temp push

[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..2ba41da 100644 (file)
--- a/src/jalview/io/gff/SequenceOntologyFactory.java
+++ b/src/jalview/io/gff/SequenceOntologyFactory.java
@@ -1,21 +1,81 @@
+/*
+ * 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;
 
-public class SequenceOntologyFactory
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+
+/**
+ * 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
+ * setSequenceOntology() can be used to set full Ontology data.
+ * 
+ * @author gmcarstairs
+ *
+ */
+public class SequenceOntologyFactory implements ApplicationSingletonI
 {
-  private static SequenceOntologyI instance;
+  /**
+   * Answers an instance of this class for the current application context. Note
+   * that this supports running two JS 'applets' on the same page, one with the
+   * full Sequence Ontology (USE_FULL_SO = true) and one with a hard-coded
+   * subset (USE_FULL_SO = false). If this is overkill, could change this method
+   * to just return a common static instance.
+   * 
+   * @return
+   */
+  private static synchronized SequenceOntologyFactory getInstance()
+  {
+    return (SequenceOntologyFactory) ApplicationSingletonProvider
+            .getInstance(SequenceOntologyFactory.class);
+  }
+
+  /**
+   * Answers the configured model of the Sequence Ontology.
+   * 
+   * @return
+   */
+  public static synchronized SequenceOntologyI getSequenceOntology()
+  {
+    SequenceOntologyFactory f = getInstance();
+    return (f.sequenceOntology == null
+            ? f.sequenceOntology = new SequenceOntologyLite()
+            : f.sequenceOntology);
+  }
 
-  public static synchronized SequenceOntologyI getInstance()
+  /**
+   * For testng only
+   * 
+   * @param so
+   */
+  public static void setSequenceOntology(SequenceOntologyI so)
   {
-    if (instance == null)
-    {
-      // instance = new SequenceOntology();
-      instance = new SequenceOntologyLite();
-    }
-    return instance;
+    getInstance().sequenceOntology = so;
   }
 
-  public static void setInstance(SequenceOntologyI so)
+  private SequenceOntologyI sequenceOntology;
+
+  private SequenceOntologyFactory()
   {
-    instance = so;
+    // private singleton
   }
+
 }