Merge branch 'develop' into trialMerge

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

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index 2ad8487..9611a4c 100644 (file)
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -194,10 +194,11 @@ public class Dna
   }
 
   /**
+   * Translates cDNA using the specified code table
    * 
    * @return
    */
-  public AlignmentI translateCdna()
+  public AlignmentI translateCdna(GeneticCodeI codeTable)
   {
     AlignedCodonFrame acf = new AlignedCodonFrame();
 
@@ -209,7 +210,7 @@ public class Dna
     for (s = 0; s < sSize; s++)
     {
       SequenceI newseq = translateCodingRegion(selection.get(s),
-              seqstring[s], acf, pepseqs);
+              seqstring[s], acf, pepseqs, codeTable);
 
       if (newseq != null)
       {
@@ -429,11 +430,12 @@ public class Dna
    * @param acf
    *          Definition of global ORF alignment reference frame
    * @param proteinSeqs
+   * @param codeTable
    * @return sequence ready to be added to alignment.
    */
   protected SequenceI translateCodingRegion(SequenceI selection,
           String seqstring, AlignedCodonFrame acf,
-          List<SequenceI> proteinSeqs)
+          List<SequenceI> proteinSeqs, GeneticCodeI codeTable)
   {
     List<int[]> skip = new ArrayList<>();
     int[] skipint = null;
@@ -466,9 +468,8 @@ public class Dna
         /*
          * Filled up a reading frame...
          */
-        AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1],
-                cdp[2]);
-        String aa = ResidueProperties.codonTranslate(new String(codon));
+        AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1], cdp[2]);
+        String aa = codeTable.translate(new String(codon));
         rf = 0;
         final String gapString = String.valueOf(gapChar);
         if (aa == null)