X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FRnamlFile.java;h=bc6b3855c6b706730a887650c62a21c15da678f9;hb=6819474b5da8df0145cfe2c65ea9445609332c20;hp=eb2e9a85b35532cfca7ed63530cc8541a4d4ecbf;hpb=1e131ab5bca8c6799d7eb9117618d8c0e3243830;p=jalview.git

diff --git a/src/jalview/io/RnamlFile.java b/src/jalview/io/RnamlFile.java
index eb2e9a8..bc6b385 100644
--- a/src/jalview/io/RnamlFile.java
+++ b/src/jalview/io/RnamlFile.java
@@ -1,9 +1,22 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ */
 package jalview.io;
 
-
-
-
-
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.SecondaryStructureAnnotation;
@@ -113,8 +126,8 @@ public class RnamlFile extends AlignFile
 		  //System.out.println(result.get(0).getAnnotations());
 		  String seq = current.getSeq();
 	
-		  int begin=0;
-		  int end = seq.length()-1;
+		  int begin=1;
+		  int end = seq.length();
 		  
 		  id = current.getName();
 		  seqs[i] = new Sequence(id, seq, begin, end);