+ }
+
+ /**
+ * 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<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
+ mappings.add(acf1);
+ mappings.add(acf2);
+ mappings.add(acf3);
+ mappings.add(acf4);
+
+ /*
+ * test for null args
+ */
+ List<AlignedCodonFrame> 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()
+ {
+ SequenceI dna = new Sequence("Seq1", "---ACG---GCATCA", 8, 16);
+ SequenceI protein = new Sequence("Seq2", "-T-AS", 5, 7);
+ dna.createDatasetSequence();
+ protein.createDatasetSequence();
+ 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<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
+ mappings.add(acf);
+
+ AlignmentI prot = new Alignment(new SequenceI[] { protein });
+ prot.setCodonFrames(mappings);
+ AlignmentI nuc = new Alignment(new SequenceI[] { dna });
+
+ /*
+ * construct and perform the edit command to turn "-T-AS" in to "-T-A--S"
+ * i.e. insert two gaps at column 4
+ */
+ EditCommand ec = new EditCommand();
+ final Edit edit = ec.new Edit(Action.INSERT_GAP,
+ new SequenceI[] { protein }, 4, 2, '-');
+ ec.appendEdit(edit, prot, true, null);
+
+ /*
+ * the mapped edit command should be to insert 6 gaps before base 4 in the
+ * nucleotide sequence, which corresponds to aligned column 12 in the dna
+ */
+ EditCommand mappedEdit = MappingUtils.mapEditCommand(ec, false, nuc,
+ '-', mappings);
+ assertEquals(1, mappedEdit.getEdits().size());
+ Edit e = mappedEdit.getEdits().get(0);
+ assertEquals(1, e.getSequences().length);
+ assertEquals(dna, e.getSequences()[0]);
+ assertEquals(12, e.getPosition());
+ assertEquals(6, e.getNumber());
+ }
+
+ /**
+ * 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
+ */
+ @Test(groups = { "Functional" })
+ public void testMapColumnSelection_hiddenColumns() throws IOException
+ {
+ setupMappedAlignments();
+
+ 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
+ */
+ proteinSelection.hideColumns(0);
+ ColumnSelection dnaSelection = MappingUtils.mapColumnSelection(
+ proteinSelection, proteinView, dnaView);
+ assertEquals("[]", dnaSelection.getSelected().toString());
+ List<int[]> 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
+ */
+ 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
+ */
+ 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
+ */
+ 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
+ */
+ 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)));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetLength()
+ {
+ assertEquals(0, MappingUtils.getLength(null));
+
+ /*
+ * [start, end] ranges
+ */
+ List<int[]> ranges = new ArrayList<int[]>();
+ assertEquals(0, MappingUtils.getLength(ranges));
+ ranges.add(new int[] { 1, 1 });
+ assertEquals(1, MappingUtils.getLength(ranges));
+ ranges.add(new int[] { 2, 10 });
+ assertEquals(10, MappingUtils.getLength(ranges));
+ ranges.add(new int[] { 20, 10 });
+ assertEquals(21, MappingUtils.getLength(ranges));
+
+ /*
+ * [start, end, start, end...] ranges
+ */
+ ranges.clear();
+ ranges.add(new int[] { 1, 5, 8, 4 });
+ ranges.add(new int[] { 8, 2 });
+ ranges.add(new int[] { 12, 12 });
+ assertEquals(18, MappingUtils.getLength(ranges));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testContains()
+ {
+ assertFalse(MappingUtils.contains(null, 1));
+ List<int[]> ranges = new ArrayList<int[]>();
+ assertFalse(MappingUtils.contains(ranges, 1));
+
+ ranges.add(new int[] { 1, 4 });
+ ranges.add(new int[] { 6, 6 });
+ ranges.add(new int[] { 8, 10 });
+ ranges.add(new int[] { 30, 20 });
+ ranges.add(new int[] { -16, -44 });
+
+ assertFalse(MappingUtils.contains(ranges, 0));
+ assertTrue(MappingUtils.contains(ranges, 1));
+ assertTrue(MappingUtils.contains(ranges, 2));
+ assertTrue(MappingUtils.contains(ranges, 3));
+ assertTrue(MappingUtils.contains(ranges, 4));
+ assertFalse(MappingUtils.contains(ranges, 5));
+
+ assertTrue(MappingUtils.contains(ranges, 6));
+ assertFalse(MappingUtils.contains(ranges, 7));
+
+ assertTrue(MappingUtils.contains(ranges, 8));
+ assertTrue(MappingUtils.contains(ranges, 9));
+ assertTrue(MappingUtils.contains(ranges, 10));
+
+ assertFalse(MappingUtils.contains(ranges, 31));
+ assertTrue(MappingUtils.contains(ranges, 30));
+ assertTrue(MappingUtils.contains(ranges, 29));
+ assertTrue(MappingUtils.contains(ranges, 20));
+ assertFalse(MappingUtils.contains(ranges, 19));
+
+ assertFalse(MappingUtils.contains(ranges, -15));
+ assertTrue(MappingUtils.contains(ranges, -16));
+ assertTrue(MappingUtils.contains(ranges, -44));
+ assertFalse(MappingUtils.contains(ranges, -45));
+ }
+
+ /**
+ * Test the method that drops positions from the start of a mapped range
+ */
+ @Test(groups = "Functional")
+ public void testRemoveStartPositions()
+ {
+ int[] ranges = new int[] { 1, 10 };
+ int[] adjusted = MappingUtils.removeStartPositions(0, ranges);
+ assertEquals("[1, 10]", Arrays.toString(adjusted));
+
+ adjusted = MappingUtils.removeStartPositions(1, ranges);
+ assertEquals("[2, 10]", Arrays.toString(adjusted));
+ assertEquals("[1, 10]", Arrays.toString(ranges));
+
+ ranges = adjusted;
+ adjusted = MappingUtils.removeStartPositions(1, ranges);
+ assertEquals("[3, 10]", Arrays.toString(adjusted));
+ assertEquals("[2, 10]", Arrays.toString(ranges));
+
+ ranges = new int[] { 2, 3, 10, 12 };
+ adjusted = MappingUtils.removeStartPositions(1, ranges);
+ assertEquals("[3, 3, 10, 12]", Arrays.toString(adjusted));
+ assertEquals("[2, 3, 10, 12]", Arrays.toString(ranges));
+
+ ranges = new int[] { 2, 2, 8, 12 };
+ adjusted = MappingUtils.removeStartPositions(1, ranges);
+ assertEquals("[8, 12]", Arrays.toString(adjusted));
+ assertEquals("[2, 2, 8, 12]", Arrays.toString(ranges));
+
+ ranges = new int[] { 2, 2, 8, 12 };
+ adjusted = MappingUtils.removeStartPositions(2, ranges);
+ assertEquals("[9, 12]", Arrays.toString(adjusted));
+ assertEquals("[2, 2, 8, 12]", Arrays.toString(ranges));
+
+ ranges = new int[] { 2, 2, 4, 4, 9, 12 };
+ adjusted = MappingUtils.removeStartPositions(1, ranges);
+ assertEquals("[4, 4, 9, 12]", Arrays.toString(adjusted));
+ assertEquals("[2, 2, 4, 4, 9, 12]", Arrays.toString(ranges));
+
+ ranges = new int[] { 2, 2, 4, 4, 9, 12 };
+ adjusted = MappingUtils.removeStartPositions(2, ranges);
+ assertEquals("[9, 12]", Arrays.toString(adjusted));
+ assertEquals("[2, 2, 4, 4, 9, 12]", Arrays.toString(ranges));
+
+ ranges = new int[] { 2, 3, 9, 12 };
+ adjusted = MappingUtils.removeStartPositions(3, ranges);
+ assertEquals("[10, 12]", Arrays.toString(adjusted));
+ assertEquals("[2, 3, 9, 12]", Arrays.toString(ranges));
+ }
+
+ /**
+ * Test the method that drops positions from the start of a mapped range, on
+ * the reverse strand
+ */
+ @Test(groups = "Functional")
+ public void testRemoveStartPositions_reverseStrand()
+ {
+ int[] ranges = new int[] { 10, 1 };
+ 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));
+ }
+