X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolParser.java;fp=src%2Fjalview%2Fext%2Fjmol%2FJmolParser.java;h=beaaf79217f4f841f35a3c3745421c0a2c2ce638;hb=ff450fad8709ae81919af7a15ea382af7292794c;hp=f08e40ed7f8c964be64ad32ff0d969342636c7f5;hpb=45fa2a2d8465e302f895576a4c841578d2209cda;p=jalview.git

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index f08e40e..beaaf79 100644
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -351,10 +351,10 @@ 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')
       {