X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FRna.java;h=3d7eab51100ee0a372ca005c7710fcc1af8c3dbb;hb=0619c67b9d65ffbe0a7ea5b2c7e12df5d125c535;hp=f2ef11887a7c1f55d334b0bb89b47a058e61d463;hpb=be415b56e8ce1bc00f5004c64793ce5d0cb17be8;p=jalview.git

diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index f2ef118..3d7eab5 100644
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -1,12 +1,13 @@
-/* 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 2.8)
+ * 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 
@@ -14,20 +15,24 @@
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
-
 /* Author: Lauren Michelle Lui 
  * Methods are based on RALEE methods http://personalpages.manchester.ac.uk/staff/sam.griffiths-jones/software/ralee/
+ * Additional Author: Jan Engelhart (2011) - Structure consensus and bug fixing
+ * Additional Author: Anne Menard (2012) - Pseudoknot support and secondary structure consensus
  * */
 
 package jalview.analysis;
 
 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 +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;
@@ -51,18 +56,22 @@ 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); 
       }
 
       i++;
@@ -76,15 +85,31 @@ 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
    * number in the 'featureGroup' member of a SequenceFeature Based off of RALEE
    * code ralee-helix-map.