X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureSettings.java;h=de9d231a63894928aa8081f58014a71a26bb43ba;hb=d053a3c980cf4318b9a19a255f9fc870e74de989;hp=4a0ae160dfe288a58e35ec846b960bed6a30fc3a;hpb=34286266321abbbab6d462c39f500650f9c860c9;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index 4a0ae16..de9d231 100755
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -291,15 +291,15 @@ public class FeatureSettings extends Panel implements ItemListener,
     SequenceFeature[] tmpfeatures;
     String group = null, type;
     Vector visibleChecks = new Vector();
-
-    for (int i = 0; i < av.alignment.getHeight(); i++)
+    AlignmentI alignment=av.getAlignment();
+    for (int i = 0; i < alignment.getHeight(); i++)
     {
-      if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
+      if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
       {
         continue;
       }
 
-      tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+      tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
       int index = 0;
       while (index < tmpfeatures.length)
       {