JAL-1705 compute peptide variants from dna; add "consequence" feature on

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

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 194e6af..2311dea 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -1394,7 +1394,7 @@ public class AlignmentUtils
 
     for (Mapping seqMapping : seqMappings)
     {
-      SequenceI cds = makeCdsSequence(dnaSeq, seqMapping, newMappings);
+      SequenceI cds = makeCdsSequence(dnaSeq, seqMapping);
       cdsSequences.add(cds);
 
       /*
@@ -1507,19 +1507,16 @@ public class AlignmentUtils
 
   /**
    * Makes and returns a CDS-only sequence, where the CDS regions are identified
-   * as the 'from' ranges of the mapping on the dna. Any sequence features on
-   * the dna which overlap the CDS regions are copied to the new sequence.
+   * as the 'from' ranges of the mapping on the dna.
    * 
    * @param dnaSeq
    *          nucleotide sequence
    * @param seqMapping
    *          mappings from CDS regions of nucleotide
-   * @param exonMappings
-   *          CDS-to-peptide mapping (to add to)
    * @return
    */
   protected static SequenceI makeCdsSequence(SequenceI dnaSeq,
-          Mapping seqMapping, AlignedCodonFrame exonMappings)
+          Mapping seqMapping)
   {
     StringBuilder newSequence = new StringBuilder(dnaSeq.getLength());
     final char[] dna = dnaSeq.getSequence();
@@ -1542,6 +1539,7 @@ public class AlignmentUtils
             newSequence.toString());
 
     transferDbRefs(seqMapping.getTo(), cds);
+
     return cds;
   }