From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 30 Aug 2018 15:31:37 +0000 (+0100)
Subject: JAL-3092 make sure base pair counter is always moved in loop that computes the helix... 
X-Git-Tag: Release_2_10_5~39
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=47fdef81050c615ce519a0deaa8a5f4c67b83f0b;p=jalview.git

JAL-3092 make sure base pair counter is always moved in loop that computes the helix count for a strand of RNA secondary structure
---

diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index 0d39abf..e5cda93 100644
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -440,8 +440,8 @@ 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 +460,6 @@ public class Rna
             break;
           }
         }
-        j -= 1;
       }
 
       // Put positions and helix information into the hashtable