Merge branch 'features/JAL-1767pcaInProject' into bug/JAL-3171_maintain_datasets_acro...

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

diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java
index f3395ca..86dcc39 100644 (file)
--- a/test/jalview/util/MapListTest.java
+++ b/test/jalview/util/MapListTest.java
@@ -391,7 +391,9 @@ public class MapListTest
     MapList ml7 = new MapList(codons, protein, 3, 1); // toShifts differ
 
     assertTrue(ml.equals(ml));
+    assertEquals(ml.hashCode(), ml.hashCode());
     assertTrue(ml.equals(ml1));
+    assertEquals(ml.hashCode(), ml1.hashCode());
     assertTrue(ml1.equals(ml));
 
     assertFalse(ml.equals(null));
@@ -426,7 +428,7 @@ public class MapListTest
   @Test(groups = { "Functional" })
   public void testGetRanges()
   {
-    List<int[]> ranges = new ArrayList<int[]>();
+    List<int[]> ranges = new ArrayList<>();
     ranges.add(new int[] { 2, 3 });
     ranges.add(new int[] { 5, 6 });
     assertEquals("[2, 3, 5, 6]", Arrays.toString(MapList.getRanges(ranges)));
@@ -603,7 +605,7 @@ public class MapListTest
   public void testAddRange()
   {
     int[] range = { 1, 5 };
-    List<int[]> ranges = new ArrayList<int[]>();
+    List<int[]> ranges = new ArrayList<>();
 
     // add to empty list:
     MapList.addRange(range, ranges);
@@ -702,7 +704,7 @@ public class MapListTest
   public void testCoalesceRanges()
   {
     assertNull(MapList.coalesceRanges(null));
-    List<int[]> ranges = new ArrayList<int[]>();
+    List<int[]> ranges = new ArrayList<>();
     assertSame(ranges, MapList.coalesceRanges(ranges));
     ranges.add(new int[] { 1, 3 });
     assertSame(ranges, MapList.coalesceRanges(ranges));
@@ -763,7 +765,7 @@ public class MapListTest
   @Test(groups = { "Functional" })
   public void testCoalesceRanges_withOverlap()
   {
-    List<int[]> ranges = new ArrayList<int[]>();
+    List<int[]> ranges = new ArrayList<>();
     ranges.add(new int[] { 1, 3 });
     ranges.add(new int[] { 2, 5 });
 
@@ -818,7 +820,7 @@ public class MapListTest
   /**
    * Test the method that compounds ('traverses') two mappings
    */
-  @Test
+  @Test(groups = "Functional")
   public void testTraverse()
   {
     /*
@@ -826,22 +828,31 @@ public class MapListTest
      */
     MapList ml1 = new MapList(new int[] { 3, 4, 8, 12 }, new int[] { 5, 8,
         11, 13 }, 1, 1);
+    assertEquals("{[3, 4], [8, 12]}", prettyPrint(ml1.getFromRanges()));
+    assertEquals("{[5, 8], [11, 13]}", prettyPrint(ml1.getToRanges()));
+
     MapList ml2 = new MapList(new int[] { 1, 50 }, new int[] { 40, 45, 70,
         75, 90, 127 }, 1, 1);
+    assertEquals("{[1, 50]}", prettyPrint(ml2.getFromRanges()));
+    assertEquals("{[40, 45], [70, 75], [90, 127]}",
+            prettyPrint(ml2.getToRanges()));
+
     MapList compound = ml1.traverse(ml2);
 
-    assertEquals(compound.getFromRatio(), 1);
-    assertEquals(compound.getToRatio(), 1);
+    assertEquals(1, compound.getFromRatio());
+    assertEquals(1, compound.getToRatio());
     List<int[]> fromRanges = compound.getFromRanges();
-    assertEquals(fromRanges.size(), 2);
+    assertEquals(2, fromRanges.size());
     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);
+    assertEquals(4, toRanges.size());
     // 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));
+    assertArrayEquals(new int[] { 44, 45 }, toRanges.get(0));
+    assertArrayEquals(new int[] { 70, 71 }, toRanges.get(1));
+    assertArrayEquals(new int[] { 74, 75 }, toRanges.get(2));
+    assertArrayEquals(new int[] { 90, 90 }, toRanges.get(3));
 
     /*
      * 1:1 over 1:1 backwards ('reverse strand')
@@ -851,14 +862,15 @@ public class MapListTest
             new int[] { 1000, 901, 600, 201 }, 1, 1);
     compound = ml1.traverse(ml2);
 
-    assertEquals(compound.getFromRatio(), 1);
-    assertEquals(compound.getToRatio(), 1);
+    assertEquals(1, compound.getFromRatio());
+    assertEquals(1, compound.getToRatio());
     fromRanges = compound.getFromRanges();
-    assertEquals(fromRanges.size(), 1);
+    assertEquals(1, fromRanges.size());
     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));
+    assertEquals(2, toRanges.size());
+    assertArrayEquals(new int[] { 931, 901 }, toRanges.get(0));
+    assertArrayEquals(new int[] { 600, 582 }, toRanges.get(1));
 
     /*
      * 1:1 plus 1:3 should result in 1:3
@@ -868,15 +880,16 @@ public class MapListTest
             1, 3);
     compound = ml1.traverse(ml2);
 
-    assertEquals(compound.getFromRatio(), 1);
-    assertEquals(compound.getToRatio(), 3);
+    assertEquals(1, compound.getFromRatio());
+    assertEquals(3, compound.getToRatio());
     fromRanges = compound.getFromRanges();
-    assertEquals(fromRanges.size(), 1);
+    assertEquals(1, fromRanges.size());
     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));
+    assertEquals(2, toRanges.size());
+    assertArrayEquals(new int[] { 31, 50 }, toRanges.get(0));
+    assertArrayEquals(new int[] { 91, 160 }, toRanges.get(1));
 
     /*
      * 3:1 plus 1:1 should result in 3:1
@@ -886,15 +899,16 @@ public class MapListTest
             1, 1);
     compound = ml1.traverse(ml2);
 
-    assertEquals(compound.getFromRatio(), 3);
-    assertEquals(compound.getToRatio(), 1);
+    assertEquals(3, compound.getFromRatio());
+    assertEquals(1, compound.getToRatio());
     fromRanges = compound.getFromRanges();
-    assertEquals(fromRanges.size(), 1);
+    assertEquals(1, fromRanges.size());
     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));
+    assertEquals(2, toRanges.size());
+    assertArrayEquals(new int[] { 11, 15 }, toRanges.get(0));
+    assertArrayEquals(new int[] { 91, 95 }, toRanges.get(1));
 
     /*
      * 1:3 plus 3:1 should result in 1:1
@@ -904,15 +918,16 @@ public class MapListTest
             3, 1);
     compound = ml1.traverse(ml2);
 
-    assertEquals(compound.getFromRatio(), 1);
-    assertEquals(compound.getToRatio(), 1);
+    assertEquals(1, compound.getFromRatio());
+    assertEquals(1, compound.getToRatio());
     fromRanges = compound.getFromRanges();
-    assertEquals(fromRanges.size(), 1);
+    assertEquals(1, fromRanges.size());
     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));
+    assertEquals(2, toRanges.size());
+    assertArrayEquals(new int[] { 55, 70 }, toRanges.get(0));
+    assertArrayEquals(new int[] { 121, 124 }, toRanges.get(1));
 
     /*
      * 3:1 plus 1:3 should result in 1:1
@@ -922,14 +937,48 @@ public class MapListTest
             1, 3);
     compound = ml1.traverse(ml2);
 
-    assertEquals(compound.getFromRatio(), 1);
-    assertEquals(compound.getToRatio(), 1);
+    assertEquals(1, compound.getFromRatio());
+    assertEquals(1, compound.getToRatio());
     fromRanges = compound.getFromRanges();
-    assertEquals(fromRanges.size(), 1);
+    assertEquals(1, fromRanges.size());
     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));
+    assertEquals(2, toRanges.size());
+    assertArrayEquals(new int[] { 47, 50 }, toRanges.get(0));
+    assertArrayEquals(new int[] { 71, 126 }, toRanges.get(1));
+
+    /*
+     * 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());
   }
 }