package jalview.io.vamsas;
import jalview.bin.Cache;
+import jalview.datamodel.DBRefEntry;
import jalview.gui.TreePanel;
import jalview.io.VamsasAppDatastore;
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;
* @author JimP
*
*/
-public class DatastoreItem
+public abstract class DatastoreItem
{
/**
*
Hashtable vobj2jv;
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
+
+ * @param jvobj
+ * @param vobj
+ */
protected void bindjvvobj(Object jvobj, uk.ac.vamsas.client.Vobject vobj)
{
VorbaId id = vobj.getVorbaId();
// JBPNote - better implementing a hybrid invertible hash.
jv2vobj.put(jvobj, vobj.getVorbaId());
}
+ /**
+ * replaces oldjvobject with newjvobject in the Jalview Object <> VorbaID
+ * binding tables
+ * note: this is taken verbatim from jalview.io.VamsasAppDatastore
+ * @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);
+ }
+ }
public DatastoreItem()
{
initDatastoreItem(datastore);
// 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()+")");
+ }
+ }
+ /**
+ * 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()+")");
+ }
+ }
+ /**
+ * 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()
+ {
+
+ 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()
+ {
+ 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;
public void initDatastoreItem(VamsasAppDatastore ds)
{
{
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;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff