X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FDatastoreItem.java;h=11c7e91f82a945781f56044ce6a446eae56a42ff;hb=a23cc416cd520ac6dec6052591575b264f5d25bc;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..11c7e91 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 jalview.util.MessageManager;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.IdentityHashMap;
import java.util.Vector;
-import org.apache.commons.logging.Log;
-
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;
@@ -133,16 +132,14 @@ public abstract class DatastoreItem
{
Cache.log.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(
"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 "
@@ -192,15 +189,13 @@ 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 +228,8 @@ 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 +255,8 @@ 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);
}