X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FDatastoreItem.java;h=e20f51e05b6757f06857a59c23c9082dad75553e;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=1560ad0d42dc932dfc2357e4e7ca1d6fbc849e3e;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git

diff --git a/src/jalview/io/vamsas/DatastoreItem.java b/src/jalview/io/vamsas/DatastoreItem.java
index 1560ad0..e20f51e 100644
--- a/src/jalview/io/vamsas/DatastoreItem.java
+++ b/src/jalview/io/vamsas/DatastoreItem.java
@@ -20,15 +20,15 @@
  */
 package jalview.io.vamsas;
 
-import jalview.bin.Cache;
-import jalview.io.VamsasAppDatastore;
-import jalview.util.MessageManager;
-
 import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.IdentityHashMap;
 import java.util.Vector;
 
+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;
 import uk.ac.vamsas.client.VorbaId;
@@ -60,8 +60,8 @@ public abstract class DatastoreItem
   /**
    * shared log instance
    */
-  protected static org.apache.log4j.Logger log = org.apache.log4j.Logger
-          .getLogger(DatastoreItem.class);
+  protected static JLoggerLog4j log = JLoggerLog4j
+          .getLogger(DatastoreItem.class.getCanonicalName());
 
   /**
    * note: this is taken verbatim from jalview.io.VamsasAppDatastore
@@ -74,10 +74,10 @@ public abstract class DatastoreItem
     {
       return cdoc.getObject((VorbaId) jv2vobj.get(jvobj));
     }
-    if (Cache.log.isDebugEnabled())
+    if (Cache.isDebugEnabled())
     {
-      Cache.log.debug("Returning null VorbaID binding for jalview object "
-              + jvobj);
+      Cache.debug(
+              "Returning null VorbaID binding for jalview object " + jvobj);
     }
     return null;
   }
@@ -95,8 +95,8 @@ public abstract class DatastoreItem
     if (id == null)
     {
       id = cdoc.registerObject(vobj);
-      Cache.log
-              .debug("Registering new object and returning null for getvObj2jv");
+      Cache.debug(
+              "Registering new object and returning null for getvObj2jv");
       return null;
     }
     if (vobj2jv.containsKey(vobj.getVorbaId()))
@@ -122,39 +122,38 @@ 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);
+                        : "unregisterable")
+                + " object " + vobj);
       }
     }
     if (vobj2jv.containsKey(vobj.getVorbaId())
             && !(vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
     {
-      Cache.log
-              .debug("Warning? Overwriting existing vamsas id binding for "
+      Cache.debug(
+              "Warning? Overwriting existing vamsas id binding for "
                       + vobj.getVorbaId(),
-                      new Exception(
-                              MessageManager
-                                      .getString("exception.overwriting_vamsas_id_binding")));
+              new Exception(MessageManager.getString(
+                      "exception.overwriting_vamsas_id_binding")));
     }
     else if (jv2vobj.containsKey(jvobj)
             && !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
     {
-      Cache.log
-              .debug("Warning? Overwriting existing jalview object binding for "
+      Cache.debug(
+              "Warning? Overwriting existing jalview object binding for "
                       + jvobj,
-                      new Exception(
-                              MessageManager
-                                      .getString("exception.overwriting_jalview_id_binding")));
+              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;
@@ -197,7 +196,8 @@ public abstract class DatastoreItem
     {
       throw new Error(MessageManager.formatMessage(
               "error.implementation_error_old_jalview_object_not_bound",
-              new String[] { oldjvobject.toString() }));
+              new String[]
+              { oldjvobject.toString() }));
     }
     if (newjvobject != null)
     {
@@ -236,13 +236,11 @@ public abstract class DatastoreItem
     tojalview = true;
     if (jvobj != null && !(boundType.isAssignableFrom(jvobj.getClass())))
     {
-      throw new Error(
-              MessageManager
-                      .formatMessage(
-                              "error.implementation_error_vamsas_doc_class_should_bind_to_type",
-                              new String[] { vobj.getClass().toString(),
-                                  boundType.toString(),
-                                  jvobj.getClass().toString() }));
+      throw new Error(MessageManager.formatMessage(
+              "error.implementation_error_vamsas_doc_class_should_bind_to_type",
+              new String[]
+              { vobj.getClass().toString(), boundType.toString(),
+                  jvobj.getClass().toString() }));
     }
     dsReg.registerDsObj(this);
   }
@@ -268,13 +266,11 @@ public abstract class DatastoreItem
     vobj = getjv2vObj(jvobj);
     if (vobj != null && !(boundToType.isAssignableFrom(vobj.getClass())))
     {
-      throw new Error(
-              MessageManager
-                      .formatMessage(
-                              "error.implementation_error_vamsas_doc_class_should_bind_to_type",
-                              new String[] { jvobj2.getClass().toString(),
-                                  boundToType.toString(),
-                                  vobj.getClass().toString() }));
+      throw new Error(MessageManager.formatMessage(
+              "error.implementation_error_vamsas_doc_class_should_bind_to_type",
+              new String[]
+              { jvobj2.getClass().toString(), boundToType.toString(),
+                  vobj.getClass().toString() }));
     }
     dsReg.registerDsObj(this);
   }
@@ -460,9 +456,9 @@ public abstract class DatastoreItem
     jalview.datamodel.Provenance jprov = new jalview.datamodel.Provenance();
     for (int i = 0; i < prov.getEntryCount(); i++)
     {
-      jprov.addEntry(prov.getEntry(i).getUser(), prov.getEntry(i)
-              .getAction(), prov.getEntry(i).getDate(), prov.getEntry(i)
-              .getId());
+      jprov.addEntry(prov.getEntry(i).getUser(),
+              prov.getEntry(i).getAction(), prov.getEntry(i).getDate(),
+              prov.getEntry(i).getId());
     }
 
     return jprov;