X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FMapping.java;h=1c196bee48d6e8564f3ccae4536ab33bde89b879;hb=1389d6cb90f34bc58df11d453d3656dc9ff34bd0;hp=a0a050fd7beed934d076a6951ce2f1314f3063e7;hpb=5133de48f4251fa73eedcda66d6e2f2c25ff876b;p=jalview.git

diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java
index a0a050f..1c196be 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++;
         }