From b4d15601e50bafd396bce2af9dded397e63cc8b8 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 5 Oct 2016 12:51:11 +0100
Subject: [PATCH] JAL-1191 use full SO in desktop application

---
 src/jalview/ext/so/SequenceOntology.java        |    5 ++++-
 src/jalview/io/gff/SequenceOntologyFactory.java |   23 +++++++++++++++++++++--
 2 files changed, 25 insertions(+), 3 deletions(-)

diff --git a/src/jalview/ext/so/SequenceOntology.java b/src/jalview/ext/so/SequenceOntology.java
index af80b7a..28ddfd9 100644
--- a/src/jalview/ext/so/SequenceOntology.java
+++ b/src/jalview/ext/so/SequenceOntology.java
@@ -77,11 +77,11 @@ public class SequenceOntology implements SequenceOntologyI
    */
   protected void loadOntologyZipFile(String ontologyFile)
   {
+    long now = System.currentTimeMillis();
     ZipInputStream zipStream = null;
     try
     {
       String zipFile = ontologyFile + ".zip";
-      System.out.println("Loading Sequence Ontology from " + zipFile);
       InputStream inStream = this.getClass().getResourceAsStream(
               "/" + zipFile);
       zipStream = new ZipInputStream(new BufferedInputStream(inStream));
@@ -93,6 +93,9 @@ public class SequenceOntology implements SequenceOntologyI
           loadOboFile(zipStream);
         }
       }
+      long elapsed = System.currentTimeMillis() - now;
+      System.out.println("Loaded Sequence Ontology from " + zipFile + " ("
+              + elapsed + "ms)");
     } catch (Exception e)
     {
       e.printStackTrace();
diff --git a/src/jalview/io/gff/SequenceOntologyFactory.java b/src/jalview/io/gff/SequenceOntologyFactory.java
index 3eaa5d1..acf90e7 100644
--- a/src/jalview/io/gff/SequenceOntologyFactory.java
+++ b/src/jalview/io/gff/SequenceOntologyFactory.java
@@ -1,5 +1,18 @@
 package jalview.io.gff;
 
+import jalview.bin.Cache;
+import jalview.ext.so.SequenceOntology;
+
+/**
+ * A factory class that returns a model of the Sequence Ontology. If the user's
+ * Jalview properties file has the line <br>
+ * USE_SO_LITE = true <br>
+ * then a hard-coded subset will be used, otherwise the full ontology (as
+ * downloaded at a point in time).
+ * 
+ * @author gmcarstairs
+ *
+ */
 public class SequenceOntologyFactory
 {
   private static SequenceOntologyI instance;
@@ -8,8 +21,14 @@ public class SequenceOntologyFactory
   {
     if (instance == null)
     {
-      // instance = new SequenceOntology();
-      instance = new SequenceOntologyLite();
+      if (Cache.getDefault("USE_SO_LITE", false))
+      {
+        instance = new SequenceOntologyLite();
+      }
+      else
+      {
+        instance = new SequenceOntology();
+      }
     }
     return instance;
   }
-- 
1.7.10.2