update author list in license for (JAL-826)

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

diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index 69a228b..66bccb9 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.
  * 
@@ -21,6 +22,7 @@
 
 package jalview.analysis;
 
+import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.Vector;
 
@@ -28,6 +30,7 @@ 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
@@ -62,7 +65,7 @@ public class Rna
         Object temp = stack.lastElement();
         stack.remove(stack.size() - 1);
         pairs.addElement(temp);
-        pairs.addElement(i);
+        pairs.addElement(i);        
       }
 
       i++;
@@ -76,13 +79,30 @@ 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 +179,6 @@ public class Rna
 
       // Record helix as featuregroup
       pairs[i].setFeatureGroup(Integer.toString(helix));
-      pairs[i].setFeatureGroup(Integer.toString(helix));
 
       lastopen = open;
       lastclose = close;