JAL-1551 tidy

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

diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index 853ebd5..3c417c3 100644 (file)
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -24,7 +24,6 @@ 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;
 
 import jalview.api.AlignViewportI;
 import jalview.commands.EditCommand;
@@ -862,6 +861,10 @@ public class MappingUtilsTest
   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 });
@@ -870,6 +873,15 @@ public class MappingUtilsTest
     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" })
@@ -911,4 +923,107 @@ public class MappingUtilsTest
     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));
+  }
+
 }