From d5c5166fcfbdaec2297d68e1e47a869e3bf2049b Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 28 Oct 2011 15:06:39 +0100
Subject: [PATCH] use stack rather than vector and throw parse exceptions

---
 src/jalview/analysis/Rna.java |   16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index ca3c6d5..ba18732 100644
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -24,6 +24,7 @@ package jalview.analysis;
 
 import java.util.ArrayList;
 import java.util.Hashtable;
+import java.util.Stack;
 import java.util.Vector;
 
 import jalview.datamodel.SequenceFeature;
@@ -43,11 +44,9 @@ 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;
@@ -57,14 +56,18 @@ 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);        
       }
@@ -187,3 +190,4 @@ public class Rna
     }
   }
 }
+
-- 
1.7.10.2