X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FRna.java;h=ba18732a982dd8cad4e18aa9f828a83dddd55e8a;hb=7796bc87c98b21f199f9dc195401223984619091;hp=69a228ba8ac0496fb8f5c42bacdc1f35341fc48a;hpb=323a457c9d0643be2406b6661246e8e988c0d0f6;p=jalview.git

diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index 69a228b..ba18732 100644
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -1,5 +1,6 @@
-/* Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -21,13 +22,16 @@
 
 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();
   /**
    * 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
@@ -40,10 +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;
@@ -53,16 +56,20 @@ 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++;
@@ -76,13 +83,30 @@ 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);
+
     }
 
     return outPairs;
   }
+  
+  
+  /**
+   * Function to get the end position corresponding to a given start position
+   * @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);
+  }*/
+  
 
   /**
    * Figures out which helix each position belongs to and stores the helix
@@ -159,7 +183,6 @@ public class Rna
 
       // Record helix as featuregroup
       pairs[i].setFeatureGroup(Integer.toString(helix));
-      pairs[i].setFeatureGroup(Integer.toString(helix));
 
       lastopen = open;
       lastclose = close;
@@ -167,3 +190,4 @@ public class Rna
     }
   }
 }
+