X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FRna.java;h=0d39abf39b213872ed425341dfb59558bce8518c;hb=bab4b08733a9543bdce5c0b9d1c32ca7d18ad9e3;hp=34233f0c3000c8e3b31e7f88b5d059df434e5256;hpb=516567645c306018e92e4556a8c120b3b2cdbc60;p=jalview.git

diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index 34233f0..0d39abf 100644
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -49,7 +49,8 @@ public class Rna
    */
   public static boolean isOpeningParenthesis(char c)
   {
-    return ('A' <= c && c <= 'Z' || c == '(' || c == '[' || c == '{' || c == '<');
+    return ('A' <= c && c <= 'Z' || c == '(' || c == '[' || c == '{'
+            || c == '<');
   }
 
   /**
@@ -74,7 +75,8 @@ public class Rna
    */
   public static boolean isClosingParenthesis(char c)
   {
-    return ('a' <= c && c <= 'z' || c == ')' || c == ']' || c == '}' || c == '>');
+    return ('a' <= c && c <= 'z' || c == ')' || c == ']' || c == '}'
+            || c == '>');
   }
 
   /**
@@ -160,8 +162,8 @@ public class Rna
         if (!stacks.containsKey(opening))
         {
           throw new WUSSParseException(MessageManager.formatMessage(
-                  "exception.mismatched_unseen_closing_char",
-                  new String[] { String.valueOf(base) }), i);
+                  "exception.mismatched_unseen_closing_char", new String[]
+                  { String.valueOf(base) }), i);
         }
 
         Stack<Integer> stack = stacks.get(opening);
@@ -169,8 +171,8 @@ public class Rna
         {
           // error whilst parsing i'th position. pass back
           throw new WUSSParseException(MessageManager.formatMessage(
-                  "exception.mismatched_closing_char",
-                  new String[] { String.valueOf(base) }), i);
+                  "exception.mismatched_closing_char", new String[]
+                  { String.valueOf(base) }), i);
         }
         int temp = stack.pop();
 
@@ -188,9 +190,9 @@ public class Rna
          * i (length of input string)
          */
         throw new WUSSParseException(MessageManager.formatMessage(
-                "exception.mismatched_opening_char",
-                new String[] { String.valueOf(opening),
-                    String.valueOf(stack.pop()) }), i);
+                "exception.mismatched_opening_char", new String[]
+                { String.valueOf(opening), String.valueOf(stack.pop()) }),
+                i);
       }
     }
     return pairs;
@@ -466,7 +468,7 @@ public class Rna
       helices.put(close, helix);
 
       // Record helix as featuregroup
-      result.add(new SequenceFeature("RNA helix", "", "", open, close,
+      result.add(new SequenceFeature("RNA helix", "", open, close,
               String.valueOf(helix)));
 
       lastopen = open;