Merge branch 'releases/Release_2_10_4_Branch' into develop

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

diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java
index 95d7efe..1acc9e1 100644 (file)
--- a/test/jalview/util/MapListTest.java
+++ b/test/jalview/util/MapListTest.java
@@ -816,4 +816,155 @@ public class MapListTest
     assertEquals(1, merged.size());
     assertArrayEquals(new int[] { 9, 0 }, merged.get(0));
   }
+
+  /**
+   * Test the method that compounds ('traverses') two mappings
+   */
+  @Test(groups = "Functional")
+  public void testTraverse()
+  {
+    /*
+     * simple 1:1 plus 1:1 forwards
+     */
+    MapList ml1 = new MapList(new int[] { 3, 4, 8, 12 }, new int[] { 5, 8,
+        11, 13 }, 1, 1);
+    MapList ml2 = new MapList(new int[] { 1, 50 }, new int[] { 40, 45, 70,
+        75, 90, 127 }, 1, 1);
+    MapList compound = ml1.traverse(ml2);
+
+    assertEquals(compound.getFromRatio(), 1);
+    assertEquals(compound.getToRatio(), 1);
+    List<int[]> fromRanges = compound.getFromRanges();
+    assertEquals(fromRanges.size(), 2);
+    assertArrayEquals(new int[] { 3, 4 }, fromRanges.get(0));
+    assertArrayEquals(new int[] { 8, 12 }, fromRanges.get(1));
+    List<int[]> toRanges = compound.getToRanges();
+    assertEquals(toRanges.size(), 2);
+    // 5-8 maps to 44-45,70-71
+    // 11-13 maps to 74-75,90
+    assertArrayEquals(new int[] { 44, 45, 70, 71 }, toRanges.get(0));
+    assertArrayEquals(new int[] { 74, 75, 90, 90 }, toRanges.get(1));
+
+    /*
+     * 1:1 over 1:1 backwards ('reverse strand')
+     */
+    ml1 = new MapList(new int[] { 1, 50 }, new int[] { 70, 119 }, 1, 1);
+    ml2 = new MapList(new int[] { 1, 500 },
+            new int[] { 1000, 901, 600, 201 }, 1, 1);
+    compound = ml1.traverse(ml2);
+
+    assertEquals(compound.getFromRatio(), 1);
+    assertEquals(compound.getToRatio(), 1);
+    fromRanges = compound.getFromRanges();
+    assertEquals(fromRanges.size(), 1);
+    assertArrayEquals(new int[] { 1, 50 }, fromRanges.get(0));
+    toRanges = compound.getToRanges();
+    assertEquals(toRanges.size(), 1);
+    assertArrayEquals(new int[] { 931, 901, 600, 582 }, toRanges.get(0));
+
+    /*
+     * 1:1 plus 1:3 should result in 1:3
+     */
+    ml1 = new MapList(new int[] { 1, 30 }, new int[] { 11, 40 }, 1, 1);
+    ml2 = new MapList(new int[] { 1, 100 }, new int[] { 1, 50, 91, 340 },
+            1, 3);
+    compound = ml1.traverse(ml2);
+
+    assertEquals(compound.getFromRatio(), 1);
+    assertEquals(compound.getToRatio(), 3);
+    fromRanges = compound.getFromRanges();
+    assertEquals(fromRanges.size(), 1);
+    assertArrayEquals(new int[] { 1, 30 }, fromRanges.get(0));
+    // 11-40 maps to 31-50,91-160
+    toRanges = compound.getToRanges();
+    assertEquals(toRanges.size(), 1);
+    assertArrayEquals(new int[] { 31, 50, 91, 160 }, toRanges.get(0));
+
+    /*
+     * 3:1 plus 1:1 should result in 3:1
+     */
+    ml1 = new MapList(new int[] { 1, 30 }, new int[] { 11, 20 }, 3, 1);
+    ml2 = new MapList(new int[] { 1, 100 }, new int[] { 1, 15, 91, 175 },
+            1, 1);
+    compound = ml1.traverse(ml2);
+
+    assertEquals(compound.getFromRatio(), 3);
+    assertEquals(compound.getToRatio(), 1);
+    fromRanges = compound.getFromRanges();
+    assertEquals(fromRanges.size(), 1);
+    assertArrayEquals(new int[] { 1, 30 }, fromRanges.get(0));
+    // 11-20 maps to 11-15, 91-95
+    toRanges = compound.getToRanges();
+    assertEquals(toRanges.size(), 1);
+    assertArrayEquals(new int[] { 11, 15, 91, 95 }, toRanges.get(0));
+
+    /*
+     * 1:3 plus 3:1 should result in 1:1
+     */
+    ml1 = new MapList(new int[] { 21, 40 }, new int[] { 13, 72 }, 1, 3);
+    ml2 = new MapList(new int[] { 1, 300 }, new int[] { 51, 70, 121, 200 },
+            3, 1);
+    compound = ml1.traverse(ml2);
+
+    assertEquals(compound.getFromRatio(), 1);
+    assertEquals(compound.getToRatio(), 1);
+    fromRanges = compound.getFromRanges();
+    assertEquals(fromRanges.size(), 1);
+    assertArrayEquals(new int[] { 21, 40 }, fromRanges.get(0));
+    // 13-72 maps 3:1 to 55-70, 121-124
+    toRanges = compound.getToRanges();
+    assertEquals(toRanges.size(), 1);
+    assertArrayEquals(new int[] { 55, 70, 121, 124 }, toRanges.get(0));
+
+    /*
+     * 3:1 plus 1:3 should result in 1:1
+     */
+    ml1 = new MapList(new int[] { 31, 90 }, new int[] { 13, 32 }, 3, 1);
+    ml2 = new MapList(new int[] { 11, 40 }, new int[] { 41, 50, 71, 150 },
+            1, 3);
+    compound = ml1.traverse(ml2);
+
+    assertEquals(compound.getFromRatio(), 1);
+    assertEquals(compound.getToRatio(), 1);
+    fromRanges = compound.getFromRanges();
+    assertEquals(fromRanges.size(), 1);
+    assertArrayEquals(new int[] { 31, 90 }, fromRanges.get(0));
+    // 13-32 maps to 47-50,71-126
+    toRanges = compound.getToRanges();
+    assertEquals(toRanges.size(), 1);
+    assertArrayEquals(new int[] { 47, 50, 71, 126 }, toRanges.get(0));
+
+    /*
+     * method returns null if not all regions are mapped through
+     */
+    ml1 = new MapList(new int[] { 1, 50 }, new int[] { 101, 150 }, 1, 1);
+    ml2 = new MapList(new int[] { 131, 180 }, new int[] { 201, 250 }, 1, 3);
+    compound = ml1.traverse(ml2);
+    assertNull(compound);
+  }
+
+  /**
+   * Test that method that inspects for the (first) forward or reverse 'to' range.
+   * Single position ranges are ignored.
+   */
+  @Test(groups = { "Functional" })
+  public void testIsToForwardsStrand()
+  {
+    // [3-9] declares forward strand
+    MapList ml = new MapList(new int[] { 20, 11 },
+            new int[]
+            { 2, 2, 3, 9, 12, 11 }, 1, 1);
+    assertTrue(ml.isToForwardStrand());
+
+    // [11-5] declares reverse strand ([13-14] is ignored)
+    ml = new MapList(new int[] { 20, 11 },
+            new int[]
+            { 2, 2, 11, 5, 13, 14 }, 1, 1);
+    assertFalse(ml.isToForwardStrand());
+
+    // all single position ranges - defaults to forward strand
+    ml = new MapList(new int[] { 3, 1 }, new int[] { 2, 2, 4, 4, 6, 6 }, 1,
+            1);
+    assertTrue(ml.isToForwardStrand());
+  }
 }