JAL-1705 ensure the right mapping is used to align CDS to cDNA

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index eb1ee4b..14e3907 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -1366,12 +1366,13 @@ public class AlignmentUtils
    * Constructs an alignment consisting of the mapped (CDS) regions in the given
    * nucleotide sequences, and updates mappings to match. The CDS sequences are
    * added to the original alignment's dataset, which is shared by the new
-   * alignment.
+   * alignment. Mappings from nucleotide to CDS, and from CDS to protein, are
+   * added to the alignment dataset.
    * 
    * @param dna
    *          aligned dna sequences
    * @param mappings
-   *          from dna to protein; these are replaced with new mappings
+   *          from dna to protein
    * @param al
    * @return an alignment whose sequences are the cds-only parts of the dna
    *         sequences (or null if no mappings are found)
@@ -2093,7 +2094,7 @@ public class AlignmentUtils
     Map<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
 
     /*
-     * report any sequences that have no mapping so can't be realigned
+     * r any sequences that have no mapping so can't be realigned
      */
     unmapped.addAll(unaligned.getSequences());
 
@@ -2106,7 +2107,7 @@ public class AlignmentUtils
         SequenceI fromSeq = mapping.findAlignedSequence(seq, aligned);
         if (fromSeq != null)
         {
-          Mapping seqMap = mapping.getMappingForSequence(seq);
+          Mapping seqMap = mapping.getMappingBetween(fromSeq, seq);
           if (addMappedPositions(seq, fromSeq, seqMap, map))
           {
             unmapped.remove(seq);
@@ -2137,6 +2138,11 @@ public class AlignmentUtils
   static boolean addMappedPositions(SequenceI seq, SequenceI fromSeq,
           Mapping seqMap, Map<Integer, Map<SequenceI, Character>> map)
   {
+    if (seqMap == null)
+    {
+      return false;
+    }
+
     char[] fromChars = fromSeq.getSequence();
     int toStart = seq.getStart();
     char[] toChars = seq.getSequence();
@@ -2193,4 +2199,19 @@ public class AlignmentUtils
     }
     return true;
   }
+
+  // strictly temporary hack until proper criteria for aligning protein to cds
+  // are in place; this is so Ensembl -> fetch xrefs Uniprot aligns the Uniprot
+  public static boolean looksLikeEnsembl(AlignmentI alignment)
+  {
+    for (SequenceI seq : alignment.getSequences())
+    {
+      String name = seq.getName();
+      if (!name.startsWith("ENSG") && !name.startsWith("ENST"))
+      {
+        return false;
+      }
+    }
+    return true;
+  }
 }

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index a56f1d4..6d6cdb5 100644 (file)
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -649,4 +649,29 @@ public class AlignedCodonFrame
   {
     return mappings == null ? "null" : mappings.toString();
   }
+
+  /**
+   * Returns the first mapping found that is from 'fromSeq' to 'toSeq', or null
+   * if none found
+   * 
+   * @param fromSeq
+   *          aligned or dataset sequence
+   * @param toSeq
+   *          aligned or dataset sequence
+   * @return
+   */
+  public Mapping getMappingBetween(SequenceI fromSeq, SequenceI toSeq)
+  {
+    for (SequenceToSequenceMapping mapping : mappings)
+    {
+      SequenceI from = mapping.fromSeq;
+      SequenceI to = mapping.mapping.to;
+      if ((from == fromSeq || from == fromSeq.getDatasetSequence())
+              && (to == toSeq || to == toSeq.getDatasetSequence()))
+      {
+        return mapping.mapping;
+      }
+    }
+    return null;
+  }
 }

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d161cfd..d1f3421 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -4779,8 +4779,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                * pending getting Embl transcripts to 'align', 
                * we are only doing this for Ensembl
                */
-              // TODO want to do this also when fetching UNIPROT for Ensembl
-              if (DBRefSource.ENSEMBL.equalsIgnoreCase(source))
+              // TODO proper criteria for 'can align as cdna'
+              if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
+                      || AlignmentUtils.looksLikeEnsembl(alignment))
               {
                 copyAlignment.alignAs(alignment);
                 copyAlignmentIsAligned = true;

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 3d3736f..7ccbf97 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -50,6 +50,7 @@ import java.util.Iterator;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.TreeMap;
 
 import org.testng.annotations.Test;
 
@@ -1953,7 +1954,65 @@ public class AlignmentUtilsTests
      */
     dna.addCodonFrame(acf);
     AlignmentUtils.alignAs(cds, dna);
-    assertEquals("---GGGTTT---", cds.getSequenceAt(0).getSequenceAsString());
+    assertEquals("---GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
     assertEquals("CCC------AAA", cds.getSequenceAt(1).getSequenceAsString());
   }
+
+  @Test(groups = { "Functional" })
+  public void testAddMappedPositions()
+  {
+    SequenceI from = new Sequence("dna", "ggAA-ATcc-TT-g");
+    SequenceI seq1 = new Sequence("cds", "AAATTT");
+    from.createDatasetSequence();
+    seq1.createDatasetSequence();
+    Mapping mapping = new Mapping(seq1, new MapList(
+            new int[] { 3, 6, 9, 10 },
+            new int[] { 1, 6 }, 1, 1));
+    Map<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
+    AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
+
+    /*
+     * verify map has seq1 residues in columns 3,4,6,7,11,12
+     */
+    assertEquals(6, map.size());
+    assertEquals('A', map.get(3).get(seq1).charValue());
+    assertEquals('A', map.get(4).get(seq1).charValue());
+    assertEquals('A', map.get(6).get(seq1).charValue());
+    assertEquals('T', map.get(7).get(seq1).charValue());
+    assertEquals('T', map.get(11).get(seq1).charValue());
+    assertEquals('T', map.get(12).get(seq1).charValue());
+
+    /*
+     * 
+     */
+  }
+
+  /**
+   * Test case where the mapping 'from' range includes a stop codon which is
+   * absent in the 'to' range
+   */
+  @Test(groups = { "Functional" })
+  public void testAddMappedPositions_withStopCodon()
+  {
+    SequenceI from = new Sequence("dna", "ggAA-ATcc-TT-g");
+    SequenceI seq1 = new Sequence("cds", "AAATTT");
+    from.createDatasetSequence();
+    seq1.createDatasetSequence();
+    Mapping mapping = new Mapping(seq1, new MapList(
+            new int[] { 3, 6, 9, 10 },
+            new int[] { 1, 6 }, 1, 1));
+    Map<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
+    AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
+  
+    /*
+     * verify map has seq1 residues in columns 3,4,6,7,11,12
+     */
+    assertEquals(6, map.size());
+    assertEquals('A', map.get(3).get(seq1).charValue());
+    assertEquals('A', map.get(4).get(seq1).charValue());
+    assertEquals('A', map.get(6).get(seq1).charValue());
+    assertEquals('T', map.get(7).get(seq1).charValue());
+    assertEquals('T', map.get(11).get(seq1).charValue());
+    assertEquals('T', map.get(12).get(seq1).charValue());
+  }
 }