JAL-3725 helper methods for computing mapped feature range overlap

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

diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java
index 71fbdfd..6bbda78 100644 (file)
--- a/test/jalview/util/MapListTest.java
+++ b/test/jalview/util/MapListTest.java
@@ -44,7 +44,7 @@ public class MapListTest
   {
     Cache.initLogger();
   }
-  
+
   @BeforeClass(alwaysRun = true)
   public void setUpJvOptionPane()
   {
@@ -303,6 +303,85 @@ public class MapListTest
   }
 
   /**
+   * Tests for method that locates the overlap of the ranges in the 'from' map
+   * for given range in the 'to' map
+   */
+  @Test(groups = { "Functional" })
+  public void testGetOverlapsInFrom_withIntrons()
+  {
+    /*
+     * Exons at positions [2, 3, 5] [6, 7, 9] [10, 12, 14] [16, 17, 18] i.e.
+     * 2-3, 5-7, 9-10, 12-12, 14-14, 16-18
+     */
+    int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
+    int[] protein = { 11, 14 };
+    MapList ml = new MapList(codons, protein, 3, 1);
+
+    assertEquals("[2, 3, 5, 5]",
+            Arrays.toString(ml.getOverlapsInFrom(11, 11)));
+    assertEquals("[2, 3, 5, 7, 9, 9]",
+            Arrays.toString(ml.getOverlapsInFrom(11, 12)));
+    // out of range 5' :
+    assertEquals("[2, 3, 5, 7, 9, 9]",
+            Arrays.toString(ml.getOverlapsInFrom(8, 12)));
+    // out of range 3' :
+    assertEquals("[10, 10, 12, 12, 14, 14, 16, 18]",
+            Arrays.toString(ml.getOverlapsInFrom(13, 16)));
+    // out of range both :
+    assertEquals("[2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18]",
+            Arrays.toString(ml.getOverlapsInFrom(1, 16)));
+    // no overlap:
+    assertNull(ml.getOverlapsInFrom(20, 25));
+  }
+
+  /**
+   * Tests for method that locates the overlap of the ranges in the 'to' map
+   * for given range in the 'from' map
+   */
+  @Test(groups = { "Functional" })
+  public void testGetOverlapsInTo_withIntrons()
+  {
+    /*
+     * Exons at positions [2, 3, 5] [6, 7, 9] [10, 12, 14] [17, 18, 19] i.e.
+     * 2-3, 5-7, 9-10, 12-12, 14-14, 17-19
+     */
+    int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 17, 19 };
+    /*
+     * Mapped proteins at positions 1, 3, 4, 6 in the sequence
+     */
+    int[] protein = { 1, 1, 3, 4, 6, 6 };
+    MapList ml = new MapList(codons, protein, 3, 1);
+
+    /*
+     * Can't map from an unmapped position
+     */
+    assertNull(ml.getOverlapsInTo(1, 1));
+    assertNull(ml.getOverlapsInTo(4, 4));
+    assertNull(ml.getOverlapsInTo(15, 16));
+    
+    /*
+     * nor from a range that includes no mapped position (exon)
+     */
+    assertNull(ml.getOverlapsInTo(15, 16));
+
+    // end of codon 1 maps to first peptide
+    assertEquals("[1, 1]", Arrays.toString(ml.getOverlapsInTo(2, 2)));
+    // end of codon 1 and start of codon 2 maps to first 2 peptides
+    assertEquals("[1, 1, 3, 3]", Arrays.toString(ml.getOverlapsInTo(3, 7)));
+
+    // range overlaps 5' end of dna:
+    assertEquals("[1, 1, 3, 3]", Arrays.toString(ml.getOverlapsInTo(1, 6)));
+   assertEquals("[1, 1, 3, 3]", Arrays.toString(ml.getOverlapsInTo(1, 8)));
+
+    // range overlaps 3' end of dna:
+    assertEquals("[6, 6]", Arrays.toString(ml.getOverlapsInTo(17, 24)));
+    assertEquals("[6, 6]", Arrays.toString(ml.getOverlapsInTo(16, 24)));
+    
+    // dna positions 8, 11 are intron but include end of exon 2 and start of exon 3
+    assertEquals("[3, 4]", Arrays.toString(ml.getOverlapsInTo(8, 11)));
+  }
+
+  /**
    * Tests for method that locates ranges in the 'to' map for given range in the
    * 'from' map.
    */
@@ -596,7 +675,8 @@ public class MapListTest
   public void testAddMapList_sameMap()
   {
     MapList ml = new MapList(new int[] { 11, 15, 20, 25, 35, 30 },
-            new int[] { 72, 22 }, 1, 3);
+            new int[]
+            { 72, 22 }, 1, 3);
     String before = ml.toString();
     ml.addMapList(ml);
     assertEquals(before, ml.toString());