X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FDatastoreItem.java;h=1aba737cd040c20cb8101c207ba25b50ac747727;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=b77cc8cf537aacae704e25151e2a3af029707b3c;hpb=9602211f8efae2e67f836bbacb2cc07a5dde3625;p=jalview.git

diff --git a/src/jalview/io/vamsas/DatastoreItem.java b/src/jalview/io/vamsas/DatastoreItem.java
index b77cc8c..1aba737 100644
--- a/src/jalview/io/vamsas/DatastoreItem.java
+++ b/src/jalview/io/vamsas/DatastoreItem.java
@@ -1,146 +1,578 @@
-package jalview.io.vamsas;
-
-import jalview.bin.Cache;
-import jalview.gui.TreePanel;
-import jalview.io.VamsasAppDatastore;
-
-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;
-
-/**
- * Holds all the common machinery for binding objects to vamsas objects
- * @author JimP
- *
- */
-public class DatastoreItem
-{
-  /**
-   * 
-   */
-  Entry provEntry = null;
-
-  IClientDocument cdoc;
-
-  Hashtable vobj2jv;
-
-  IdentityHashMap jv2vobj;
-  /**
-   * @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(uk.ac.vamsas.client.Vobject vobj)
-  {
-    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;
-  }
-
-  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)
-      {
-        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))
-    {
-      Cache.log.debug("Warning? Overwriting existing vamsas id binding for " +
-                      vobj.getVorbaId(),
-                      new 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.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());
-  }
-
-  public DatastoreItem() {
-    super();
-  }
-  public DatastoreItem(VamsasAppDatastore datastore)
-  {
-    this();
-    initDatastoreItem(datastore);
-    // TODO Auto-generated constructor stub
-  }
-
-  public void initDatastoreItem(VamsasAppDatastore ds)
-  {
-    initDatastoreItem(ds.getProvEntry(), ds.getClientDocument(), ds.getVamsasObjectBinding(), ds.getJvObjectBinding());
-  }
-  public 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;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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 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(uk.ac.vamsas.client.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, 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)
+      {
+        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(
+                      "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.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(
+              "IMPLEMENTATION ERROR: old jalview object is not bound ! ("
+                      + oldjvobject + ")");
+    }
+    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("Implementation Error: Vamsas Document Class "
+              + vobj.getClass() + " should bind to a " + boundType
+              + " (found a " + jvobj.getClass() + ")");
+    }
+    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("Implementation Error: Jalview Class "
+              + jvobj2.getClass() + " should bind to a " + boundToType
+              + " (found a " + vobj.getClass() + ")");
+    }
+    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!
+  }
+
+}