vamsas connects and updates are threaded with a progress bar.

[jalview.git] / src / jalview / gui / VamsasApplication.java

diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index 65212a6..bfe5487 100644 (file)
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -149,6 +149,8 @@ public class VamsasApplication
           vclient = clientfactory.getIClient(app, sess);
         }
       }
+      // set some properties for our VAMSAS interaction
+      setVclientConfig();
       user = vclient.getUserHandle();
 
     } catch (Exception e)
@@ -160,6 +162,30 @@ public class VamsasApplication
     return true;
   }
 
+  private void setVclientConfig()
+  {
+    if (vclient==null)
+    {
+      return;
+    }
+    try {
+      if (vclient instanceof uk.ac.vamsas.client.simpleclient.SimpleClient)
+      {
+        uk.ac.vamsas.client.simpleclient.SimpleClientConfig cfg = ((uk.ac.vamsas.client.simpleclient.SimpleClient)  vclient).getSimpleClientConfig();
+        cfg._validatemergedroots = false;
+        cfg._validateupdatedroots= true; //we may write rubbish otherwise. 
+      }
+    }
+    catch (Error e)
+    {
+      Cache.log.warn("Probable SERIOUS VAMSAS client incompatibility - carrying on regardless",e);
+    }
+    catch (Exception e)
+    {
+      Cache.log.warn("Probable VAMSAS client incompatibility - carrying on regardless",e);
+    }
+  }
+
   /**
    * make the appHandle for Jalview
    * 
@@ -192,6 +218,7 @@ public class VamsasApplication
               "Impementation error! Vamsas Operations when client not initialised and connected.");
     }
     addDocumentUpdateHandler();
+    addStoreDocumentHandler();
     startSession();
     Cache.log
             .debug("Jalview loading the Vamsas Session for the first time.");
@@ -236,17 +263,27 @@ public class VamsasApplication
 
   public void push_update()
   {
-    Cache.log.info("Jalview updating to the Vamsas Session.");
-    dealWithDocumentUpdate(true);
-    /*
-     * IClientDocument cdoc=null; try { cdoc = vclient.getClientDocument(); }
-     * catch (Exception e) { Cache.log.error("Failed to get client document for
-     * update."); // RAISE A WARNING DIALOG disableGui(false); return; }
-     * updateVamsasDocument(cdoc); updateJalviewGui();
-     * cdoc.setVamsasRoots(cdoc.getVamsasRoots()); // propagate update flags
-     * back vclient.updateDocument(cdoc);
-     */
-    Cache.log.info("Jalview finished updating to the Vamsas Session.");
+    Thread udthread = new Thread(new Runnable() {
+
+      public void run()
+      {
+        Cache.log.info("Jalview updating to the Vamsas Session.");
+    
+        dealWithDocumentUpdate(true);
+        /*
+         * IClientDocument cdoc=null; try { cdoc = vclient.getClientDocument(); }
+         * catch (Exception e) { Cache.log.error("Failed to get client document for
+         * update."); // RAISE A WARNING DIALOG disableGui(false); return; }
+         * updateVamsasDocument(cdoc); updateJalviewGui();
+         * cdoc.setVamsasRoots(cdoc.getVamsasRoots()); // propagate update flags
+         * back vclient.updateDocument(cdoc);
+         */
+        Cache.log.info("Jalview finished updating to the Vamsas Session.");
+        // TODO Auto-generated method stub
+      }
+      
+    });
+    udthread.start();
   }
 
   public void end_session()
@@ -283,7 +320,7 @@ public class VamsasApplication
     Cache.log.debug("Jalview updating from sesion document ..");
     ensureJvVamsas();
     VamsasAppDatastore vds = new VamsasAppDatastore(cdoc, vobj2jv, jv2vobj,
-            baseProvEntry());
+            baseProvEntry(), alRedoState);
     vds.updateToJalview();
     Cache.log.debug(".. finished updating from sesion document.");
 
@@ -295,6 +332,7 @@ public class VamsasApplication
     {
       jv2vobj = new IdentityHashMap();
       vobj2jv = new Hashtable();
+      alRedoState = new Hashtable();
     }
   }
 
@@ -304,12 +342,12 @@ public class VamsasApplication
   IdentityHashMap jv2vobj = null;
 
   Hashtable vobj2jv = null;
-
+  Hashtable alRedoState = null;
   public void updateVamsasDocument(IClientDocument doc)
   {
     ensureJvVamsas();
     VamsasAppDatastore vds = new VamsasAppDatastore(doc, vobj2jv, jv2vobj,
-            baseProvEntry());
+            baseProvEntry(), alRedoState);
     // wander through frames
     JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 
@@ -441,6 +479,30 @@ public class VamsasApplication
     Cache.log.debug("Added Jalview handler for vamsas document updates.");
   }
 
+  private void addStoreDocumentHandler()
+  {
+    final VamsasApplication client = this;
+    vclient.addVorbaEventHandler(uk.ac.vamsas.client.Events.DOCUMENT_REQUESTTOCLOSE, new PropertyChangeListener()
+    {
+      public void propertyChange(PropertyChangeEvent evt)
+      {
+        Cache.log.debug("Asking user if the vamsas session should be stored.");
+        int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+                "The current VAMSAS session has unsaved data - do you want to save it ?",
+            "VAMSAS Session Shutdown",
+            JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
+        
+            if(reply==JOptionPane.YES_OPTION)
+            {
+              Cache.log.debug("Prompting for vamsas store filename.");
+              Desktop.instance.vamsasSave_actionPerformed(null);
+              Cache.log.debug("Finished attempt at storing document.");
+            } 
+            Cache.log.debug("finished dealing with REQUESTTOCLOSE event.");
+      }
+    });
+    Cache.log.debug("Added Jalview handler for vamsas document updates.");
+  }
   public void disableGui(boolean b)
   {
     Desktop.instance.setVamsasUpdate(b);