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

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

diff --git a/src/jalview/io/vamsas/DatastoreItem.java b/src/jalview/io/vamsas/DatastoreItem.java
index a1d8380..e20f51e 100644 (file)
--- a/src/jalview/io/vamsas/DatastoreItem.java
+++ b/src/jalview/io/vamsas/DatastoreItem.java
@@ -25,11 +25,9 @@ import java.util.Hashtable;
 import java.util.IdentityHashMap;
 import java.util.Vector;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
 import jalview.bin.Cache;
 import jalview.io.VamsasAppDatastore;
+import jalview.log.JLoggerLog4j;
 import jalview.util.MessageManager;
 import uk.ac.vamsas.client.IClientDocument;
 import uk.ac.vamsas.client.Vobject;
@@ -62,7 +60,8 @@ public abstract class DatastoreItem
   /**
    * shared log instance
    */
-  protected static Logger log = LogManager.getLogger(DatastoreItem.class);
+  protected static JLoggerLog4j log = JLoggerLog4j
+          .getLogger(DatastoreItem.class.getCanonicalName());
 
   /**
    * note: this is taken verbatim from jalview.io.VamsasAppDatastore
@@ -75,9 +74,9 @@ public abstract class DatastoreItem
     {
       return cdoc.getObject((VorbaId) jv2vobj.get(jvobj));
     }
-    if (Cache.log.isDebugEnabled())
+    if (Cache.isDebugEnabled())
     {
-      Cache.log.debug(
+      Cache.debug(
               "Returning null VorbaID binding for jalview object " + jvobj);
     }
     return null;
@@ -96,7 +95,7 @@ public abstract class DatastoreItem
     if (id == null)
     {
       id = cdoc.registerObject(vobj);
-      Cache.log.debug(
+      Cache.debug(
               "Registering new object and returning null for getvObj2jv");
       return null;
     }
@@ -123,7 +122,7 @@ public abstract class DatastoreItem
       if (id == null || vobj.getVorbaId() == null
               || cdoc.getObject(id) != vobj)
       {
-        Cache.log.error("Failed to get id for "
+        Cache.error("Failed to get id for "
                 + (vobj.isRegisterable() ? "registerable"
                         : "unregisterable")
                 + " object " + vobj);
@@ -132,7 +131,7 @@ public abstract class DatastoreItem
     if (vobj2jv.containsKey(vobj.getVorbaId())
             && !(vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
     {
-      Cache.log.debug(
+      Cache.debug(
               "Warning? Overwriting existing vamsas id binding for "
                       + vobj.getVorbaId(),
               new Exception(MessageManager.getString(
@@ -141,20 +140,20 @@ public abstract class DatastoreItem
     else if (jv2vobj.containsKey(jvobj)
             && !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
     {
-      Cache.log.debug(
+      Cache.debug(
               "Warning? Overwriting existing jalview object binding for "
                       + jvobj,
               new Exception(MessageManager.getString(
                       "exception.overwriting_jalview_id_binding")));
     }
     /*
-     * Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id "
+     * Cache.error("Attempt to make conflicting object binding! "+vobj+" id "
      * +vobj.getVorbaId()+" already bound to "+getvObj2jv(vobj)+" and "+jvobj+"
      * already bound to "+getjv2vObj(jvobj),new Exception("Excessive call to
      * bindjvvobj")); }
      */
     // we just update the hash's regardless!
-    Cache.log.debug("Binding " + vobj.getVorbaId() + " to " + jvobj);
+    Cache.debug("Binding " + vobj.getVorbaId() + " to " + jvobj);
     vobj2jv.put(vobj.getVorbaId(), jvobj);
     // JBPNote - better implementing a hybrid invertible hash.
     jv2vobj.put(jvobj, vobj.getVorbaId());
@@ -172,8 +171,8 @@ public abstract class DatastoreItem
   {
     if (this.jvobj != null && this.vobj != null)
     {
-      Cache.log.debug("updating dsobj registry. ("
-              + this.getClass().getName() + ")");
+      Cache.debug("updating dsobj registry. (" + this.getClass().getName()
+              + ")");
     }
     this.jvobj = jvobj;
     this.vobj = vobj;