X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignedCodonFrame.java;h=0f6a5f3ac0c307556bd126029bcdf19664c53a98;hb=34cd990de2acbfc60802d2ab0c869481749a2406;hp=5240f0cf7bb1bbdc035c3e8e46bfe3622ac7b75c;hpb=b3ab81b9e34fbb6de969ec0c3230c887661c3b48;p=jalview.git

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 5240f0c..0f6a5f3 100644
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -402,40 +402,6 @@ public class AlignedCodonFrame
   }
 
   /**
-   * Returns the DNA codon positions (base 1) for the given position (base 1) in
-   * a mapped protein sequence, or null if no mapping is found.
-   * 
-   * Intended for use in aligning cDNA to match aligned protein. Only the first
-   * mapping found is returned, so not suitable for use if multiple protein
-   * sequences are mapped to the same cDNA (but aligning cDNA as protein is
-   * ill-defined for this case anyway).
-   * 
-   * @param seq
-   *          the DNA dataset sequence
-   * @param aaPos
-   *          residue position (base 1) in a protein sequence
-   * @return
-   */
-  public int[] getDnaPosition(SequenceI seq, int aaPos)
-  {
-    /*
-     * Adapted from markMappedRegion().
-     */
-    MapList ml = null;
-    int i = 0;
-    for (SequenceToSequenceMapping ssm : mappings)
-    {
-      if (ssm.fromSeq == seq)
-      {
-        ml = getdnaToProt()[i];
-        break;
-      }
-      i++;
-    }
-    return ml == null ? null : ml.locateInFrom(aaPos, aaPos);
-  }
-
-  /**
    * Convenience method to return the first aligned sequence in the given
    * alignment whose dataset has a mapping with the given (aligned or dataset)
    * sequence.