X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FRna.java;h=800e70ac7bdab45720fb1db9466e692776a8f2f4;hb=d7c00f48b00e3ede57c46ae4daf6a9203b9b6059;hp=ba18732a982dd8cad4e18aa9f828a83dddd55e8a;hpb=d5c5166fcfbdaec2297d68e1e47a869e3bf2049b;p=jalview.git

diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index ba18732..800e70a 100644
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -54,12 +54,12 @@ public class Rna
     {
       char base = line.charAt(i);
 
-      if ((base == '<') || (base == '(') || (base == '{') || (base == '['))
+      if ((base == '<') || (base == '(') || (base == '{') || (base == '[')|| (base == 'A')|| (base == 'B')|| (base == 'C')|| (base == 'D')|| (base == '1')|| (base == 'F')|| (base == 'G')|| (base == '2')|| (base == 'I')|| (base == 'J')|| (base == 'K')|| (base == 'L')|| (base == 'M')|| (base == 'N')|| (base == 'O')|| (base == 'P')|| (base == 'Q')|| (base == 'R')|| (base == 'S')|| (base == 'T')|| (base == 'U')|| (base == 'V')|| (base == 'W')|| (base == 'X')|| (base == 'Y')|| (base == 'Z'))
       {
         stack.push(i);
       }
-      else if ((base == '>') || (base == ')') || (base == '}')
-              || (base == ']'))
+      else if ((base == '>') || (base == ')') || (base == '}')|| (base == ']')|| (base == 'a')|| (base == 'b')|| (base == 'c')|| (base == 'd')|| (base == 'e')|| (base == 'f')|| (base == 'g')|| (base == 'h')|| (base == 'i')|| (base == 'j')|| (base == 'k')|| (base == 'l')|| (base == 'm')|| (base == 'n')|| (base == 'o')|| (base == 'p')|| (base == 'q')|| (base == 'r')|| (base == 's')|| (base == 't')|| (base == 'u')|| (base == 'v')|| (base == 'w')|| (base == 'x')|| (base == 'y')|| (base == 'z'))
+      
       {
 
         if (stack.isEmpty())
@@ -69,7 +69,8 @@ public class Rna
         }
         Object temp = stack.pop();
         pairs.addElement(temp);
-        pairs.addElement(i);        
+        pairs.addElement(i); 
+        //System.out.println(pairs);
       }
 
       i++;