JAL-629 Change all stdout and stderr output to use Console.outPrintln and Console...

[jalview.git] / src / jalview / analysis / Rna.java

diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index 0d39abf..911ee04 100644 (file)
--- 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 +421,8 @@ 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 +436,12 @@ 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 +456,6 @@ public class Rna
             break;
           }
         }
-        j -= 1;
       }
 
       // Put positions and helix information into the hashtable