X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FMappingUtilsTest.java;h=7100381d38a178d458f4dfe9afd34f1c6a81bc8c;hb=a6b324e3f5edac3df0b968f0037b1cc8b651598e;hp=51c99af3486577424bd4d86eec02b1bbb27b2971;hpb=5b079109d33a4596a8c3017dbf93b7de5b0300c5;p=jalview.git diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java index 51c99af..7100381 100644 --- a/test/jalview/util/MappingUtilsTest.java +++ b/test/jalview/util/MappingUtilsTest.java @@ -43,12 +43,9 @@ 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.Test; @@ -77,7 +74,8 @@ 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 @@ -129,7 +127,8 @@ 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] @@ -209,7 +208,8 @@ 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); @@ -343,8 +343,10 @@ 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", @@ -373,7 +375,8 @@ 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); @@ -442,7 +445,7 @@ 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, @@ -474,7 +477,8 @@ 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); @@ -556,7 +560,8 @@ 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 +656,7 @@ 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); @@ -707,7 +712,7 @@ 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 }); @@ -738,6 +743,45 @@ public class MappingUtilsTest } /** + * 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 @@ -747,62 +791,66 @@ public class MappingUtilsTest { setupMappedAlignments(); - ColumnSelection colsel = new ColumnSelection(); + 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 */ - colsel.hideColumns(0); - ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, + proteinSelection.hideColumns(0); + ColumnSelection dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView); - assertEquals("[]", cs.getSelected().toString()); - List hidden = cs.getHiddenColumns(); + 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 */ - colsel.revealAllHiddenColumns(); - colsel.hideColumns(1); - cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView); - hidden = cs.getHiddenColumns(); + 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 */ - colsel.revealAllHiddenColumns(); - colsel.clear(); - colsel.hideColumns(2); - cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView); - assertTrue(cs.getHiddenColumns().isEmpty()); + 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 */ - colsel.revealAllHiddenColumns(); - colsel.clear(); - colsel.hideColumns(3); // 5-10 hidden in dna - colsel.addElement(1); // 0-3 selected in dna - cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView); - assertEquals("[0, 1, 2, 3]", cs.getSelected().toString()); - hidden = cs.getHiddenColumns(); + 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 */ - colsel.revealAllHiddenColumns(); - colsel.clear(); - colsel.hideColumns(1); - colsel.hideColumns(3); - cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView); - hidden = cs.getHiddenColumns(); + 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)));