X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FRna.java;h=626e4792e3d9b029ad1189ef200485a8adc3afea;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=66bccb934c48ccc85b735bda573c99f5cb292003;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index 66bccb9..626e479 100644
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -24,13 +24,15 @@ package jalview.analysis;
 
 import java.util.ArrayList;
 import java.util.Hashtable;
+import java.util.Stack;
 import java.util.Vector;
 
 import jalview.datamodel.SequenceFeature;
 
 public class Rna
 {
-	static Hashtable<Integer, Integer> pairHash = new Hashtable();
+  static Hashtable<Integer, Integer> pairHash = new Hashtable();
+
   /**
    * Based off of RALEE code ralee-get-base-pairs. Keeps track of open bracket
    * positions in "stack" vector. When a close bracket is reached, pair this
@@ -43,10 +45,10 @@ public class Rna
    * @return Array of SequenceFeature; type = RNA helix, begin is open base
    *         pair, end is close base pair
    */
-  public static SequenceFeature[] GetBasePairs(String line)
+  public static SequenceFeature[] GetBasePairs(CharSequence line)
+          throws WUSSParseException
   {
-
-    Vector stack = new Vector();
+    Stack stack = new Stack();
     Vector pairs = new Vector();
 
     int i = 0;
@@ -56,16 +58,20 @@ public class Rna
 
       if ((base == '<') || (base == '(') || (base == '{') || (base == '['))
       {
-        stack.addElement(i);
+        stack.push(i);
       }
       else if ((base == '>') || (base == ')') || (base == '}')
               || (base == ']'))
       {
 
-        Object temp = stack.lastElement();
-        stack.remove(stack.size() - 1);
+        if (stack.isEmpty())
+        {
+          // error whilst parsing i'th position. pass back
+          throw new WUSSParseException("Mismatched closing bracket", i);
+        }
+        Object temp = stack.pop();
         pairs.addElement(temp);
-        pairs.addElement(i);        
+        pairs.addElement(i);
       }
 
       i++;
@@ -79,30 +85,29 @@ public class Rna
     {
       int begin = Integer.parseInt(pairs.elementAt(p).toString());
       int end = Integer.parseInt(pairs.elementAt(p + 1).toString());
-      
-       outPairs[p / 2] = new SequenceFeature("RNA helix", "", "", begin,
+
+      outPairs[p / 2] = new SequenceFeature("RNA helix", "", "", begin,
               end, "");
-       //pairHash.put(begin, end);
+      // pairHash.put(begin, end);
 
     }
 
     return outPairs;
   }
-  
-  
+
   /**
    * Function to get the end position corresponding to a given start position
-   * @param indice - start position of a base pair
+   * 
+   * @param indice
+   *          - start position of a base pair
    * @return - end position of a base pair
    */
-  /*makes no sense at the moment :(
-  public int findEnd(int indice){
-	  //TODO: Probably extend this to find the start to a given end?
-	  //could be done by putting everything twice to the hash
-	  ArrayList<Integer> pair = new ArrayList<Integer>();
-	  return pairHash.get(indice);
-  }*/
-  
+  /*
+   * makes no sense at the moment :( public int findEnd(int indice){ //TODO:
+   * Probably extend this to find the start to a given end? //could be done by
+   * putting everything twice to the hash ArrayList<Integer> pair = new
+   * ArrayList<Integer>(); return pairHash.get(indice); }
+   */
 
   /**
    * Figures out which helix each position belongs to and stores the helix