X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FRnamlFile.java;h=f8c384d1b321677892a8e597c81de5b68f8a825d;hb=94ca0419cc7afa75b3c51917a8beaf46a7c05540;hp=4d3ddc17241ba7cdd0b60123fd438e363efcc4a2;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git

diff --git a/src/jalview/io/RnamlFile.java b/src/jalview/io/RnamlFile.java
index 4d3ddc1..f8c384d 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()];
 
@@ -210,8 +212,8 @@ public class RnamlFile extends AlignFile
   // public static void main(String[] args) {
   // Pattern p= Pattern.compile("(.+)[.][^.]+");
   // Matcher m = p.matcher("toto.xml.zip");
-  // System.out.println(m.matches());
-  // System.out.println(m.group(1));
+  // jalview.bin.Console.outPrintln(m.matches());
+  // jalview.bin.Console.outPrintln(m.group(1));
   // }
   /**
    * make a friendly ID string.