From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Sat, 17 Nov 2012 21:02:51 +0000 (+0000)
Subject: sequence numbering from 1
X-Git-Tag: Jalview_2_9~265^2~12
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4e5806da22df848f52f8a4d9b72d7945cac1fbce;p=jalview.git

sequence numbering from 1
---

diff --git a/src/jalview/io/RnamlFile.java b/src/jalview/io/RnamlFile.java
index da64607..bc6b385 100644
--- a/src/jalview/io/RnamlFile.java
+++ b/src/jalview/io/RnamlFile.java
@@ -126,8 +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);