X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolParser.java;h=dc3d0eef52d3591a0bcdeafbf858ef2af27ec4ea;hb=refs%2Fheads%2Ffeatures%2FJAL-2446NCList;hp=ddf3b1a6639cfaac5b762d1c6d72b165c080906e;hpb=e327ac5df98f528afeb347ac9a79085ad0d0975b;p=jalview.git

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index ddf3b1a..dc3d0ee 100644
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -355,10 +355,10 @@ public class JmolParser extends StructureFile implements JmolStatusListener
           SequenceI sq, char[] secstr, char[] secstrcode, String chainId,
           int firstResNum)
   {
-    char[] seq = sq.getSequence();
+    int length = sq.getLength();
     boolean ssFound = false;
-    Annotation asecstr[] = new Annotation[seq.length + firstResNum - 1];
-    for (int p = 0; p < seq.length; p++)
+    Annotation asecstr[] = new Annotation[length + firstResNum - 1];
+    for (int p = 0; p < length; p++)
     {
       if (secstr[p] >= 'A' && secstr[p] <= 'z')
       {