-package jalview.io.vamsas;\r
-\r
-import jalview.bin.Cache;\r
-import jalview.gui.TreePanel;\r
-import jalview.io.VamsasAppDatastore;\r
-\r
-import java.util.Enumeration;\r
-import java.util.Hashtable;\r
-import java.util.IdentityHashMap;\r
-import java.util.Vector;\r
-\r
-import uk.ac.vamsas.client.IClientDocument;\r
-import uk.ac.vamsas.client.Vobject;\r
-import uk.ac.vamsas.client.VorbaId;\r
-import uk.ac.vamsas.objects.core.Entry;\r
-\r
-/**\r
- * Holds all the common machinery for binding objects to vamsas objects\r
- * @author JimP\r
- *\r
- */\r
-public class DatastoreItem\r
-{\r
- /**\r
- * \r
- */\r
- Entry provEntry = null;\r
-\r
- IClientDocument cdoc;\r
-\r
- Hashtable vobj2jv;\r
-\r
- IdentityHashMap jv2vobj;\r
- /**\r
- * @return the Vobject bound to Jalview datamodel object\r
- */\r
- protected Vobject getjv2vObj(Object jvobj)\r
- {\r
- if (jv2vobj.containsKey(jvobj))\r
- {\r
- return cdoc.getObject( (VorbaId) jv2vobj.get(jvobj));\r
- }\r
- if (Cache.log.isDebugEnabled())\r
- {\r
- Cache.log.debug("Returning null VorbaID binding for jalview object "+jvobj);\r
- }\r
- return null;\r
- }\r
-\r
- /**\r
- *\r
- * @param vobj\r
- * @return Jalview datamodel object bound to the vamsas document object\r
- */\r
- protected Object getvObj2jv(uk.ac.vamsas.client.Vobject vobj)\r
- {\r
- VorbaId id = vobj.getVorbaId();\r
- if (id == null)\r
- {\r
- id = cdoc.registerObject(vobj);\r
- Cache.log\r
- .debug("Registering new object and returning null for getvObj2jv");\r
- return null;\r
- }\r
- if (vobj2jv.containsKey(vobj.getVorbaId()))\r
- {\r
- return vobj2jv.get(vobj.getVorbaId());\r
- }\r
- return null;\r
- }\r
-\r
- protected void bindjvvobj(Object jvobj, uk.ac.vamsas.client.Vobject vobj)\r
- {\r
- VorbaId id = vobj.getVorbaId();\r
- if (id == null)\r
- {\r
- id = cdoc.registerObject(vobj);\r
- if (id == null || vobj.getVorbaId() == null || cdoc.getObject(id)!=vobj)\r
- {\r
- Cache.log.error("Failed to get id for " +\r
- (vobj.isRegisterable() ? "registerable" :\r
- "unregisterable") + " object " + vobj);\r
- }\r
- }\r
-\r
- if (vobj2jv.containsKey(vobj.getVorbaId()) &&\r
- ! ( (VorbaId) vobj2jv.get(vobj.getVorbaId())).equals(jvobj))\r
- {\r
- Cache.log.debug("Warning? Overwriting existing vamsas id binding for " +\r
- vobj.getVorbaId(),\r
- new Exception("Overwriting vamsas id binding."));\r
- }\r
- else if (jv2vobj.containsKey(jvobj) &&\r
- ! ( (VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))\r
- {\r
- Cache.log.debug(\r
- "Warning? Overwriting existing jalview object binding for " + jvobj,\r
- new Exception("Overwriting jalview object binding."));\r
- }\r
- /* 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"));\r
- }*/\r
- // we just update the hash's regardless!\r
- Cache.log.debug("Binding "+vobj.getVorbaId()+" to "+jvobj);\r
- vobj2jv.put(vobj.getVorbaId(), jvobj);\r
- // JBPNote - better implementing a hybrid invertible hash.\r
- jv2vobj.put(jvobj, vobj.getVorbaId());\r
- }\r
-\r
- public DatastoreItem() {\r
- super();\r
- }\r
- public DatastoreItem(VamsasAppDatastore datastore)\r
- {\r
- this();\r
- initDatastoreItem(datastore);\r
- // TODO Auto-generated constructor stub\r
- }\r
-\r
- public void initDatastoreItem(VamsasAppDatastore ds)\r
- {\r
- initDatastoreItem(ds.getProvEntry(), ds.getClientDocument(), ds.getVamsasObjectBinding(), ds.getJvObjectBinding());\r
- }\r
- public void initDatastoreItem(Entry provEntry, IClientDocument cdoc, Hashtable vobj2jv, IdentityHashMap jv2vobj)\r
- {\r
- this.provEntry = provEntry;\r
- this.cdoc = cdoc;\r
- this.vobj2jv = vobj2jv;\r
- this.jv2vobj = jv2vobj;\r
- }\r
-\r
- protected boolean isModifiable(String modifiable)\r
- {\r
- return modifiable==null; // TODO: USE VAMSAS LIBRARY OBJECT LOCK METHODS)\r
- }\r
-\r
- protected Vector getjv2vObjs(Vector alsq)\r
- {\r
- Vector vObjs = new Vector();\r
- Enumeration elm = alsq.elements();\r
- while (elm.hasMoreElements())\r
- {\r
- vObjs.addElement(getjv2vObj(elm.nextElement()));\r
- }\r
- return vObjs;\r
- }\r
-}\r
+/*
+ * 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.
+ *
+ * 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.io.VamsasAppDatastore;
+import jalview.util.MessageManager;
+
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Vector;
+
+import uk.ac.vamsas.client.IClientDocument;
+import uk.ac.vamsas.client.Vobject;
+import uk.ac.vamsas.client.VorbaId;
+import uk.ac.vamsas.objects.core.Entry;
+import uk.ac.vamsas.objects.core.Provenance;
+import uk.ac.vamsas.objects.core.Seg;
+
+/**
+ * Holds all the common machinery for binding objects to vamsas objects
+ *
+ * @author JimP
+ *
+ */
+public abstract class DatastoreItem
+{
+ /**
+ *
+ */
+ Entry provEntry = null;
+
+ IClientDocument cdoc;
+
+ 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));
+ }
+ if (Cache.log.isDebugEnabled())
+ {
+ 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(Vobject vobj)
+ {
+ 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");
+ return null;
+ }
+ if (vobj2jv.containsKey(vobj.getVorbaId()))
+ {
+ return vobj2jv.get(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, Vobject vobj)
+ {
+ VorbaId id = vobj.getVorbaId();
+ if (id == null)
+ {
+ id = cdoc.registerObject(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);
+ }
+ }
+ 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(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(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")); }
+ */
+ // we just update the hash's regardless!
+ 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);
+ }
+ }
+
+ /**
+ * 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;
+ dsReg = ds.getDatastoreRegisty();
+ initDatastoreItem(ds.getProvEntry(), ds.getClientDocument(),
+ ds.getVamsasObjectBinding(), ds.getJvObjectBinding());
+ }
+
+ private void initDatastoreItem(Entry provEntry, IClientDocument cdoc,
+ Hashtable vobj2jv, IdentityHashMap jv2vobj)
+ {
+ this.provEntry = provEntry;
+ this.cdoc = cdoc;
+ this.vobj2jv = vobj2jv;
+ this.jv2vobj = jv2vobj;
+ }
+
+ protected boolean isModifiable(String modifiable)
+ {
+ return modifiable == null; // TODO: USE VAMSAS LIBRARY OBJECT LOCK METHODS)
+ }
+
+ protected Vector getjv2vObjs(Vector alsq)
+ {
+ Vector vObjs = new Vector();
+ Enumeration elm = alsq.elements();
+ while (elm.hasMoreElements())
+ {
+ vObjs.addElement(getjv2vObj(elm.nextElement()));
+ }
+ 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.
+ */
+ public int[] getSegRange(Seg visSeg, boolean ensureDirection)
+ {
+ boolean incl = visSeg.getInclusive();
+ // adjust for inclusive flag.
+ int pol = (visSeg.getStart() <= visSeg.getEnd()) ? 1 : -1; // polarity of
+ // region.
+ int start = visSeg.getStart() + (incl ? 0 : pol);
+ int end = visSeg.getEnd() + (incl ? 0 : -pol);
+ if (ensureDirection && pol == -1)
+ {
+ // jalview doesn't deal with inverted ranges, yet.
+ int t = end;
+ end = start;
+ start = t;
+ }
+ return new int[]
+ { start, end, pol < 0 ? 1 : 0 };
+ }
+
+ /**
+ * provenance bits
+ */
+ 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());
+ }
+
+ return jprov;
+ }
+
+ /**
+ *
+ * @return default initial provenance list for a Jalview created vamsas
+ * object.
+ */
+ Provenance dummyProvenance()
+ {
+ return dummyProvenance(null);
+ }
+
+ protected Entry dummyPEntry(String action)
+ {
+ Entry entry = new Entry();
+ entry.setApp(this.provEntry.getApp());
+ if (action != null)
+ {
+ entry.setAction(action);
+ }
+ else
+ {
+ entry.setAction("created.");
+ }
+ entry.setDate(new java.util.Date());
+ entry.setUser(this.provEntry.getUser());
+ return entry;
+ }
+
+ protected Provenance dummyProvenance(String action)
+ {
+ Provenance prov = new Provenance();
+ prov.addEntry(dummyPEntry(action));
+ return prov;
+ }
+
+ protected void addProvenance(Provenance p, String action)
+ {
+ 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