JAL-3949 Complete new abstracted logging framework in jalview.log. Updated log calls...

[jalview.git] / src / jalview / io / vamsas / DatastoreRegistry.java

diff --git a/src/jalview/io/vamsas/DatastoreRegistry.java b/src/jalview/io/vamsas/DatastoreRegistry.java
index b58c90b..fe5a917 100644 (file)
--- a/src/jalview/io/vamsas/DatastoreRegistry.java
+++ b/src/jalview/io/vamsas/DatastoreRegistry.java
@@ -1,16 +1,35 @@
+/*
+ * 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.vamsas;
 
-import java.util.Enumeration;
 import java.util.IdentityHashMap;
 import java.util.Iterator;
 import java.util.Map;
 
-import uk.ac.vamsas.client.Vobject;
+import jalview.log.JLoggerLog4j;
 
-public class DatastoreRegistry
+public class DatastoreRegistry implements AutoCloseable
 {
-  protected static org.apache.log4j.Logger log = org.apache.log4j.Logger
-          .getLogger(DatastoreRegistry.class);
+  protected static JLoggerLog4j log = JLoggerLog4j
+          .getLogger(DatastoreRegistry.class.getCanonicalName());
 
   /**
    * map between Datastore objects and the objects they are handling- used to
@@ -66,8 +85,7 @@ public class DatastoreRegistry
     if (dsregitem == null)
     {
       // create a new item entry
-      dsregitem = new Object[]
-      { dsitem.jvobj, dsitem.vobj };
+      dsregitem = new Object[] { dsitem.jvobj, dsitem.vobj };
       dsItemReg.put(dsitem, dsregitem);
       dsObjReg.put(dsitem.jvobj, dsitem);
       dsObjReg.put(dsitem.vobj, dsitem);
@@ -136,7 +154,8 @@ public class DatastoreRegistry
     return dsregitem;
   }
 
-  protected void finalize()
+  @Override
+  public void close()
   {
     if (dsObjReg != null)
     {
@@ -155,5 +174,6 @@ public class DatastoreRegistry
     {
       dsItemReg.clear();
     }
+    // super.finalize();
   }
 }