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JAL-1140 use the Reader provided by the jalview.io.FileParse framework
author
jprocter
<jprocter@compbio.dundee.ac.uk>
Mon, 20 Aug 2012 15:04:10 +0000
(16:04 +0100)
committer
jprocter
<jprocter@compbio.dundee.ac.uk>
Mon, 20 Aug 2012 15:07:58 +0000
(16:07 +0100)
src/jalview/io/RnamlFile.java
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diff --git
a/src/jalview/io/RnamlFile.java
b/src/jalview/io/RnamlFile.java
index
b1589b6
..
c93201f
100644
(file)
--- 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
{
@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());
System.out.println("this is the secondary scructure:" +result.size());
//System.out.println("this is the secondary scructure:" +result.toString());