Merge branch 'develop' into menard

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

diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index 800e70a..1583f84 100644 (file)
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -1,13 +1,13 @@
 /*
- * 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
+ * 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 
@@ -15,14 +15,12 @@
  * 
  * 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/
  * */
 
 package jalview.analysis;
 
-import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.Stack;
 import java.util.Vector;
@@ -31,7 +29,8 @@ import jalview.datamodel.SequenceFeature;
 
 public class Rna
 {
-       static Hashtable<Integer, Integer> pairHash = new Hashtable();
+  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
@@ -44,7 +43,8 @@ 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 SequenceFeature[] GetBasePairs(CharSequence line)
+          throws WUSSParseException
   {
     Stack stack = new Stack();
     Vector pairs = new Vector();
@@ -70,7 +70,6 @@ public class Rna
         Object temp = stack.pop();
         pairs.addElement(temp);
         pairs.addElement(i); 
-        //System.out.println(pairs);
       }
 
       i++;
@@ -84,30 +83,29 @@ 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);
+      // 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
+   * 
+   * @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
@@ -191,4 +189,3 @@ public class Rna
     }
   }
 }
-