X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fanalysis%2FRna.java;h=0157b9144a43786cc64e57f47d638cb50f3e14e2;hb=85299bc2db43c8b108169661ebc1c4d9b2d3d2e5;hp=0d39abf39b213872ed425341dfb59558bce8518c;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git

diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index 0d39abf..0157b91 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
    * 
@@ -425,8 +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
       /*
@@ -440,12 +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))
         {
@@ -460,7 +458,6 @@ public class Rna
             break;
           }
         }
-        j -= 1;
       }
 
       // Put positions and helix information into the hashtable