JAL-1705 align CDS and peptide products to transcripts

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

diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java
index 22a3ad9..c442b6f 100644 (file)
--- a/test/jalview/util/MapListTest.java
+++ b/test/jalview/util/MapListTest.java
@@ -25,6 +25,7 @@ import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -666,4 +667,124 @@ public class MapListTest
             1);
     assertTrue(ml.isFromForwardStrand());
   }
+
+  /**
+   * Test the method that merges a list of ranges where possible
+   */
+  @Test(groups = { "Functional" })
+  public void testCoalesceRanges()
+  {
+    assertNull(MapList.coalesceRanges(null));
+    List<int[]> ranges = new ArrayList<int[]>();
+    assertSame(ranges, MapList.coalesceRanges(ranges));
+    ranges.add(new int[] { 1, 3 });
+    assertSame(ranges, MapList.coalesceRanges(ranges));
+
+    // add non-contiguous range:
+    ranges.add(new int[] { 5, 6 });
+    assertSame(ranges, MapList.coalesceRanges(ranges));
+
+    // 'contiguous' range in opposite direction is not merged:
+    ranges.add(new int[] { 7, 6 });
+    assertSame(ranges, MapList.coalesceRanges(ranges));
+
+    // merging in forward direction:
+    ranges.clear();
+    ranges.add(new int[] { 1, 3 });
+    ranges.add(new int[] { 4, 5 });
+    ranges.add(new int[] { 5, 5 });
+    ranges.add(new int[] { 5, 7 });
+    List<int[]> merged = MapList.coalesceRanges(ranges);
+    assertEquals(1, merged.size());
+    assertArrayEquals(new int[] { 1, 7 }, merged.get(0));
+    // verify input list is unchanged
+    assertEquals(4, ranges.size());
+    assertArrayEquals(new int[] { 1, 3 }, ranges.get(0));
+    assertArrayEquals(new int[] { 4, 5 }, ranges.get(1));
+    assertArrayEquals(new int[] { 5, 5 }, ranges.get(2));
+    assertArrayEquals(new int[] { 5, 7 }, ranges.get(3));
+
+    // merging in reverse direction:
+    ranges.clear();
+    ranges.add(new int[] { 7, 5 });
+    ranges.add(new int[] { 5, 4 });
+    ranges.add(new int[] { 4, 4 });
+    ranges.add(new int[] { 3, 1 });
+    merged = MapList.coalesceRanges(ranges);
+    assertEquals(1, merged.size());
+    assertArrayEquals(new int[] { 7, 1 }, merged.get(0));
+
+    // merging with switches of direction:
+    ranges.clear();
+    ranges.add(new int[] { 1, 3 });
+    ranges.add(new int[] { 4, 5 });
+    ranges.add(new int[] { 5, 5 });
+    ranges.add(new int[] { 6, 6 });
+    ranges.add(new int[] { 12, 10 });
+    ranges.add(new int[] { 9, 8 });
+    ranges.add(new int[] { 8, 8 });
+    ranges.add(new int[] { 7, 7 });
+    merged = MapList.coalesceRanges(ranges);
+    assertEquals(2, merged.size());
+    assertArrayEquals(new int[] { 1, 6 }, merged.get(0));
+    assertArrayEquals(new int[] { 12, 7 }, merged.get(1));
+  }
+
+  /**
+   * Test the method that merges a list of ranges where possible
+   */
+  @Test(groups = { "Functional" })
+  public void testCoalesceRanges_withOverlap()
+  {
+    List<int[]> ranges = new ArrayList<int[]>();
+    ranges.add(new int[] { 1, 3 });
+    ranges.add(new int[] { 2, 5 });
+
+    /*
+     * [2, 5] should extend [1, 3]
+     */
+    List<int[]> merged = MapList.coalesceRanges(ranges);
+    assertEquals(1, merged.size());
+    assertArrayEquals(new int[] { 1, 5 }, merged.get(0));
+
+    /*
+     * a subsumed interval should be dropped
+     */
+    ranges.clear();
+    ranges.add(new int[] { 1, 6 });
+    ranges.add(new int[] { 2, 4 });
+    merged = MapList.coalesceRanges(ranges);
+    assertEquals(1, merged.size());
+    assertArrayEquals(new int[] { 1, 6 }, merged.get(0));
+
+    ranges.clear();
+    ranges.add(new int[] { 1, 5 });
+    ranges.add(new int[] { 1, 6 });
+    merged = MapList.coalesceRanges(ranges);
+    assertEquals(1, merged.size());
+    assertArrayEquals(new int[] { 1, 6 }, merged.get(0));
+
+    /*
+     * merge duplicate ranges
+     */
+    ranges.clear();
+    ranges.add(new int[] { 1, 3 });
+    ranges.add(new int[] { 1, 3 });
+    merged = MapList.coalesceRanges(ranges);
+    assertEquals(1, merged.size());
+    assertArrayEquals(new int[] { 1, 3 }, merged.get(0));
+
+    /*
+     * reverse direction
+     */
+    ranges.clear();
+    ranges.add(new int[] { 9, 5 });
+    ranges.add(new int[] { 9, 4 });
+    ranges.add(new int[] { 8, 3 });
+    ranges.add(new int[] { 3, 2 });
+    ranges.add(new int[] { 1, 0 });
+    merged = MapList.coalesceRanges(ranges);
+    assertEquals(1, merged.size());
+    assertArrayEquals(new int[] { 9, 0 }, merged.get(0));
+  }
 }