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;
/**
* 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
{
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;
if (id == null)
{
id = cdoc.registerObject(vobj);
- Cache.log.debug(
+ Cache.debug(
"Registering new object and returning null for getvObj2jv");
return null;
}
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);
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(
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());
{
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;