mungo merge

[jalview.git] / src / jalview / datamodel / Mapping.java

diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java
index 6c619ce..bd83fe9 100644 (file)
--- a/src/jalview/datamodel/Mapping.java
+++ b/src/jalview/datamodel/Mapping.java
@@ -155,8 +155,9 @@ public class Mapping
       int[] alignedCodon = getAlignedCodon(codon);
 
       String peptide = getPeptide();
+      int peptideCol = toPosition - 1 - Mapping.this.to.getStart();
       return new AlignedCodon(alignedCodon[0], alignedCodon[1],
-              alignedCodon[2], peptide);
+              alignedCodon[2], peptide, peptideCol);
     }
 
     /**
@@ -164,6 +165,8 @@ public class Mapping
      * sequence.
      * 
      * @return
+     * @throws NoSuchElementException
+     *           if the 'toRange' is exhausted (nothing to map to)
      */
     private String getPeptide()
     {
@@ -693,6 +696,7 @@ public class Mapping
    * 
    * @see java.lang.Object#finalize()
    */
+  @Override
   protected void finalize() throws Throwable
   {
     map = null;
@@ -700,9 +704,28 @@ public class Mapping
     super.finalize();
   }
 
+  /**
+   * Returns an iterator which can serve up the aligned codon column positions
+   * and their corresponding peptide products
+   * 
+   * @param seq
+   *          an aligned (i.e. possibly gapped) sequence
+   * @param gapChar
+   * @return
+   */
   public Iterator<AlignedCodon> getCodonIterator(SequenceI seq, char gapChar)
   {
     return new AlignedCodonIterator(seq, gapChar);
   }
 
+  /**
+   * Readable representation for debugging only, not guaranteed not to change
+   */
+  @Override
+  public String toString()
+  {
+    return String.format("%s %s", this.map.toString(), this.to == null ? ""
+            : this.to.getName());
+  }
+
 }