JAL-2029 many-to-many EnsemblCDS-to-Uniprot mappings

[jalview.git] / test / jalview / util / MappingUtilsTest.java

diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index 7100381..b53d513 100644 (file)
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -21,6 +21,7 @@
 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;
 
@@ -855,4 +856,161 @@ public class MappingUtilsTest
     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));
+    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));
+  }
+
+  @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));
+  }
+
 }