JAL-1705 tweak to MapList.toString for debugging

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

diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java
index 54e8311..d4ed0ea 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;
@@ -534,7 +535,7 @@ public class MapListTest
     MapList ml = new MapList(new int[] { 1, 5, 10, 15, 25, 20 }, new int[] {
         51, 1 }, 1, 3);
     String s = ml.toString();
-    assertEquals("From (1:3) [ [1, 5] [10, 15] [25, 20] ] To [ [51, 1] ]",
+    assertEquals("[ [1, 5] [10, 15] [25, 20] ] 1:3 to [ [51, 1] ]",
             s);
   }
 
@@ -558,7 +559,7 @@ public class MapListTest
 
     String s = ml.toString();
     assertEquals(
-            "From (1:3) [ [11, 15] [20, 25] [35, 30] [2, 4] [37, 40] ] To [ [72, 22] [12, 17] [78, 83] [88, 96] ]",
+            "[ [11, 15] [20, 25] [35, 30] [2, 4] [37, 40] ] 1:3 to [ [72, 22] [12, 17] [78, 83] [88, 96] ]",
             s);
   }
 
@@ -571,7 +572,7 @@ public class MapListTest
     MapList ml2 = new MapList(new int[] { 15, 16 }, new int[] { 58, 53 },
             1, 3);
     ml.addMapList(ml2);
-    assertEquals("From (1:3) [ [11, 16] ] To [ [72, 53] ]", ml.toString());
+    assertEquals("[ [11, 16] ] 1:3 to [ [72, 53] ]", ml.toString());
   }
 
   @Test(groups = "Functional")
@@ -646,4 +647,147 @@ public class MapListTest
     assertEquals(79, ml.getToLowest());
     assertEquals(100, ml.getToHighest());
   }
+
+  /**
+   * Test that method that inspects for the (first) forward or reverse from
+   * range. Single position ranges are ignored.
+   */
+  @Test(groups = { "Functional" })
+  public void testIsFromForwardStrand()
+  {
+    // [3-9] declares forward strand
+    MapList ml = new MapList(new int[] { 2, 2, 3, 9, 12, 11 },
+            new int[] { 20, 11 }, 1, 1);
+    assertTrue(ml.isFromForwardStrand());
+
+    // [11-5] declares reverse strand ([13-14] is ignored)
+    ml = new MapList(new int[] { 2, 2, 11, 5, 13, 14 },
+            new int[] { 20, 11 }, 1, 1);
+    assertFalse(ml.isFromForwardStrand());
+
+    // all single position ranges - defaults to forward strand
+    ml = new MapList(new int[] { 2, 2, 4, 4, 6, 6 }, new int[] { 3, 1 }, 1,
+            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));
+  }
 }