JAL-3253 jalview.bin.Instance streamlining

[jalview.git] / src / jalview / io / gff / SequenceOntologyFactory.java

diff --git a/src/jalview/io/gff/SequenceOntologyFactory.java b/src/jalview/io/gff/SequenceOntologyFactory.java
index 3eaa5d1..258b16a 100644 (file)
--- a/src/jalview/io/gff/SequenceOntologyFactory.java
+++ b/src/jalview/io/gff/SequenceOntologyFactory.java
@@ -1,21 +1,69 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io.gff;
 
+import jalview.bin.Instance;
+
+/**
+ * A factory class that returns a model of the Sequence Ontology. By default a
+ * hard-coded subset is used (for the applet, or testing), or setInstance() can
+ * be used to set full Ontology data.
+ * 
+ * @author gmcarstairs
+ *
+ */
 public class SequenceOntologyFactory
 {
-  private static SequenceOntologyI instance;
 
-  public static synchronized SequenceOntologyI getInstance()
+  public static synchronized SequenceOntologyI getSequenceOntology()
   {
-    if (instance == null)
-    {
-      // instance = new SequenceOntology();
-      instance = new SequenceOntologyLite();
-    }
-    return instance;
+    SequenceOntologyFactory j = getInstance();
+    return (j.sequenceOntology == null
+            ? j.sequenceOntology = new SequenceOntologyLite()
+            : j.sequenceOntology);
   }
 
+  /**
+   * For testng only
+   * 
+   * @param so
+   */
   public static void setInstance(SequenceOntologyI so)
   {
-    instance = so;
+    getInstance().sequenceOntology = so;
+  }
+
+  private SequenceOntologyI sequenceOntology;
+
+  private SequenceOntologyFactory()
+  {
+    // private singleton
   }
+
+  private static synchronized SequenceOntologyFactory getInstance()
+  {
+    Instance j = Instance.getInstance();
+    return (j.sequenceOntologyFactory == null
+            ? j.sequenceOntologyFactory = new SequenceOntologyFactory()
+            : j.sequenceOntologyFactory);
+  }
+
 }