Merge branch 'develop' into features/JAL-2446NCList

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

diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java
index fe396ce..328b96a 100644 (file)
--- 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();
@@ -176,7 +176,7 @@ 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);
       }
@@ -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++;
@@ -530,9 +531,8 @@ public class Mapping
         SequenceFeature[] vf = new SequenceFeature[frange.length / 2];
         for (int i = 0, v = 0; i < frange.length; i += 2, v++)
         {
-          vf[v] = new SequenceFeature(f);
-          vf[v].setBegin(frange[i]);
-          vf[v].setEnd(frange[i + 1]);
+          vf[v] = new SequenceFeature(f, frange[i], frange[i + 1],
+                  f.getFeatureGroup(), f.getScore());
           if (frange.length > 2)
           {
             vf[v].setDescription(f.getDescription() + "\nPart " + (v + 1));
@@ -541,27 +541,7 @@ public class Mapping
         return vf;
       }
     }
-    if (false) // else
-    {
-      int[] word = getWord(f.getBegin());
-      if (word[0] < word[1])
-      {
-        f.setBegin(word[0]);
-      }
-      else
-      {
-        f.setBegin(word[1]);
-      }
-      word = getWord(f.getEnd());
-      if (word[0] > word[1])
-      {
-        f.setEnd(word[0]);
-      }
-      else
-      {
-        f.setEnd(word[1]);
-      }
-    }
+
     // give up and just return the feature.
     return new SequenceFeature[] { f };
   }