X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignedCodon.java;h=345099a473aa99b325b828bb4c2d1f885684a7df;hb=3ab582bfeeab1563bedf60e97994e63e672d2e31;hp=f88d5a6a467a8fcc3860a399354637b2b42f6c99;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git

diff --git a/src/jalview/datamodel/AlignedCodon.java b/src/jalview/datamodel/AlignedCodon.java
index f88d5a6..345099a 100644
--- a/src/jalview/datamodel/AlignedCodon.java
+++ b/src/jalview/datamodel/AlignedCodon.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
  * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -27,32 +27,38 @@ package jalview.datamodel;
  * 
  * Example: in "G-AT-C-GA" the aligned codons are (0, 2, 3) and (5, 7, 8).
  * 
- * JBPComment: Is this useful anywhere other than jalview.analysis.Dna ?
- * 
  * @author gmcarstairs
  *
  */
 public final class AlignedCodon
 {
+  // base 1 aligned sequence position (base 0)
   public final int pos1;
 
+  // base 2 aligned sequence position (base 0)
   public final int pos2;
 
+  // base 3 aligned sequence position (base 0)
   public final int pos3;
 
+  // peptide aligned sequence position (base 0)
+  public final int peptideCol;
+
+  // peptide coded for by this codon
   public final String product;
 
   public AlignedCodon(int i, int j, int k)
   {
-    this(i, j, k, null);
+    this(i, j, k, null, 0);
   }
 
-  public AlignedCodon(int i, int j, int k, String prod)
+  public AlignedCodon(int i, int j, int k, String prod, int prodCol)
   {
     pos1 = i;
     pos2 = j;
     pos3 = k;
     product = prod;
+    peptideCol = prodCol;
   }
 
   /**