X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=ce29f0127727842246d5b49bf6a5e17b85c958ba;hb=bfe4fa22a61ee595f0d6595a3ee625c966000c6d;hp=3294c2608dcade73a6f73906befa5c33c7a648e0;hpb=3a5e7da51af0166273109f98bdf942e733105233;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 3294c26..ce29f01 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -23,6 +23,7 @@ package jalview.bin;
 import groovy.lang.Binding;
 import groovy.util.GroovyScriptEngine;
 
+import jalview.ext.so.SequenceOntology;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.PromptUserConfig;
@@ -33,6 +34,7 @@ import jalview.io.FormatAdapter;
 import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
 import jalview.io.NewickFile;
+import jalview.io.gff.SequenceOntologyFactory;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.UserColourScheme;
@@ -288,6 +290,14 @@ public class Jalview
       }
     }
 
+    /*
+     * configure 'full' SO model unless preferences say not to
+     */
+    if (!Cache.getDefault("USE_SO_LITE", false))
+    {
+      SequenceOntologyFactory.setInstance(new SequenceOntology());
+    }
+
     if (!headless)
     {
       desktop = new Desktop();