/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * 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.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;
{
jv2vobj.put(newjvobject, vobject);
vobj2jv.put(vobject, newjvobject);
- updateRegistryEntry(newjvobject, (Vobject) vobject);
+ updateRegistryEntry(newjvobject, vobj);
}
}
{
datastore = ds;
dsReg = ds.getDatastoreRegisty();
- initDatastoreItem(ds.getProvEntry(), ds.getClientDocument(), ds
- .getVamsasObjectBinding(), ds.getJvObjectBinding());
+ initDatastoreItem(ds.getProvEntry(), ds.getClientDocument(),
+ ds.getVamsasObjectBinding(), ds.getJvObjectBinding());
}
private void initDatastoreItem(Entry provEntry, IClientDocument cdoc,