X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Futil%2FMappingUtilsTest.java;h=b84e770ad970f29e6bb004492612bdba0b5a4c61;hb=693e17575680c94d9bdc5797faa0b328bb6f7c05;hp=6ba69b0ba67d222dfeb9f045ebce6bf3ebb94113;hpb=8b27085fa7fc5f2877e078421284c2636b85b8c6;p=jalview.git diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java index 6ba69b0..b84e770 100644 --- a/test/jalview/util/MappingUtilsTest.java +++ b/test/jalview/util/MappingUtilsTest.java @@ -33,12 +33,13 @@ 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.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 +51,19 @@ 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 +93,9 @@ 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 +146,9 @@ 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()); @@ -711,7 +721,7 @@ public class MappingUtilsTest * subselect the mapping search */ @Test(groups = { "Functional" }) - public void testFindMappingsBetweenSequenceAndOthers() + public void testFindMappingsForSequenceAndOthers() { SequenceI seq1 = new Sequence("Seq1", "ABC"); SequenceI seq2 = new Sequence("Seq2", "ABC"); @@ -723,7 +733,7 @@ public class MappingUtilsTest seq4.createDatasetSequence(); /* - * Create mappings from seq1 to seq2, seq2 to seq1, seq3 to seq1 + * 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); @@ -732,23 +742,54 @@ public class MappingUtilsTest 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); /* - * Seq1 has three mappings + * test for null args */ List result = MappingUtils - .findMappingsForSequenceAndOthers(seq1, mappings, - new Alignment(new SequenceI[] { seq1, seq2 })); + .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)); - assertEquals(2, result.size()); + 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" }) @@ -839,7 +880,7 @@ public class MappingUtilsTest public void testMapColumnSelection_hiddenColumns() throws IOException { setupMappedAlignments(); - + ColumnSelection proteinSelection = new ColumnSelection(); /* @@ -847,8 +888,8 @@ public class MappingUtilsTest * in dna respectively, overall 0-4 */ proteinSelection.hideColumns(0); - ColumnSelection dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, - proteinView, dnaView); + ColumnSelection dnaSelection = MappingUtils.mapColumnSelection( + proteinSelection, proteinView, dnaView); assertEquals("[]", dnaSelection.getSelected().toString()); List hidden = dnaSelection.getHiddenColumns(); assertEquals(1, hidden.size()); @@ -863,7 +904,8 @@ public class MappingUtilsTest // deselect these or hideColumns will be expanded to include 0 proteinSelection.clear(); proteinSelection.hideColumns(1); - dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView); + dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, + proteinView, dnaView); hidden = dnaSelection.getHiddenColumns(); assertEquals(1, hidden.size()); assertEquals("[0, 3]", Arrays.toString(hidden.get(0))); @@ -874,7 +916,8 @@ public class MappingUtilsTest proteinSelection.revealAllHiddenColumns(); proteinSelection.clear(); proteinSelection.hideColumns(2); - dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView); + dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, + proteinView, dnaView); assertTrue(dnaSelection.getHiddenColumns().isEmpty()); /* @@ -885,7 +928,8 @@ public class MappingUtilsTest proteinSelection.clear(); proteinSelection.hideColumns(3); // 5-10 hidden in dna proteinSelection.addElement(1); // 0-3 selected in dna - dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView); + dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, + proteinView, dnaView); assertEquals("[0, 1, 2, 3]", dnaSelection.getSelected().toString()); hidden = dnaSelection.getHiddenColumns(); assertEquals(1, hidden.size()); @@ -898,7 +942,8 @@ public class MappingUtilsTest proteinSelection.clear(); proteinSelection.hideColumns(1); proteinSelection.hideColumns(3); - dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView); + dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, + proteinView, dnaView); hidden = dnaSelection.getHiddenColumns(); assertEquals(2, hidden.size()); assertEquals("[0, 3]", Arrays.toString(hidden.get(0))); @@ -1032,42 +1077,42 @@ 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));