+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 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.
+ *
+ * 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/>.
+ * 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 jalview.util.MessageManager;
import java.util.Enumeration;
import java.util.Hashtable;
/**
* Holds all the common machinery for binding objects to vamsas objects
+ *
* @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)
{
if (jv2vobj.containsKey(jvobj))
{
- return cdoc.getObject( (VorbaId) jv2vobj.get(jvobj));
+ return cdoc.getObject((VorbaId) jv2vobj.get(jvobj));
}
if (Cache.log.isDebugEnabled())
{
- Cache.log.debug("Returning null VorbaID binding for jalview object "+jvobj);
+ Cache.log.debug("Returning null VorbaID binding for jalview object "
+ + jvobj);
}
return null;
}
/**
- *
+ *
* @param vobj
* @return Jalview datamodel object bound to the vamsas document object
*/
protected Object getvObj2jv(uk.ac.vamsas.client.Vobject vobj)
{
- if (vobj2jv==null)
+ if (vobj2jv == null)
return null;
VorbaId id = vobj.getVorbaId();
if (id == null)
{
id = cdoc.registerObject(vobj);
Cache.log
- .debug("Registering new object and returning null for getvObj2jv");
+ .debug("Registering new object and returning null for getvObj2jv");
return null;
}
if (vobj2jv.containsKey(vobj.getVorbaId()))
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();
if (id == null)
{
id = cdoc.registerObject(vobj);
- if (id == null || vobj.getVorbaId() == null || cdoc.getObject(id)!=vobj)
+ if (id == null || vobj.getVorbaId() == null
+ || cdoc.getObject(id) != vobj)
{
- Cache.log.error("Failed to get id for " +
- (vobj.isRegisterable() ? "registerable" :
- "unregisterable") + " object " + vobj);
+ Cache.log.error("Failed to get id for "
+ + (vobj.isRegisterable() ? "registerable"
+ : "unregisterable") + " object " + vobj);
}
}
-
- if (vobj2jv.containsKey(vobj.getVorbaId()) &&
- ! ( (VorbaId) vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
+ if (vobj2jv.containsKey(vobj.getVorbaId())
+ && !(vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
{
- Cache.log.debug("Warning? Overwriting existing vamsas id binding for " +
- vobj.getVorbaId(),
- new Exception("Overwriting vamsas id binding."));
+ Cache.log
+ .debug("Warning? Overwriting existing vamsas id binding for "
+ + vobj.getVorbaId(),
+ new Exception(
+ MessageManager
+ .getString("exception.overwriting_vamsas_id_binding")));
}
- else if (jv2vobj.containsKey(jvobj) &&
- ! ( (VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
+ 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."));
+ Cache.log
+ .debug("Warning? Overwriting existing jalview object binding for "
+ + jvobj,
+ new Exception(
+ MessageManager
+ .getString("exception.overwriting_jalview_id_binding")));
}
- /* Cache.log.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"));
- }*/
+ /*
+ * Cache.log.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);
+ Cache.log.debug("Binding " + vobj.getVorbaId() + " to " + jvobj);
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);
+ }
}
- public DatastoreItem() {
+ /**
+ * 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(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, vobj);
+ }
+ }
+
+ public DatastoreItem()
+ {
super();
}
+
public DatastoreItem(VamsasAppDatastore datastore)
{
this();
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(
+ 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);
+ }
+
+ /**
+ * 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(
+ 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);
+ }
+
+ /**
+ * 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, Hashtable vobj2jv, IdentityHashMap jv2vobj)
+
+ private void initDatastoreItem(Entry provEntry, IClientDocument cdoc,
+ Hashtable vobj2jv, IdentityHashMap jv2vobj)
{
this.provEntry = provEntry;
this.cdoc = cdoc;
protected boolean isModifiable(String modifiable)
{
- return modifiable==null; // TODO: USE VAMSAS LIBRARY OBJECT LOCK METHODS)
+ return modifiable == null; // TODO: USE VAMSAS LIBRARY OBJECT LOCK METHODS)
}
protected Vector getjv2vObjs(Vector alsq)
}
return vObjs;
}
+
// utility functions
/**
* get start<end range of segment, adjusting for inclusivity flag and
* polarity.
- *
+ *
* @param visSeg
- * @param ensureDirection when true - always ensure start is less than end.
- * @return int[] { start, end, direction} where direction==1 for range running from end to start.
+ * @param ensureDirection
+ * when true - always ensure start is less than end.
+ * @return int[] { start, end, direction} where direction==1 for range running
+ * from end to start.
*/
public int[] getSegRange(Seg visSeg, boolean ensureDirection)
{
end = start;
start = t;
}
- return new int[]
- {
- start, end, pol < 0 ? 1 : 0};
+ return new int[] { start, end, pol < 0 ? 1 : 0 };
}
+
/**
* provenance bits
*/
- protected jalview.datamodel.Provenance getJalviewProvenance(Provenance prov)
+ protected jalview.datamodel.Provenance getJalviewProvenance(
+ Provenance prov)
{
// TODO: fix App and Action entries and check use of provenance in jalview.
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;
}
/**
- *
+ *
* @return default initial provenance list for a Jalview created vamsas
* object.
*/
{
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!
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff