X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FMapping.java;h=5a4689db423f2b35e1fc5251bb8a1492b6b01a62;hb=3fade939d6e42625c486678ef8df8accc4aa9ca5;hp=a0a050fd7beed934d076a6951ce2f1314f3063e7;hpb=5133de48f4251fa73eedcda66d6e2f2c25ff876b;p=jalview.git

diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java
index a0a050f..5a4689d 100644
--- a/src/jalview/datamodel/Mapping.java
+++ b/src/jalview/datamodel/Mapping.java
@@ -20,6 +20,7 @@
  */
 package jalview.datamodel;
 
+import jalview.util.Comparison;
 import jalview.util.MapList;
 
 import java.util.Iterator;
@@ -258,7 +259,8 @@ public class Mapping
       int truePos = sequencePos - (start - 1);
       while (alignedBases < truePos && alignedColumn < alignedSeq.length)
       {
-        if (alignedSeq[alignedColumn++] != gap)
+        char c = alignedSeq[alignedColumn++];
+        if (c != gap && !Comparison.isGap(c))
         {
           alignedBases++;
         }
@@ -528,9 +530,8 @@ 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());
           if (frange.length > 2)
           {
             vf[v].setDescription(f.getDescription() + "\nPart " + (v + 1));
@@ -539,27 +540,7 @@ 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 };
   }