X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FDatastoreItem.java;h=de82beb1e164359b449fbfaa92383fc37ff065d4;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=42e494f9fb76cc27f9a6d70a0b9aff7e70486f18;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/io/vamsas/DatastoreItem.java b/src/jalview/io/vamsas/DatastoreItem.java
index 42e494f..de82beb 100644
--- a/src/jalview/io/vamsas/DatastoreItem.java
+++ b/src/jalview/io/vamsas/DatastoreItem.java
@@ -1,26 +1,28 @@
 /*
- * 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 2.9.0b1)
+ * Copyright (C) 2015 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 jalview.util.MessageManager;
 
 import java.util.Enumeration;
 import java.util.Hashtable;
@@ -40,7 +42,7 @@ import uk.ac.vamsas.objects.core.Seg;
  * @author JimP
  * 
  */
-public class DatastoreItem
+public abstract class DatastoreItem
 {
   /**
    * 
@@ -53,7 +55,17 @@ public 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)
@@ -94,6 +106,13 @@ 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();
@@ -108,22 +127,25 @@ public class DatastoreItem
                         : "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 "
-                      + 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()))
     {
-      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 "
@@ -136,6 +158,53 @@ public class DatastoreItem
     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()
@@ -150,16 +219,184 @@ public class 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(
+              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,
+  private void initDatastoreItem(Entry provEntry, IClientDocument cdoc,
           Hashtable vobj2jv, IdentityHashMap jv2vobj)
   {
     this.provEntry = provEntry;
@@ -191,7 +428,7 @@ public class DatastoreItem
    * 
    * @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.
    */
@@ -210,8 +447,7 @@ public class DatastoreItem
       end = start;
       start = t;
     }
-    return new int[]
-    { start, end, pol < 0 ? 1 : 0 };
+    return new int[] { start, end, pol < 0 ? 1 : 0 };
   }
 
   /**
@@ -270,4 +506,87 @@ public class DatastoreItem
   {
     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!
+  }
+
 }