X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FMapping.java;h=328b96a05ae88ba1e8ec40bc6e974e32c2a16f0c;hb=e3f8846ad3af97c5b26e09f7a4e3bcc901f758ca;hp=c74160339f1023fb54aa779a226e10ccdcc5a625;hpb=b9d3d1f71c6a8aee09cd23e1303b062cbe43a239;p=jalview.git

diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java
index c741603..328b96a 100644
--- a/src/jalview/datamodel/Mapping.java
+++ b/src/jalview/datamodel/Mapping.java
@@ -46,7 +46,7 @@ public class Mapping
     /*
      * The characters of the aligned sequence e.g. "-cGT-ACgTG-"
      */
-    private final char[] alignedSeq;
+    private final SequenceI alignedSeq;
 
     /*
      * the sequence start residue
@@ -102,7 +102,7 @@ public class Mapping
      */
     public AlignedCodonIterator(SequenceI seq, char gapChar)
     {
-      this.alignedSeq = seq.getSequence();
+      this.alignedSeq = seq;
       this.start = seq.getStart();
       this.gap = gapChar;
       fromRanges = map.getFromRanges().iterator();
@@ -176,14 +176,14 @@ public class Mapping
       if (toPosition <= currentToRange[1])
       {
         SequenceI seq = Mapping.this.to;
-        char pep = seq.getSequence()[toPosition - seq.getStart()];
+        char pep = seq.getCharAt(toPosition - seq.getStart());
         toPosition++;
         return String.valueOf(pep);
       }
       if (!toRanges.hasNext())
       {
-        throw new NoSuchElementException("Ran out of peptide at position "
-                + toPosition);
+        throw new NoSuchElementException(
+                "Ran out of peptide at position " + toPosition);
       }
       currentToRange = toRanges.next();
       toPosition = currentToRange[0];
@@ -257,9 +257,10 @@ public class Mapping
        * allow for offset e.g. treat pos 8 as 2 if sequence starts at 7
        */
       int truePos = sequencePos - (start - 1);
-      while (alignedBases < truePos && alignedColumn < alignedSeq.length)
+      int length = alignedSeq.getLength();
+      while (alignedBases < truePos && alignedColumn < length)
       {
-        char c = alignedSeq[alignedColumn++];
+        char c = alignedSeq.getCharAt(alignedColumn++);
         if (c != gap && !Comparison.isGap(c))
         {
           alignedBases++;
@@ -666,8 +667,8 @@ public class Mapping
         to[f * 2] = r[0];
         to[f * 2 + 1] = r[1];
       }
-      copy.setMap(new MapList(from, to, map.getFromRatio(), map
-              .getToRatio()));
+      copy.setMap(
+              new MapList(from, to, map.getFromRatio(), map.getToRatio()));
     }
     return copy;
   }
@@ -714,7 +715,8 @@ public class Mapping
    * @param gapChar
    * @return
    */
-  public Iterator<AlignedCodon> getCodonIterator(SequenceI seq, char gapChar)
+  public Iterator<AlignedCodon> getCodonIterator(SequenceI seq,
+          char gapChar)
   {
     return new AlignedCodonIterator(seq, gapChar);
   }
@@ -725,8 +727,8 @@ public class Mapping
   @Override
   public String toString()
   {
-    return String.format("%s %s", this.map.toString(), this.to == null ? ""
-            : this.to.getName());
+    return String.format("%s %s", this.map.toString(),
+            this.to == null ? "" : this.to.getName());
   }
 
   /**