package jalview.util;
import static org.testng.AssertJUnit.assertEquals;
+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;
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()
+ public void testGetLength()
{
+ assertEquals(0, MappingUtils.getLength(null));
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();
+ assertEquals(0, MappingUtils.getLength(ranges));
ranges.add(new int[] { 1, 1 });
- ranges.add(new int[] { 3, 4 });
+ 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));
+ }
+
+ @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, 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));
+ 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));
}
+
}