revised RNA stem/loop processing code that copes with pseudoknots

diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index 3d7eab5..c5207f7 100644 (file)
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -23,16 +23,60 @@
 
 package jalview.analysis;
 
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.Stack;
 import java.util.Vector;
 
+
+import jalview.analysis.SecStrConsensus.SimpleBP;
 import jalview.datamodel.SequenceFeature;
 
 public class Rna
 {
-  static Hashtable<Integer, Integer> pairHash = new Hashtable();
+       
+       static Hashtable<Integer, Integer> pairHash = new Hashtable();
+       
+  private static final Character[] openingPars = {'(','[','{','<','A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z'}; 
+  private static final Character[] closingPars = {')',']','}','>','a','b','c','d','e','f','g','h','i','j','k','l','m','n','o','p','q','r','s','t','u','v','w','x','y','z'}; 
+  
+  private static HashSet<Character> openingParsSet = new HashSet<Character>(Arrays.asList(openingPars)); 
+  private static HashSet<Character> closingParsSet = new HashSet<Character>(Arrays.asList(closingPars));
+  private static Hashtable<Character,Character> closingToOpening = new Hashtable<Character,Character>()
+  // Initializing final data structure
+  {
+       private static final long serialVersionUID = 1L;
+       {
+         for(int i=0;i<openingPars.length;i++)
+         {
+                 System.out.println(closingPars[i]+"->"+openingPars[i]);
+                 put(closingPars[i],openingPars[i]);             
+         }
+  }};
+       
+  private static boolean isOpeningParenthesis(char c)
+  {
+         return openingParsSet.contains(c);
+  }
+       
+  private static boolean isClosingParenthesis(char c)
+  {
+         return closingParsSet.contains(c);
+  }
 
+  private static char matchingOpeningParenthesis(char closingParenthesis) throws WUSSParseException
+  {
+         if (!isClosingParenthesis(closingParenthesis))
+         {
+                 throw new WUSSParseException("Querying matching opening parenthesis for non-closing parenthesis character "+closingParenthesis, -1);
+         }
+       
+         return closingToOpening.get(closingParenthesis);
+  }
+  
   /**
    * 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
@@ -45,69 +89,89 @@ public class Rna
    * @return Array of SequenceFeature; type = RNA helix, begin is open base
    *         pair, end is close base pair
    */
-  public static SequenceFeature[] GetBasePairs(CharSequence line)
-          throws WUSSParseException
+  public static Vector<SimpleBP> GetSimpleBPs(CharSequence line) throws WUSSParseException
   {
-    Stack stack = new Stack();
-    Vector pairs = new Vector();
-
+    System.out.println(line);
+       Hashtable<Character,Stack<Integer>> stacks = new Hashtable<Character,Stack<Integer>>();
+    Vector<SimpleBP> pairs = new Vector<SimpleBP>();
     int i = 0;
     while (i < line.length())
     {
       char base = line.charAt(i);
-
-      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'))
+     
+      if (isOpeningParenthesis(base))
       {
-        stack.push(i);
+         if (!stacks.containsKey(base)){
+                 stacks.put(base, new Stack<Integer>());
+         }
+        stacks.get(base).push(i);
+       
       }
-      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'))
-      
+      else if (isClosingParenthesis(base))
       {
-
+       
+         char opening = matchingOpeningParenthesis(base);
+         
+         if (!stacks.containsKey(opening)){
+                 throw new WUSSParseException("Mismatched (unseen) closing character "+base, i);
+         }
+         
+        Stack<Integer> stack = stacks.get(opening);
         if (stack.isEmpty())
         {
           // error whilst parsing i'th position. pass back
-          throw new WUSSParseException("Mismatched closing bracket", i);
+                 throw new WUSSParseException("Mismatched closing character "+base, i);
         }
-        Object temp = stack.pop();
-        pairs.addElement(temp);
-        pairs.addElement(i); 
+        int temp = stack.pop();
+        
+        pairs.add(new SimpleBP(temp,i));
       }
-
       i++;
     }
-
-    int numpairs = pairs.size() / 2;
-    SequenceFeature[] outPairs = new SequenceFeature[numpairs];
-
-    // Convert pairs to array
-    for (int p = 0; p < pairs.size(); p += 2)
+    for(char opening: stacks.keySet())
     {
-      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,
-              end, "");
-      // pairHash.put(begin, end);
-
+       Stack<Integer> stack = stacks.get(opening);
+       if (!stack.empty())
+       {
+                 throw new WUSSParseException("Mismatched opening character "+opening+" at "+stack.pop(), i);                  
+       }
+    }
+    return pairs;
+  }
+  
+  public static SequenceFeature[] GetBasePairs(CharSequence line) throws WUSSParseException
+  {
+         Vector<SimpleBP> bps = GetSimpleBPs(line);
+         SequenceFeature[] outPairs = new SequenceFeature[bps.size()];
+    for (int p = 0; p < bps.size(); p++)
+    {
+       SimpleBP bp = bps.elementAt(p);
+       outPairs[p] = new SequenceFeature("RNA helix", "", "", bp.getBP5(),bp.getBP3(), "");
     }
-
     return outPairs;
   }
-
+  
+  
+  public static  ArrayList<SimpleBP> GetModeleBP(CharSequence line) throws WUSSParseException
+  {
+         Vector<SimpleBP> bps = GetSimpleBPs(line);
+         return new ArrayList<SimpleBP>(bps);
+  }
+  
+  
   /**
    * 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
@@ -191,3 +255,4 @@ public class Rna
     }
   }
 }
+