JAL-1620 version bump and release notes

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

diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index 4c05ece..05573d7 100644 (file)
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 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;
@@ -33,9 +37,6 @@ import java.util.Hashtable;
 import java.util.Stack;
 import java.util.Vector;
 
-import jalview.analysis.SecStrConsensus.SimpleBP;
-import jalview.datamodel.SequenceFeature;
-
 public class Rna
 {
 
@@ -64,7 +65,7 @@ public class Rna
     {
       for (int i = 0; i < openingPars.length; i++)
       {
-        System.out.println(closingPars[i] + "->" + openingPars[i]);
+        // System.out.println(closingPars[i] + "->" + openingPars[i]);
         put(closingPars[i], openingPars[i]);
       }
     }
@@ -85,9 +86,7 @@ public class Rna
   {
     if (!isClosingParenthesis(closingParenthesis))
     {
-      throw new WUSSParseException(
-              "Querying matching opening parenthesis for non-closing parenthesis character "
-                      + closingParenthesis, -1);
+      throw new WUSSParseException(MessageManager.formatMessage("exception.querying_matching_opening_parenthesis_for_non_closing_parenthesis", new String[]{new StringBuffer(closingParenthesis).toString()}), -1);
     }
 
     return closingToOpening.get(closingParenthesis);
@@ -108,7 +107,6 @@ 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;
@@ -132,16 +130,14 @@ public class Rna
 
         if (!stacks.containsKey(opening))
         {
-          throw new WUSSParseException(
-                  "Mismatched (unseen) closing character " + base, i);
+          throw new WUSSParseException(MessageManager.formatMessage("exception.mismatched_unseen_closing_char", new String[]{new StringBuffer(base).toString()}), i);
         }
 
         Stack<Integer> stack = stacks.get(opening);
         if (stack.isEmpty())
         {
           // error whilst parsing i'th position. pass back
-          throw new WUSSParseException("Mismatched closing character "
-                  + base, i);
+          throw new WUSSParseException(MessageManager.formatMessage("exception.mismatched_closing_char", new String[]{new StringBuffer(base).toString()}), i);
         }
         int temp = stack.pop();
 
@@ -154,8 +150,7 @@ public class Rna
       Stack<Integer> stack = stacks.get(opening);
       if (!stack.empty())
       {
-        throw new WUSSParseException("Mismatched opening character "
-                + opening + " at " + stack.pop(), i);
+        throw new WUSSParseException(MessageManager.formatMessage("exception.mismatched_opening_char", new String[]{new StringBuffer(opening).toString(),Integer.valueOf(stack.pop()).toString()}), i);
       }
     }
     return pairs;