From: Jim Procter Date: Fri, 28 Jan 2022 17:08:35 +0000 (+0000) Subject: Merge branch 'merge/develop_JAL-3725' into develop X-Git-Tag: Release_2_11_2_0~13^2~6^2~1 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0aa7f6fab658c9a203b410d4bead72217da5c9a0;p=jalview.git Merge branch 'merge/develop_JAL-3725' into develop Conflicts: src/jalview/gui/PopupMenu.java --- 0aa7f6fab658c9a203b410d4bead72217da5c9a0 diff --cc src/jalview/gui/PopupMenu.java index 6cd763b,d1e8e32..7b284a9 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@@ -839,15 -839,13 +839,14 @@@ public class PopupMenu extends JPopupMe /* * show local rather than linked feature coordinates */ - int[] beginRange = mf.getMappedPositions(start, start); - int[] endRange = mf.getMappedPositions(end, end); - if (beginRange == null || endRange == null) + int[] localRange = mf.getMappedPositions(start, end); + if (localRange == null) { + // e.g. variant extending to stop codon so not mappable return; } - start = beginRange[0]; - end = endRange[endRange.length - 1]; + start = localRange[0]; + end = localRange[localRange.length - 1]; } StringBuilder desc = new StringBuilder(); desc.append(sf.getType()).append(" ").append(String.valueOf(start)); diff --cc test/jalview/util/MappingUtilsTest.java index bd81d30,4b7c75c..1fdfb16 --- a/test/jalview/util/MappingUtilsTest.java +++ b/test/jalview/util/MappingUtilsTest.java @@@ -1340,132 -1330,20 +1341,121 @@@ public class MappingUtilsTes } @Test(groups = "Functional") - public void testListToArray() + public void testFindOverlap() { List ranges = new ArrayList<>(); - - int[] result = MappingUtils.rangeListToArray(ranges); - assertEquals(result.length, 0); - ranges.add(new int[] { 24, 12 }); - result = MappingUtils.rangeListToArray(ranges); - assertEquals(result.length, 2); - assertEquals(result[0], 24); - assertEquals(result[1], 12); - ranges.add(new int[] { -7, 30 }); - result = MappingUtils.rangeListToArray(ranges); - assertEquals(result.length, 4); - assertEquals(result[0], 24); - assertEquals(result[1], 12); - assertEquals(result[2], -7); - assertEquals(result[3], 30); - try - { - MappingUtils.rangeListToArray(null); - fail("Expected exception"); - } catch (NullPointerException e) - { - // expected - } + ranges.add(new int[] { 4, 8 }); + ranges.add(new int[] { 10, 12 }); + ranges.add(new int[] { 16, 19 }); + + int[] overlap = MappingUtils.findOverlap(ranges, 5, 13); + assertArrayEquals(overlap, new int[] { 5, 12 }); + overlap = MappingUtils.findOverlap(ranges, -100, 100); + assertArrayEquals(overlap, new int[] { 4, 19 }); + overlap = MappingUtils.findOverlap(ranges, 7, 17); + assertArrayEquals(overlap, new int[] { 7, 17 }); + overlap = MappingUtils.findOverlap(ranges, 13, 15); + assertNull(overlap); } + + /** + * Test mapping a sequence group where sequences in and outside the group + * share a dataset sequence (e.g. alternative CDS for the same gene) + *

+ * This scenario doesn't arise after JAL-3763 changes, but test left as still valid + * @throws IOException + */ + @Test(groups = { "Functional" }) + public void testMapSequenceGroup_sharedDataset() throws IOException + { + /* + * Set up dna and protein Seq1/2/3 with mappings (held on the protein + * viewport). CDS sequences share the same 'gene' dataset sequence. + */ + SequenceI dna = new Sequence("dna", "aaatttgggcccaaatttgggccc"); + SequenceI cds1 = new Sequence("cds1/1-6", "aaattt"); + SequenceI cds2 = new Sequence("cds1/4-9", "tttggg"); + SequenceI cds3 = new Sequence("cds1/19-24", "gggccc"); + + cds1.setDatasetSequence(dna); + cds2.setDatasetSequence(dna); + cds3.setDatasetSequence(dna); + + SequenceI pep1 = new Sequence("pep1", "KF"); + SequenceI pep2 = new Sequence("pep2", "FG"); + SequenceI pep3 = new Sequence("pep3", "GP"); + pep1.createDatasetSequence(); + pep2.createDatasetSequence(); + pep3.createDatasetSequence(); + + /* + * add mappings from coding positions of dna to respective peptides + */ + AlignedCodonFrame acf = new AlignedCodonFrame(); + acf.addMap(dna, pep1, + new MapList(new int[] + { 1, 6 }, new int[] { 1, 2 }, 3, 1)); + acf.addMap(dna, pep2, + new MapList(new int[] + { 4, 9 }, new int[] { 1, 2 }, 3, 1)); + acf.addMap(dna, pep3, + new MapList(new int[] + { 19, 24 }, new int[] { 1, 2 }, 3, 1)); + + List acfList = Arrays + .asList(new AlignedCodonFrame[] + { acf }); + + AlignmentI cdna = new Alignment(new SequenceI[] { cds1, cds2, cds3 }); + AlignmentI protein = new Alignment( + new SequenceI[] + { pep1, pep2, pep3 }); + AlignViewportI cdnaView = new AlignViewport(cdna); + AlignViewportI peptideView = new AlignViewport(protein); + protein.setCodonFrames(acfList); + + /* + * Select pep1 and pep3 in the protein alignment + */ + SequenceGroup sg = new SequenceGroup(); + sg.setColourText(true); + sg.setIdColour(Color.GREEN); + sg.setOutlineColour(Color.LIGHT_GRAY); + sg.addSequence(pep1, false); + sg.addSequence(pep3, false); + sg.setEndRes(protein.getWidth() - 1); + + /* + * Verify the mapped sequence group in dna is cds1 and cds3 + */ + SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, + peptideView, cdnaView); + assertTrue(mappedGroup.getColourText()); + assertSame(sg.getIdColour(), mappedGroup.getIdColour()); + assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour()); + assertEquals(2, mappedGroup.getSequences().size()); + assertSame(cds1, mappedGroup.getSequences().get(0)); + assertSame(cds3, mappedGroup.getSequences().get(1)); + // columns 1-6 selected (0-5 base zero) + assertEquals(0, mappedGroup.getStartRes()); + assertEquals(5, mappedGroup.getEndRes()); + + /* + * Select mapping sequence group from dna to protein + */ + sg.clear(); + sg.addSequence(cds2, false); + sg.addSequence(cds1, false); + sg.setStartRes(0); + sg.setEndRes(cdna.getWidth() - 1); + mappedGroup = MappingUtils.mapSequenceGroup(sg, cdnaView, peptideView); + assertTrue(mappedGroup.getColourText()); + assertSame(sg.getIdColour(), mappedGroup.getIdColour()); + assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour()); + assertEquals(2, mappedGroup.getSequences().size()); + assertSame(protein.getSequenceAt(1), mappedGroup.getSequences().get(0)); + assertSame(protein.getSequenceAt(0), mappedGroup.getSequences().get(1)); + assertEquals(0, mappedGroup.getStartRes()); + assertEquals(1, mappedGroup.getEndRes()); // two columns + } }