X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FMappingUtilsTest.java;fp=test%2Fjalview%2Futil%2FMappingUtilsTest.java;h=d0ec3e83898476032815524bc73a127a7287fdda;hb=9f70ff4b6d193b340031997634c9e3602486bc8e;hp=b84e770ad970f29e6bb004492612bdba0b5a4c61;hpb=76844c43faeeeba369deaf42f1998ca0fb33d956;p=jalview.git diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java index b84e770..d0ec3e8 100644 --- a/test/jalview/util/MappingUtilsTest.java +++ b/test/jalview/util/MappingUtilsTest.java @@ -33,6 +33,7 @@ import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.SearchResultMatchI; import jalview.datamodel.SearchResultsI; import jalview.datamodel.Sequence; @@ -300,49 +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()); } @@ -407,14 +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()); /* @@ -424,7 +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()); } @@ -432,8 +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()); } @@ -670,7 +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); @@ -745,7 +764,7 @@ public class MappingUtilsTest AlignedCodonFrame acf4 = new AlignedCodonFrame(); acf4.addMap(seq3.getDatasetSequence(), seq4.getDatasetSequence(), map); - List mappings = new ArrayList(); + List mappings = new ArrayList<>(); mappings.add(acf1); mappings.add(acf2); mappings.add(acf3); @@ -802,7 +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 }); @@ -882,69 +901,80 @@ public class MappingUtilsTest 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))); @@ -958,7 +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)); @@ -981,7 +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 });