X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;h=d1217bfa2d67c2303c777e532b642c360ea5cc65;hb=948bd3bcbacc509da0cefaae3eedd97300a6ccce;hp=aa1a98b98dd4a91d7f2811e89da76b9997b29a09;hpb=241bd0223b016b5ad5ec78520310a8de32842722;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index aa1a98b..d1217bf 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -1888,7 +1888,7 @@ 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 +1913,15 @@ 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 +1946,12 @@ 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 +2066,11 @@ 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 +2247,13 @@ 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();
@@ -2430,11 +2443,14 @@ public class AlignmentUtils
         {
           for (String base : alleles.split(","))
           {
-            if (!base1.equals(base))
+            if (!base1.equalsIgnoreCase(base))
             {
-              String codon = base + base2 + base3;
+              String codon = base.toUpperCase() + base2.toLowerCase()
+                      + base3.toLowerCase();
+              String canonical = base1.toUpperCase() + base2.toLowerCase()
+                      + base3.toLowerCase();
               if (addPeptideVariant(peptide, peptidePos, residue, var,
-                      codon))
+                      codon, canonical))
               {
                 count++;
               }
@@ -2456,11 +2472,14 @@ public class AlignmentUtils
         {
           for (String base : alleles.split(","))
           {
-            if (!base2.equals(base))
+            if (!base2.equalsIgnoreCase(base))
             {
-              String codon = base1 + base + base3;
+              String codon = base1.toLowerCase() + base.toUpperCase()
+                      + base3.toLowerCase();
+              String canonical = base1.toLowerCase() + base2.toUpperCase()
+                      + base3.toLowerCase();
               if (addPeptideVariant(peptide, peptidePos, residue, var,
-                      codon))
+                      codon, canonical))
               {
                 count++;
               }
@@ -2482,11 +2501,14 @@ public class AlignmentUtils
         {
           for (String base : alleles.split(","))
           {
-            if (!base3.equals(base))
+            if (!base3.equalsIgnoreCase(base))
             {
-              String codon = base1 + base2 + base;
+              String codon = base1.toLowerCase() + base2.toLowerCase()
+                      + base.toUpperCase();
+              String canonical = base1.toLowerCase() + base2.toLowerCase()
+                      + base3.toUpperCase();
               if (addPeptideVariant(peptide, peptidePos, residue, var,
-                      codon))
+                      codon, canonical))
               {
                 count++;
               }
@@ -2509,10 +2531,13 @@ public class AlignmentUtils
    * @param residue
    * @param var
    * @param codon
+   *          the variant codon e.g. aCg
+   * @param canonical
+   *          the 'normal' codon e.g. aTg
    * @return true if a feature was added, else false
    */
   static boolean addPeptideVariant(SequenceI peptide, int peptidePos,
-          String residue, DnaVariant var, String codon)
+          String residue, DnaVariant var, String codon, String canonical)
   {
     /*
      * get peptide translation of codon e.g. GAT -> D
@@ -2527,7 +2552,7 @@ public class AlignmentUtils
     {
       return false;
     }
-    String desc = codon;
+    String desc = canonical + "/" + codon;
     String featureType = "";
     if (trans.equals(residue))
     {