JAL-1807 Bob's first commit -- Applet loaded; needs image

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

diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index e4a0d76..6b93dcb 100644 (file)
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -26,6 +26,10 @@
 
 package jalview.analysis;
 
+import jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.datamodel.SequenceFeature;
+import jalview.util.MessageManager;
+
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashSet;
@@ -33,10 +37,6 @@ import java.util.Hashtable;
 import java.util.Stack;
 import java.util.Vector;
 
-import jalview.analysis.SecStrConsensus.SimpleBP;
-import jalview.datamodel.SequenceFeature;
-import jalview.util.MessageManager;
-
 public class Rna
 {
 
@@ -58,17 +58,16 @@ public class Rna
   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;
-    {
+  private static Hashtable<Character, Character> closingToOpening = new Hashtable<Character, Character>();
+  
+  
+  static {
+    // Initializing final data structure
       for (int i = 0; i < openingPars.length; i++)
       {
-        System.out.println(closingPars[i] + "->" + openingPars[i]);
-        put(closingPars[i], openingPars[i]);
+        // System.out.println(closingPars[i] + "->" + openingPars[i]);
+        closingToOpening.put(closingPars[i], openingPars[i]);
       }
-    }
   };
 
   private static boolean isOpeningParenthesis(char c)
@@ -107,7 +106,6 @@ public class Rna
   public static Vector<SimpleBP> GetSimpleBPs(CharSequence line)
           throws WUSSParseException
   {
-    System.out.println(line);
     Hashtable<Character, Stack<Integer>> stacks = new Hashtable<Character, Stack<Integer>>();
     Vector<SimpleBP> pairs = new Vector<SimpleBP>();
     int i = 0;