From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Mon, 20 Aug 2012 15:04:10 +0000 (+0100)
Subject: JAL-1140 use the Reader provided by the jalview.io.FileParse framework
X-Git-Tag: Jalview_2_9~265^2~37
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b1fba751ea5ad4f84c71e3d2c388a6e650c8a8e2;p=jalview.git

JAL-1140 use the Reader provided by the jalview.io.FileParse framework
---

diff --git a/src/jalview/io/RnamlFile.java b/src/jalview/io/RnamlFile.java
index b1589b6..c93201f 100644
--- a/src/jalview/io/RnamlFile.java
+++ b/src/jalview/io/RnamlFile.java
@@ -93,16 +93,7 @@ public class RnamlFile extends AlignFile
 	@SuppressWarnings("unchecked")
 	public void parse() throws FileNotFoundException, ExceptionPermissionDenied, ExceptionLoadingFailed, ExceptionFileFormatOrSyntax
 	{
-		 FileReader fr = null;
-		  fr = new FileReader(inFile); 
-		  
-		  BufferedReader r = new BufferedReader (fr);
-	
-		  //ArrayList<String> seq =new ArrayList();
-		  //System.out.println(r);
-		   
-		  
-		 result = RNAFactory.loadSecStrRNAML(r);
+		 result = RNAFactory.loadSecStrRNAML(getReader());
 		  
 		 System.out.println("this is the secondary scructure:" +result.size());
 		  //System.out.println("this is the secondary scructure:" +result.toString());