JAL-3763 test coverage for AlignedCodonFrame.markMappedRegion

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 0f6a5f3..a9875b4 100644 (file)
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -383,7 +383,8 @@ public class AlignedCodonFrame
 
   /**
    * Add search results for regions in other sequences that translate or are
-   * translated from a particular position in seq
+   * translated from a particular position in seq (which may be an aligned or
+   * dataset sequence)
    * 
    * @param seq
    * @param index
@@ -395,6 +396,10 @@ public class AlignedCodonFrame
           SearchResultsI results)
   {
     SequenceI ds = seq.getDatasetSequence();
+    if (ds == null)
+    {
+      ds = seq;
+    }
     for (SequenceToSequenceMapping ssm : mappings)
     {
       ssm.markMappedRegion(ds, index, results);

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index 0074d2a..6b067c8 100755 (executable)
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -329,8 +329,10 @@ public class SearchResults implements SearchResultsI
   }
 
   /**
-   * Two SearchResults are considered equal if they contain the same matches in
-   * the same order.
+   * Two SearchResults are considered equal if they contain the same matches
+   * (Sequence, start position, end position) in the same order
+   * 
+   * @see Match#equals(Object)
    */
   @Override
   public boolean equals(Object obj)

diff --git a/test/jalview/datamodel/AlignedCodonFrameTest.java b/test/jalview/datamodel/AlignedCodonFrameTest.java
index e3fa027..0cfc380 100644 (file)
--- a/test/jalview/datamodel/AlignedCodonFrameTest.java
+++ b/test/jalview/datamodel/AlignedCodonFrameTest.java
@@ -100,52 +100,67 @@ public class AlignedCodonFrameTest
   public void testGetMappedRegion()
   {
     // introns lower case, exons upper case
-    final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T");
-    seq1.createDatasetSequence();
-    final Sequence seq2 = new Sequence("Seq2", "-TA-gG-Gg-CG-a");
-    seq2.createDatasetSequence();
+    final Sequence dna1 = new Sequence("Seq1/10-18", "c-G-TA-gC-gT-T");
+    dna1.createDatasetSequence();
+    final Sequence dna2 = new Sequence("Seq2/20-28", "-TA-gG-Gg-CG-a");
+    dna2.createDatasetSequence();
 
-    final Sequence aseq1 = new Sequence("Seq1", "-P-R");
-    aseq1.createDatasetSequence();
-    final Sequence aseq2 = new Sequence("Seq2", "-LY-Q");
-    aseq2.createDatasetSequence();
+    final Sequence pep1 = new Sequence("Seq1/3-4", "-P-R");
+    pep1.createDatasetSequence();
+    final Sequence pep2 = new Sequence("Seq2/7-9", "-LY-Q");
+    pep2.createDatasetSequence();
 
     /*
      * First with no mappings
      */
     AlignedCodonFrame acf = new AlignedCodonFrame();
 
-    assertNull(acf.getMappedRegion(seq1, aseq1, 1));
+    assertNull(acf.getMappedRegion(dna1, pep1, 3));
 
     /*
      * Set up the mappings for the exons (upper-case bases)
      * Note residue Q is unmapped
      */
-    MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 }, new int[] {
-        1, 2 }, 3, 1);
-    acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
-    map = new MapList(new int[] { 1, 2, 4, 5, 7, 8 }, new int[] { 1, 2 },
+    MapList map1 = new MapList(new int[] { 11, 13, 15, 15, 17, 18 }, new int[] {
+        3, 4 }, 3, 1);
+    acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map1);
+    MapList map2 = new MapList(new int[] { 20, 21, 23, 24, 26, 27 }, new int[] { 7, 9 },
             3, 1);
-    acf.addMap(seq2.getDatasetSequence(), aseq2.getDatasetSequence(), map);
+    acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map2);
 
-    assertArrayEquals(new int[] { 2, 4 },
-            acf.getMappedRegion(seq1, aseq1, 1));
-    assertArrayEquals(new int[] { 6, 6, 8, 9 },
-            acf.getMappedRegion(seq1, aseq1, 2));
-    assertArrayEquals(new int[] { 1, 2, 4, 4 },
-            acf.getMappedRegion(seq2, aseq2, 1));
-    assertArrayEquals(new int[] { 5, 5, 7, 8 },
-            acf.getMappedRegion(seq2, aseq2, 2));
+    /*
+     * get codon positions for peptide position
+     */
+    assertArrayEquals(new int[] { 11, 13 },
+            acf.getMappedRegion(dna1, pep1, 3));
+    assertArrayEquals(new int[] { 15, 15, 17, 18 },
+            acf.getMappedRegion(dna1, pep1, 4));
+    assertArrayEquals(new int[] { 20, 21, 23, 23 },
+            acf.getMappedRegion(dna2, pep2, 7));
+    assertArrayEquals(new int[] { 24, 24, 26, 27 },
+            acf.getMappedRegion(dna2, pep2, 8));
 
     /*
-     * No mapping from seq2 to Q
+     * No mapping from dna2 to Q
      */
-    assertNull(acf.getMappedRegion(seq2, aseq2, 3));
+    assertNull(acf.getMappedRegion(dna2, pep2, 9));
 
     /*
-     * No mapping from sequence 1 to sequence 2
+     * No mapping from dna1 to pep2
+     */
+    assertNull(acf.getMappedRegion(dna1, pep2, 7));
+    
+    /*
+     * get peptide position for codon position
      */
-    assertNull(acf.getMappedRegion(seq1, aseq2, 1));
+    assertArrayEquals(new int[] { 3, 3 },
+            acf.getMappedRegion(pep1, dna1, 11));
+    assertArrayEquals(new int[] { 3, 3 },
+            acf.getMappedRegion(pep1, dna1, 12));
+    assertArrayEquals(new int[] { 3, 3 },
+            acf.getMappedRegion(pep1, dna1, 13));
+    assertNull(acf.getMappedRegion(pep1, dna1, 14)); // intron base, not mapped
+
   }
 
   @Test(groups = { "Functional" })
@@ -545,4 +560,92 @@ public class AlignedCodonFrameTest
     mapping = acf.getCoveringMapping(cds2,  pep);
     assertNotNull(mapping);
   }
+
+  /**
+   * Test the method that adds mapped positions to SearchResults
+   */
+  @Test(groups = { "Functional" })
+  public void testMarkMappedRegion()
+  {
+    // introns lower case, exons upper case
+    final Sequence dna1 = new Sequence("Seq1/10-18", "c-G-TA-gC-gT-T");
+    dna1.createDatasetSequence();
+    final Sequence dna2 = new Sequence("Seq2/20-28", "-TA-gG-Gg-CG-a");
+    dna2.createDatasetSequence();
+  
+    final Sequence pep1 = new Sequence("Seq1/3-4", "-P-R");
+    pep1.createDatasetSequence();
+    final Sequence pep2 = new Sequence("Seq2/7-9", "-LY-Q");
+    pep2.createDatasetSequence();
+  
+    /*
+     * First with no mappings
+     */
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+    SearchResults sr = new SearchResults();
+    acf.markMappedRegion(dna1, 12, sr);
+    assertTrue(sr.isEmpty());
+  
+    /*
+     * Set up the mappings for the exons (upper-case bases)
+     * Note residue Q is unmapped
+     */
+    MapList map1 = new MapList(new int[] { 11, 13, 15, 15, 17, 18 }, new int[] {
+        3, 4 }, 3, 1);
+    acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map1);
+    MapList map2 = new MapList(new int[] { 20, 21, 23, 24, 26, 27 }, new int[] { 7, 8 },
+            3, 1);
+    acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map2);
+    
+    /*
+     * intron bases are not mapped
+     */
+    acf.markMappedRegion(dna1, 10, sr);
+    assertTrue(sr.isEmpty());
+  
+    /*
+     * Q is not mapped
+     */
+    acf.markMappedRegion(pep2, 9, sr);
+    assertTrue(sr.isEmpty());
+
+    /*
+     * mark peptide position for exon position (of aligned sequence)
+     */
+    acf.markMappedRegion(dna1, 11, sr);
+    SearchResults expected = new SearchResults();
+    expected.addResult(pep1.getDatasetSequence(),  3, 3);
+    assertEquals(sr, expected);
+
+    /*
+     * mark peptide position for exon position of dataset sequence - same result
+     */
+    sr = new SearchResults();
+    acf.markMappedRegion(dna1.getDatasetSequence(), 11, sr);
+    assertEquals(sr, expected);
+    
+    /*
+     * marking the same position a second time should not create a duplicate match
+     */
+    acf.markMappedRegion(dna1.getDatasetSequence(), 12, sr);
+    assertEquals(sr, expected);
+    
+    /*
+     * mark exon positions for peptide position (of aligned sequence)
+     */
+    sr = new SearchResults();
+    acf.markMappedRegion(pep2, 7, sr); // codon positions 20, 21, 23
+    expected = new SearchResults();
+    expected.addResult(dna2.getDatasetSequence(),  20, 21);
+    expected.addResult(dna2.getDatasetSequence(),  23, 23);
+    assertEquals(sr, expected);
+    
+    /*
+     * add another codon to the same SearchResults
+     */
+    acf.markMappedRegion(pep1.getDatasetSequence(), 4, sr); // codon positions 15, 17, 18
+    expected.addResult(dna1.getDatasetSequence(),  15, 15);
+    expected.addResult(dna1.getDatasetSequence(),  17, 18);
+    assertEquals(sr, expected);
+  }
 }