JAL-2738 use GeneLocus extends DBRefEntry to hold chromosomal mappings

[jalview.git] / src / jalview / analysis / AlignmentUtils.java

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 5e11446..0bc8180 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -74,12 +74,15 @@ import java.util.TreeMap;
  */
 public class AlignmentUtils
 {
-
   private static final int CODON_LENGTH = 3;
 
   private static final String SEQUENCE_VARIANT = "sequence_variant:";
 
-  private static final String ID = "ID";
+  /*
+   * the 'id' attribute is provided for variant features fetched from
+   * Ensembl using its REST service with JSON format 
+   */
+  public static final String VARIANT_ID = "id";
 
   /**
    * A data model to hold the 'normal' base value at a position, and an optional
@@ -1867,7 +1870,7 @@ public class AlignmentUtils
       return;
     }
 
-    MapList newMap = targetToFrom.traverse(fromLoci.getMap());
+    MapList newMap = targetToFrom.traverse(fromLoci.getMapping());
 
     if (newMap != null)
     {
@@ -1888,7 +1891,7 @@ public class AlignmentUtils
    * @param seqMappings
    *          the set of mappings involving dnaSeq
    * @param aMapping
-   *          an initial candidate from seqMappings
+   *          a transcript-to-peptide mapping
    * @return
    */
   static SequenceI findCdsForProtein(List<AlignedCodonFrame> mappings,
@@ -1913,7 +1916,15 @@ public class AlignmentUtils
     if (mappedFromLength == dnaLength
             || mappedFromLength == dnaLength - CODON_LENGTH)
     {
-      return seqDss;
+      /*
+       * if sequence has CDS features, this is a transcript with no UTR
+       * - do not take this as the CDS sequence! (JAL-2789)
+       */
+      if (seqDss.getFeatures().getFeaturesByOntology(SequenceOntologyI.CDS)
+              .isEmpty())
+      {
+        return seqDss;
+      }
     }
 
     /*
@@ -1938,10 +1949,12 @@ public class AlignmentUtils
           {
             /*
             * found a 3:1 mapping to the protein product which covers
-            * the whole dna sequence i.e. is from CDS; finally check it
-            * is from the dna start sequence
+            * the whole dna sequence i.e. is from CDS; finally check the CDS
+            * is mapped from the given dna start sequence
             */
             SequenceI cdsSeq = map.getFromSeq();
+            // todo this test is weak if seqMappings contains multiple mappings;
+            // we get away with it if transcript:cds relationship is 1:1
             List<AlignedCodonFrame> dnaToCdsMaps = MappingUtils
                     .findMappingsForSequence(cdsSeq, seqMappings);
             if (!dnaToCdsMaps.isEmpty())
@@ -2056,9 +2069,11 @@ public class AlignmentUtils
   protected static List<DBRefEntry> propagateDBRefsToCDS(SequenceI cdsSeq,
           SequenceI contig, SequenceI proteinProduct, Mapping mapping)
   {
+
     // gather direct refs from contig congruent with mapping
     List<DBRefEntry> direct = new ArrayList<>();
     HashSet<String> directSources = new HashSet<>();
+
     if (contig.getDBRefs() != null)
     {
       for (DBRefEntry dbr : contig.getDBRefs())
@@ -2235,12 +2250,13 @@ public class AlignmentUtils
     int mappedDnaLength = MappingUtils.getLength(ranges);
 
     /*
-     * if not a whole number of codons, something is wrong,
-     * abort mapping
+     * if not a whole number of codons, truncate mapping
      */
-    if (mappedDnaLength % CODON_LENGTH > 0)
+    int codonRemainder = mappedDnaLength % CODON_LENGTH;
+    if (codonRemainder > 0)
     {
-      return null;
+      mappedDnaLength -= codonRemainder;
+      MappingUtils.removeEndPositions(codonRemainder, ranges);
     }
 
     int proteinLength = proteinSeq.getLength();
@@ -2562,15 +2578,15 @@ public class AlignmentUtils
             peptidePos, var.getSource());
 
     StringBuilder attributes = new StringBuilder(32);
-    String id = (String) var.variant.getValue(ID);
+    String id = (String) var.variant.getValue(VARIANT_ID);
     if (id != null)
     {
       if (id.startsWith(SEQUENCE_VARIANT))
       {
         id = id.substring(SEQUENCE_VARIANT.length());
       }
-      sf.setValue(ID, id);
-      attributes.append(ID).append("=").append(id);
+      sf.setValue(VARIANT_ID, id);
+      attributes.append(VARIANT_ID).append("=").append(id);
       // TODO handle other species variants JAL-2064
       StringBuilder link = new StringBuilder(32);
       try