last version stay many bugs ..

[jalview.git] / src / jalview / analysis / Rna.java

diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index 69a228b..800e70a 100644 (file)
--- 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;
@@ -51,18 +54,23 @@ public class Rna
     {
       char base = line.charAt(i);
 
-      if ((base == '<') || (base == '(') || (base == '{') || (base == '['))
+      if ((base == '<') || (base == '(') || (base == '{') || (base == '[')|| (base == 'A')|| (base == 'B')|| (base == 'C')|| (base == 'D')|| (base == '1')|| (base == 'F')|| (base == 'G')|| (base == '2')|| (base == 'I')|| (base == 'J')|| (base == 'K')|| (base == 'L')|| (base == 'M')|| (base == 'N')|| (base == 'O')|| (base == 'P')|| (base == 'Q')|| (base == 'R')|| (base == 'S')|| (base == 'T')|| (base == 'U')|| (base == 'V')|| (base == 'W')|| (base == 'X')|| (base == 'Y')|| (base == 'Z'))
       {
-        stack.addElement(i);
+        stack.push(i);
       }
-      else if ((base == '>') || (base == ')') || (base == '}')
-              || (base == ']'))
+      else if ((base == '>') || (base == ')') || (base == '}')|| (base == ']')|| (base == 'a')|| (base == 'b')|| (base == 'c')|| (base == 'd')|| (base == 'e')|| (base == 'f')|| (base == 'g')|| (base == 'h')|| (base == 'i')|| (base == 'j')|| (base == 'k')|| (base == 'l')|| (base == 'm')|| (base == 'n')|| (base == 'o')|| (base == 'p')|| (base == 'q')|| (base == 'r')|| (base == 's')|| (base == 't')|| (base == 'u')|| (base == 'v')|| (base == 'w')|| (base == 'x')|| (base == 'y')|| (base == 'z'))
+      
       {
 
-        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); 
+        //System.out.println(pairs);
       }
 
       i++;
@@ -76,13 +84,30 @@ 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 +184,6 @@ 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 +191,4 @@ public class Rna
     }
   }
 }
+