X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStructureFile.java;h=76281157dcebe3b4e966f8e4c91ad86d64ea00d1;hb=723d61f29b94cbdbe9e9398e9a31a069f20fd288;hp=5ff1a02e3b243e29d4fc7da83627f80582926310;hpb=705db65374af9295e31e695ae0643b17423fa382;p=jalview.git

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index 5ff1a02..7628115 100644
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -392,8 +392,10 @@ public abstract class StructureFile extends AlignFile
 
   public static boolean isRNA(SequenceI seq)
   {
-    for (char c : seq.getSequence())
+    int length = seq.getLength();
+    for (int i = 0; i < length; i++)
     {
+      char c = seq.getCharAt(i);
       if ((c != 'A') && (c != 'C') && (c != 'G') && (c != 'U'))
       {
         return false;
@@ -406,7 +408,8 @@ public abstract class StructureFile extends AlignFile
    * make a friendly ID string.
    * 
    * @param dataName
-   * @return truncated dataName to after last '/'
+   * @return truncated dataName to after last '/' and pruned .extension if
+   *         present
    */
   protected String safeName(String dataName)
   {