X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FRna.java;h=9649240bc3b809dffc222199c762dbd5d18a471c;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=0d39abf39b213872ed425341dfb59558bce8518c;hpb=be762d8d9c71a7aa3121e845c45911c7192b7827;p=jalview.git

diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index 0d39abf..9649240 100644
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -198,10 +198,6 @@ public class Rna
     return pairs;
   }
 
-  
-
-  
-
   /**
    * Function to get the end position corresponding to a given start position
    * 
@@ -440,8 +436,8 @@ 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();
 
@@ -460,7 +456,6 @@ public class Rna
             break;
           }
         }
-        j -= 1;
       }
 
       // Put positions and helix information into the hashtable