X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FDatastoreItem.java;h=11c7e91f82a945781f56044ce6a446eae56a42ff;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=4cc540d465a1428fd178a380731c06ce738d3e2b;hpb=cfa406a916d754e600c60f7dae29b053bf045ace;p=jalview.git diff --git a/src/jalview/io/vamsas/DatastoreItem.java b/src/jalview/io/vamsas/DatastoreItem.java index 4cc540d..11c7e91 100644 --- a/src/jalview/io/vamsas/DatastoreItem.java +++ b/src/jalview/io/vamsas/DatastoreItem.java @@ -1,8 +1,28 @@ +/* + * 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 . + * 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; @@ -18,10 +38,11 @@ import uk.ac.vamsas.objects.core.Seg; /** * Holds all the common machinery for binding objects to vamsas objects + * * @author JimP - * + * */ -public class DatastoreItem +public abstract class DatastoreItem { /** * @@ -33,37 +54,49 @@ public 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())) @@ -73,59 +106,280 @@ public class DatastoreItem 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.")); + "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; @@ -135,7 +389,7 @@ public class DatastoreItem 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) @@ -148,14 +402,17 @@ public class DatastoreItem } return vObjs; } + // utility functions /** * get start