From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 5 Oct 2016 14:59:59 +0000 (+0100)
Subject: Merge branch 'develop' of http://source.jalview.org/git/jalview into develop
X-Git-Tag: Release_2_10_0~10^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=23819c49b73c64e6c2bc45059d47919b7d49575b;hp=e5ff0544866ec954e311b7401f5c3989c0016a5e;p=jalview.git

Merge branch 'develop' of source.jalview.org/git/jalview into develop
---

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);
       }
     }