/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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.
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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.gui.TreePanel;
import jalview.io.VamsasAppDatastore;
import java.util.Enumeration;
* @author JimP
*
*/
-public class DatastoreItem
+public abstract class DatastoreItem
{
/**
*
IdentityHashMap jv2vobj;
+ boolean tojalview = false;
+
+ /**
+ * shared log instance
+ */
+ protected static org.apache.log4j.Logger log = org.apache.log4j.Logger
+ .getLogger(DatastoreItem.class);
+
/**
+ * note: this is taken verbatim from jalview.io.VamsasAppDatastore
+ *
* @return the Vobject bound to Jalview datamodel object
*/
protected Vobject getjv2vObj(Object jvobj)
return null;
}
+ /**
+ * note: this is taken verbatim from jalview.io.VamsasAppDatastore with added
+ * call to updateRegistryEntry
+ *
+ * @param jvobj
+ * @param vobj
+ */
protected void bindjvvobj(Object jvobj, uk.ac.vamsas.client.Vobject vobj)
{
VorbaId id = vobj.getVorbaId();
: "unregisterable") + " object " + vobj);
}
}
-
if (vobj2jv.containsKey(vobj.getVorbaId())
- && !((VorbaId) vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
+ && !(vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
{
Cache.log.debug(
"Warning? Overwriting existing vamsas id binding for "
vobj2jv.put(vobj.getVorbaId(), jvobj);
// JBPNote - better implementing a hybrid invertible hash.
jv2vobj.put(jvobj, vobj.getVorbaId());
+ if (jvobj == this.jvobj || vobj == this.vobj)
+ {
+ updateRegistryEntry(jvobj, vobj);
+ }
+ }
+
+ /**
+ * update the vobj and jvobj references and the registry entry for this
+ * datastore object called by bindjvvobj and replacejvobjmapping
+ */
+ private void updateRegistryEntry(Object jvobj, Vobject vobj)
+ {
+ if (this.jvobj != null && this.vobj != null)
+ {
+ Cache.log.debug("updating dsobj registry. ("
+ + this.getClass().getName() + ")");
+ }
+ this.jvobj = jvobj;
+ this.vobj = vobj;
+ dsReg.registerDsObj(this);
+ }
+
+ /**
+ * replaces oldjvobject with newjvobject in the Jalview Object <> VorbaID
+ * binding tables note: originally taken verbatim from
+ * jalview.io.VamsasAppDatastore with added call to updateRegistryEntry
+ *
+ * @param oldjvobject
+ * @param newjvobject
+ * (may be null to forget the oldjvobject's document mapping)
+ *
+ */
+ protected void replaceJvObjMapping(Object oldjvobject, Object newjvobject)
+ {
+ Object vobject = jv2vobj.remove(oldjvobject);
+ if (vobject == null)
+ {
+ throw new Error(
+ "IMPLEMENTATION ERROR: old jalview object is not bound ! ("
+ + oldjvobject + ")");
+ }
+ if (newjvobject != null)
+ {
+ jv2vobj.put(newjvobject, vobject);
+ vobj2jv.put(vobject, newjvobject);
+ updateRegistryEntry(newjvobject, vobj);
+ }
}
public DatastoreItem()
// TODO Auto-generated constructor stub
}
+ /**
+ * construct and initialise datastore object and retrieve object bound to
+ * vobj2 and validate it against boundType
+ *
+ * @param datastore2
+ * @param vobj2
+ * @param boundType
+ */
+ public DatastoreItem(VamsasAppDatastore datastore2, Vobject vobj2,
+ Class boundType)
+ {
+ this(datastore2);
+ vobj = vobj2;
+ jvobj = getvObj2jv(vobj2);
+ 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() + ")");
+ }
+ dsReg.registerDsObj(this);
+ }
+
+ /**
+ * construct and initialise datastore object and retrieve document object
+ * bound to Jalview object jvobj2 and validate it against boundType
+ *
+ * @param datastore2
+ * the datastore
+ * @param jvobj2
+ * the jalview object
+ * @param boundToType
+ * - the document object class that the bound object should be
+ * assignable from
+ */
+ public DatastoreItem(VamsasAppDatastore datastore2, Object jvobj2,
+ Class boundToType)
+ {
+ this(datastore2);
+ jvobj = jvobj2;
+ tojalview = false;
+ 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() + ")");
+ }
+ dsReg.registerDsObj(this);
+ }
+
+ /**
+ * create a new vobj to be added to the document for the jalview object jvobj
+ * (jvobj!=null, vobj==null)
+ */
+ public abstract void addToDocument();
+
+ /**
+ * handle a conflict where both an existing vobj has been updated and a local
+ * jalview object has been updated. This method is only called from doSync,
+ * when an incoming update from the vamsas session conflicts with local
+ * modifications made by the Jalview user. (jvobj!=null, vobj!=null)
+ */
+ public abstract void conflict();
+
+ /**
+ * update an existing vobj in the document with the data and settings from
+ * jvobj (jvobj!=null, vobj!=null)
+ */
+ public abstract void updateToDoc();
+
+ /**
+ * update the local jalview object with the data from an existing vobj in the
+ * document (jvobj!=null, vobj!=null)
+ */
+ public abstract void updateFromDoc();
+
+ /**
+ * create a new local jvobj bound to the vobj in the document. (jvobj==null,
+ * vobj!=null)
+ */
+ public abstract void addFromDocument();
+
+ boolean addtodoc = false, conflicted = false, updated = false,
+ addfromdoc = false, success = false;
+
+ private boolean updatedtodoc;
+
+ private boolean updatedfromdoc;
+
+ /**
+ * Sync jalview to document. Enact addToDocument, conflict or update dependent
+ * on existence of a vobj bound to the local jvobj.
+ */
+ protected void doSync()
+ {
+ dsReg.registerDsObj(this);
+ if (vobj == null)
+ {
+ log.debug("adding new vobject to document.");
+ addtodoc = true;
+ addToDocument();
+ }
+ else
+ {
+ if (vobj.isUpdated())
+ {
+ log.debug("Handling update conflict for existing bound vobject.");
+ conflicted = true;
+ conflict();
+ }
+ else
+ {
+ log.debug("updating existing vobject in document.");
+ updatedtodoc = true;
+ updateToDoc();
+ }
+ }
+ // no exceptions were encountered...
+ success = true;
+ }
+
+ /**
+ * Update jalview from document. enact addFromDocument if no local jvobj
+ * exists, or update iff jvobj exists and the vobj.isUpdated() flag is set.
+ */
+ protected void doJvUpdate()
+ {
+ dsReg.registerDsObj(this);
+ if (jvobj == null)
+ {
+ log.debug("adding new vobject to Jalview from Document");
+ addfromdoc = true;
+ addFromDocument();
+ }
+ else
+ {
+ if (vobj.isUpdated())
+ {
+ log.debug("updating Jalview from existing bound vObject");
+ updatedfromdoc = true;
+ updateFromDoc();
+ }
+ }
+ }
+
VamsasAppDatastore datastore = null;
+ /**
+ * object in vamsas document
+ */
+ protected Vobject vobj = null;
+
+ /**
+ * local jalview object
+ */
+ protected Object jvobj = null;
+
+ protected DatastoreRegistry dsReg;
+
public void initDatastoreItem(VamsasAppDatastore ds)
{
datastore = ds;
- initDatastoreItem(ds.getProvEntry(), ds.getClientDocument(), ds
- .getVamsasObjectBinding(), ds.getJvObjectBinding());
+ dsReg = ds.getDatastoreRegisty();
+ initDatastoreItem(ds.getProvEntry(), ds.getClientDocument(),
+ ds.getVamsasObjectBinding(), ds.getJvObjectBinding());
}
- public void initDatastoreItem(Entry provEntry, IClientDocument cdoc,
+ private void initDatastoreItem(Entry provEntry, IClientDocument cdoc,
Hashtable vobj2jv, IdentityHashMap jv2vobj)
{
this.provEntry = provEntry;
*
* @param visSeg
* @param ensureDirection
- * when true - always ensure start is less than end.
+ * when true - always ensure start is less than end.
* @return int[] { start, end, direction} where direction==1 for range running
* from end to start.
*/
{
p.addEntry(dummyPEntry(action));
}
+
+ /**
+ * @return true if jalview was being updated from the vamsas document
+ */
+ public boolean isTojalview()
+ {
+ return tojalview;
+ }
+
+ /**
+ * @return true if addToDocument() was called.
+ */
+ public boolean isAddtodoc()
+ {
+ return addtodoc;
+ }
+
+ /**
+ * @return true if conflict() was called
+ */
+ public boolean isConflicted()
+ {
+ return conflicted;
+ }
+
+ /**
+ * @return true if updateFromDoc() was called
+ */
+ public boolean isUpdatedFromDoc()
+ {
+ return updatedfromdoc;
+ }
+
+ /**
+ * @return true if updateToDoc() was called
+ */
+ public boolean isUpdatedToDoc()
+ {
+ return updatedtodoc;
+ }
+
+ /**
+ * @return true if addFromDocument() was called.
+ */
+ public boolean isAddfromdoc()
+ {
+ return addfromdoc;
+ }
+
+ /**
+ * @return true if object sync logic completed normally.
+ */
+ public boolean isSuccess()
+ {
+ return success;
+ }
+
+ /**
+ * @return the vobj
+ */
+ public Vobject getVobj()
+ {
+ return vobj;
+ }
+
+ /**
+ * @return the jvobj
+ */
+ public Object getJvobj()
+ {
+ return jvobj;
+ }
+
+ public boolean docWasUpdated()
+ {
+ return (this.addtodoc || this.updated) && this.success;
+ }
+
+ public boolean jvWasUpdated()
+ {
+ return (success); // TODO : Implement this properly!
+ }
+
}