import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
-import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
import jalview.api.AlignViewportI;
import jalview.commands.EditCommand;
assertEquals(0, result.size());
}
+ /**
+ * just like the one above, but this time, we provide a set of sequences to
+ * subselect the mapping search
+ */
+ @Test(groups = { "Functional" })
+ public void testFindMappingsBetweenSequenceAndOthers()
+ {
+ 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
+ */
+ 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);
+
+ List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
+ mappings.add(acf1);
+ mappings.add(acf2);
+ mappings.add(acf3);
+
+ /*
+ * Seq1 has three mappings
+ */
+ List<AlignedCodonFrame> result = MappingUtils
+ .findMappingsForSequenceAndOthers(seq1, mappings,
+ new Alignment(new SequenceI[] { seq1, seq2 }));
+ 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());
+ }
+
@Test(groups = { "Functional" })
public void testMapEditCommand()
{
assertEquals("[5, 10]", Arrays.toString(hidden.get(1)));
}
- /**
- * Tests for the method that removes the trailing stop codon from a mapping
- * range i.e. the last 3 positions (whether split or not)
- */
- @Test(groups = { "Functional" })
- public void testUnmapStopCodon()
- {
- List<int[]> ranges = new ArrayList<int[]>();
-
- // simple case, forward strand:
- ranges.add(new int[] { 1, 3 });
- ranges.add(new int[] { 9, 14 });
- MappingUtils.unmapStopCodon(ranges, 9);
- assertEquals(2, ranges.size());
- assertArrayEquals(new int[] { 1, 3 }, ranges.get(0));
- assertArrayEquals(new int[] { 9, 11 }, ranges.get(1));
-
- // split stop codon, forward strand:
- ranges.clear();
- ranges.add(new int[] { 1, 8 });
- ranges.add(new int[] { 10, 10 });
- MappingUtils.unmapStopCodon(ranges, 9);
- assertEquals(1, ranges.size());
- assertArrayEquals(new int[] { 1, 6 }, ranges.get(0));
-
- // very split stop codon, forward strand:
- ranges.clear();
- ranges.add(new int[] { 1, 1 });
- ranges.add(new int[] { 3, 4 });
- ranges.add(new int[] { 6, 6 });
- ranges.add(new int[] { 8, 8 });
- ranges.add(new int[] { 10, 10 });
- MappingUtils.unmapStopCodon(ranges, 6);
- assertEquals(2, ranges.size());
- assertArrayEquals(new int[] { 1, 1 }, ranges.get(0));
- assertArrayEquals(new int[] { 3, 4 }, ranges.get(1));
-
- // simple case, reverse strand:
- ranges.clear();
- ranges.add(new int[] { 12, 10 });
- ranges.add(new int[] { 6, 1 });
- MappingUtils.unmapStopCodon(ranges, 9);
- assertEquals(2, ranges.size());
- assertArrayEquals(new int[] { 12, 10 }, ranges.get(0));
- assertArrayEquals(new int[] { 6, 4 }, ranges.get(1));
-
- // split stop codon, reverse strand:
- ranges.clear();
- ranges.add(new int[] { 12, 6 });
- ranges.add(new int[] { 4, 3 });
- MappingUtils.unmapStopCodon(ranges, 9);
- assertEquals(1, ranges.size());
- assertArrayEquals(new int[] { 12, 7 }, ranges.get(0));
- }
-
@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(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" })
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));
+ }
+
}