 1, 2, 3]", dnaSelection.getSelected().toString()); - hidden = dnaSelection.getHiddenColumns(); + 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 */ - proteinSelection.revealAllHiddenColumns(); + dnaSelection = new ColumnSelection(); + dnaHidden = new HiddenColumns(); + hiddenCols.revealAllHiddenColumns(proteinSelection); proteinSelection.clear(); - proteinSelection.hideColumns(1); - proteinSelection.hideColumns(3); - dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView); - hidden = dnaSelection.getHiddenColumns(); + 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))); @@ -868,7 +988,7 @@ public class MappingUtilsTest /* * [start, end] ranges */ - List ranges = new ArrayList(); + List ranges = new ArrayList<>(); assertEquals(0, MappingUtils.getLength(ranges)); ranges.add(new int[] { 1, 1 }); assertEquals(1, MappingUtils.getLength(ranges)); @@ -891,7 +1011,7 @@ public class MappingUtilsTest public void testContains() { assertFalse(MappingUtils.contains(null, 1)); - List ranges = new ArrayList(); + List ranges = new ArrayList<>(); assertFalse(MappingUtils.contains(ranges, 1)); ranges.add(new int[] { 1, 4 }); @@ -987,46 +1107,135 @@ public class MappingUtilsTest 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 })); + } + }