From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 5 Oct 2016 14:12:01 +0000 (+0100)
Subject: JAL-1191 revert to using SequenceOntologyLite due to downstream
X-Git-Tag: Release_2_10_0~12
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5326cbb4462396e84cdbbc178040f42b436c9146;hp=-c;p=jalview.git

JAL-1191 revert to using SequenceOntologyLite due to downstream
dependencies
---

5326cbb4462396e84cdbbc178040f42b436c9146
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index ce29f01..763b10b 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -291,9 +291,10 @@ public class Jalview
     }
 
     /*
-     * configure 'full' SO model unless preferences say not to
+     * configure 'full' SO model if preferences say to, 
+     * else use the default (SO Lite)
      */
-    if (!Cache.getDefault("USE_SO_LITE", false))
+    if (Cache.getDefault("USE_FULL_SO", false))
     {
       SequenceOntologyFactory.setInstance(new SequenceOntology());
     }
diff --git a/src/jalview/io/gff/SequenceOntologyLite.java b/src/jalview/io/gff/SequenceOntologyLite.java
index 61b34ad..d46dcbe 100644
--- a/src/jalview/io/gff/SequenceOntologyLite.java
+++ b/src/jalview/io/gff/SequenceOntologyLite.java
@@ -181,9 +181,11 @@ public class SequenceOntologyLite implements SequenceOntologyI
     {
       if (!termsNotFound.contains(term))
       {
-        System.out.println("SO term " + term
-                + " not known - add to model if needed in "
-                + getClass().getName());
+        // suppress logging here as it reports Uniprot sequence features
+        // (which do not use SO terms) when auto-configuring feature colours
+        // System.out.println("SO term " + term
+        // + " not known - add to model if needed in "
+        // + getClass().getName());
         termsNotFound.add(term);
       }
     }