X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FRnamlFile.java;fp=src%2Fjalview%2Fio%2FRnamlFile.java;h=3041a23d525f7a1244111b3dc7c50b359b8c06d5;hb=cfd38a33612b73a5b050c9f19d0fb0d81a7b646a;hp=4d3ddc17241ba7cdd0b60123fd438e363efcc4a2;hpb=de9592c0781569ccefd4c115bb36524d6c9deaab;p=jalview.git

diff --git a/src/jalview/io/RnamlFile.java b/src/jalview/io/RnamlFile.java
index 4d3ddc1..3041a23 100644
--- a/src/jalview/io/RnamlFile.java
+++ b/src/jalview/io/RnamlFile.java
@@ -160,8 +160,10 @@ public class RnamlFile extends AlignFile
         }
       }
       sqs[i] = new Sequence(id, seq, begin, end);
-
-      sqs[i].setEnd(sqs[i].findPosition(sqs[i].getLength()));
+      if (seq.length()!=(end-begin+1))
+      {
+        sqs[i].setEnd(sqs[i].findPosition(sqs[i].getLength()));
+      }
       String[] annot = new String[rna.length()];
       Annotation[] ann = new Annotation[rna.length()];