revised RNA stem/loop processing code that copes with pseudoknots

[jalview.git] / src / jalview / io / RnamlFile.java

diff --git a/src/jalview/io/RnamlFile.java b/src/jalview/io/RnamlFile.java
index b1589b6..bc6b385 100644 (file)
--- 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;
@@ -93,16 +106,7 @@ 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());
@@ -122,10 +126,10 @@ 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 = safeName(getDataName());
+                 id = current.getName();
                  seqs[i] = new Sequence(id, seq, begin, end);
                  //System.out.println(seq);
                  System.out.println("Rna is still "+rna);