Merge branch 'Release_2_9_0b1_Branch'

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

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index d0b2731..05492e8 100644 (file)
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,12 +20,12 @@
  */
 package jalview.datamodel;
 
-import java.util.ArrayList;
-import java.util.List;
-
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
 
+import java.util.ArrayList;
+import java.util.List;
+
 /**
  * Stores mapping between the columns of a protein alignment and a DNA alignment
  * and a list of individual codon to amino acid mappings between sequences.
@@ -33,12 +33,12 @@ import jalview.util.MappingUtils;
 public class AlignedCodonFrame
 {
 
-  /*
+  /**
    * tied array of na Sequence objects.
    */
   private SequenceI[] dnaSeqs = null;
 
-  /*
+  /**
    * tied array of Mappings to protein sequence Objects and SequenceI[]
    * aaSeqs=null; MapLists where each maps from the corresponding dnaSeqs
    * element to corresponding aaSeqs element
@@ -373,7 +373,8 @@ public class AlignedCodonFrame
       if (dnaSeqs[mi] == targetDs && dnaToProt[mi].to == sourceDs)
       {
         int[] codon = dnaToProt[mi].map.locateInFrom(pos, pos);
-        if (codon != null) {
+        if (codon != null)
+        {
           return codon;
         }
       }
@@ -398,13 +399,13 @@ public class AlignedCodonFrame
       return null;
     }
     MapList ml = null;
-    char[] dnaSeq = null;
+    SequenceI dnaSeq = null;
     for (int i = 0; i < dnaToProt.length; i++)
     {
       if (dnaToProt[i].to == protein)
       {
         ml = getdnaToProt()[i];
-        dnaSeq = dnaSeqs[i].getSequence();
+        dnaSeq = dnaSeqs[i];
         break;
       }
     }
@@ -422,9 +423,10 @@ public class AlignedCodonFrame
      * Read off the mapped nucleotides (converting to position base 0)
      */
     codonPos = MappingUtils.flattenRanges(codonPos);
-    return new char[]
-    { dnaSeq[codonPos[0] - 1], dnaSeq[codonPos[1] - 1],
-        dnaSeq[codonPos[2] - 1] };
+    char[] dna = dnaSeq.getSequence();
+    int start = dnaSeq.getStart();
+    return new char[] { dna[codonPos[0] - start], dna[codonPos[1] - start],
+        dna[codonPos[2] - start] };
   }
 
   /**
@@ -444,7 +446,7 @@ public class AlignedCodonFrame
     List<SequenceI> related = new ArrayList<SequenceI>();
     SequenceI seqDs = seq.getDatasetSequence();
     seqDs = seqDs != null ? seqDs : seq;
-  
+
     for (int ds = 0; ds < dnaSeqs.length; ds++)
     {
       final Mapping mapping = dnaToProt[ds];