X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=61194cea9314e715c93104ca3f8e15b2fba6fc98;hb=5247711ab4a6453614e2a9fb9307e6bae6a7b4a9;hp=33596788d2bfe4c5e491372f21d02d74712ce8d2;hpb=fddf3084802b37e5cee17829e32692a4aac3e60d;p=jalview.git

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 3359678..61194ce 100644
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -47,6 +47,12 @@ import com.stevesoft.pat.Regex;
 
 public class AnnotationRenderer
 {
+  private static final int UPPER_TO_LOWER = 'a' - 'A'; // 32
+
+  private static final int CHAR_A = 'A'; // 65
+
+  private static final int CHAR_Z = 'Z'; // 90
+
   /**
    * flag indicating if timing and redraw parameter info should be output
    */
@@ -715,14 +721,14 @@ public class AnnotationRenderer
 
               }
             }
-            if (ss >= 65)
+            if (isRNA && (ss >= CHAR_A) && (ss <= CHAR_Z))
             {
               // distinguish between forward/backward base-pairing
-              if (displayChar.indexOf(ss + 32) > -1)
+              int ssLowerCase = ss + UPPER_TO_LOWER;
+              // TODO would .equals() be safer here? or charAt(0)?
+              if (displayChar.indexOf(ssLowerCase) > -1)
               {
-
-                ss = (char) (ss + 32);
-
+                ss = (char) ssLowerCase;
               }
             }