X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FDatastoreItem.java;h=a65e77515b6a67bbe4601dcdafd0a84453ca59b3;hb=cb8e52fbbc5f725e3f7f48c672cdddb0690bd978;hp=f2d49e7045ee22ecfbbe6ad4d02d29aeae770c21;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git
diff --git a/src/jalview/io/vamsas/DatastoreItem.java b/src/jalview/io/vamsas/DatastoreItem.java
index f2d49e7..a65e775 100644
--- a/src/jalview/io/vamsas/DatastoreItem.java
+++ b/src/jalview/io/vamsas/DatastoreItem.java
@@ -1,38 +1,37 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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.
- *
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.vamsas;
-import jalview.bin.Cache;
-import jalview.datamodel.DBRefEntry;
-import jalview.gui.TreePanel;
-import jalview.io.VamsasAppDatastore;
-
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.IdentityHashMap;
import java.util.Vector;
-import org.apache.commons.logging.Log;
-
+import jalview.bin.Console;
+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;
-import uk.ac.vamsas.objects.core.DbRef;
import uk.ac.vamsas.objects.core.Entry;
import uk.ac.vamsas.objects.core.Provenance;
import uk.ac.vamsas.objects.core.Seg;
@@ -61,8 +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
@@ -75,10 +74,10 @@ public abstract class DatastoreItem
{
return cdoc.getObject((VorbaId) jv2vobj.get(jvobj));
}
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.debug("Returning null VorbaID binding for jalview object "
- + jvobj);
+ Console.debug(
+ "Returning null VorbaID binding for jalview object " + jvobj);
}
return null;
}
@@ -96,8 +95,8 @@ public abstract class DatastoreItem
if (id == null)
{
id = cdoc.registerObject(vobj);
- Cache.log
- .debug("Registering new object and returning null for getvObj2jv");
+ Console.debug(
+ "Registering new object and returning null for getvObj2jv");
return null;
}
if (vobj2jv.containsKey(vobj.getVorbaId()))
@@ -123,35 +122,38 @@ public abstract class DatastoreItem
if (id == null || vobj.getVorbaId() == null
|| cdoc.getObject(id) != vobj)
{
- Cache.log.error("Failed to get id for "
+ Console.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(
+ Console.debug(
"Warning? Overwriting existing vamsas id binding for "
- + vobj.getVorbaId(), new Exception(
- "Overwriting vamsas id binding."));
+ + vobj.getVorbaId(),
+ new Exception(MessageManager.getString(
+ "exception.overwriting_vamsas_id_binding")));
}
else if (jv2vobj.containsKey(jvobj)
&& !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
{
- Cache.log.debug(
+ Console.debug(
"Warning? Overwriting existing jalview object binding for "
- + jvobj, new Exception(
- "Overwriting jalview object binding."));
+ + 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);
+ Console.debug("Binding " + vobj.getVorbaId() + " to " + jvobj);
vobj2jv.put(vobj.getVorbaId(), jvobj);
// JBPNote - better implementing a hybrid invertible hash.
jv2vobj.put(jvobj, vobj.getVorbaId());
@@ -169,8 +171,8 @@ public abstract class DatastoreItem
{
if (this.jvobj != null && this.vobj != null)
{
- Cache.log.debug("updating dsobj registry. ("
- + this.getClass().getName() + ")");
+ Console.debug("updating dsobj registry. (" + this.getClass().getName()
+ + ")");
}
this.jvobj = jvobj;
this.vobj = vobj;
@@ -192,15 +194,16 @@ public abstract class DatastoreItem
Object vobject = jv2vobj.remove(oldjvobject);
if (vobject == null)
{
- throw new Error(
- "IMPLEMENTATION ERROR: old jalview object is not bound ! ("
- + oldjvobject + ")");
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_old_jalview_object_not_bound",
+ new String[]
+ { oldjvobject.toString() }));
}
if (newjvobject != null)
{
jv2vobj.put(newjvobject, vobject);
vobj2jv.put(vobject, newjvobject);
- updateRegistryEntry(newjvobject, (Vobject) vobject);
+ updateRegistryEntry(newjvobject, vobj);
}
}
@@ -233,9 +236,11 @@ public abstract class DatastoreItem
tojalview = true;
if (jvobj != null && !(boundType.isAssignableFrom(jvobj.getClass())))
{
- throw new Error("Implementation Error: Vamsas Document Class "
- + vobj.getClass() + " should bind to a " + boundType
- + " (found a " + 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() }));
}
dsReg.registerDsObj(this);
}
@@ -261,9 +266,11 @@ public abstract class DatastoreItem
vobj = getjv2vObj(jvobj);
if (vobj != null && !(boundToType.isAssignableFrom(vobj.getClass())))
{
- throw new Error("Implementation Error: Jalview Class "
- + jvobj2.getClass() + " should bind to a " + boundToType
- + " (found a " + 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() }));
}
dsReg.registerDsObj(this);
}
@@ -436,8 +443,7 @@ public abstract class DatastoreItem
end = start;
start = t;
}
- return new int[]
- { start, end, pol < 0 ? 1 : 0 };
+ return new int[] { start, end, pol < 0 ? 1 : 0 };
}
/**
@@ -450,9 +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;