X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignedCodonFrame.java;h=2f33e43ceb7ae9ceaa866fa728220fe868fcdd54;hb=36f083dc674297be2157d9f291a7cddba9d3250a;hp=5240f0cf7bb1bbdc035c3e8e46bfe3622ac7b75c;hpb=0a2ec403c08a1747b7e876f00f468867f8329d36;p=jalview.git

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 5240f0c..2f33e43 100644
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -383,7 +383,8 @@ public class AlignedCodonFrame
 
   /**
    * Add search results for regions in other sequences that translate or are
-   * translated from a particular position in seq
+   * translated from a particular position in seq (which may be an aligned or
+   * dataset sequence)
    * 
    * @param seq
    * @param index
@@ -395,44 +396,14 @@ public class AlignedCodonFrame
           SearchResultsI results)
   {
     SequenceI ds = seq.getDatasetSequence();
-    for (SequenceToSequenceMapping ssm : mappings)
+    if (ds == null)
     {
-      ssm.markMappedRegion(ds, index, results);
+      ds = seq;
     }
-  }
-
-  /**
-   * 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++;
+      ssm.markMappedRegion(ds, index, results);
     }
-    return ml == null ? null : ml.locateInFrom(aaPos, aaPos);
   }
 
   /**
@@ -872,9 +843,9 @@ public class AlignedCodonFrame
   }
 
   /**
-   * Returns the first mapping found which is between the given sequence and
-   * another, is a triplet mapping (3:1 or 1:3), and covers the full extent of
-   * both sequences involved.
+   * Returns the first mapping found which is between the given dataset sequence
+   * and another, is a triplet mapping (3:1 or 1:3), and covers the full extent
+   * of both sequences involved
    * 
    * @param seq
    * @return