X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FRna.java;h=0157b9144a43786cc64e57f47d638cb50f3e14e2;hb=85299bc2db43c8b108169661ebc1c4d9b2d3d2e5;hp=3108ef3de319eb34aec6a6f42f389f7274e59322;hpb=b9d3d1f71c6a8aee09cd23e1303b062cbe43a239;p=jalview.git

diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index 3108ef3..0157b91 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();
 
@@ -188,18 +190,14 @@ 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;
   }
 
-  
-
-  
-
   /**
    * Function to get the end position corresponding to a given start position
    * 
@@ -423,8 +421,9 @@ public class Rna
       final int open = basePair.getBP5();
       final int close = basePair.getBP3();
 
-      // System.out.println("open " + open + " close " + close);
-      // System.out.println("lastclose " + lastclose + " lastopen " + lastopen);
+      // jalview.bin.Console.outPrintln("open " + open + " close " + close);
+      // jalview.bin.Console.outPrintln("lastclose " + lastclose + " lastopen "
+      // + lastopen);
 
       // we're moving from right to left based on closing pair
       /*
@@ -438,12 +437,13 @@ public class Rna
       /*
        * catch things like <<..<<..>>..<<..>>>> |
        */
-      int j = bps.size() - 1;
-      while (j >= 0)
+      int j = bps.size();
+      while (--j >= 0)
       {
         int popen = bps.get(j).getBP5();
 
-        // System.out.println("j " + j + " popen " + popen + " lastopen "
+        // jalview.bin.Console.outPrintln("j " + j + " popen " + popen + "
+        // lastopen "
         // +lastopen + " open " + open);
         if ((popen < lastopen) && (popen > open))
         {
@@ -458,7 +458,6 @@ public class Rna
             break;
           }
         }
-        j -= 1;
       }
 
       // Put positions and helix information into the hashtable