fix for bug #8333

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

diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index 2879c2f..777d71b 100644 (file)
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -72,18 +72,21 @@ public class VamsasApplication implements SelectionSource
 
   Desktop jdesktop = null; // our jalview desktop reference
 
+  private boolean inInitialUpdate=true;
+
   // Cache.preferences for vamsas client session arena
   // preferences for check for default session at startup.
   // user and organisation stuff.
-  public VamsasApplication(Desktop jdesktop, File sessionPath)
+  public VamsasApplication(Desktop jdesktop, File sessionPath, String sessionName)
   {
     // JBPNote:
     // we should create a session URI from the sessionPath and pass it to
     // the clientFactory - but the vamsas api doesn't cope with that yet.
     this.jdesktop = jdesktop;
-    initClientSession(null, sessionPath);
+    initClientSession(null, sessionPath, sessionName);
   }
 
+
   private static uk.ac.vamsas.client.IClientFactory getClientFactory()
           throws IOException
   {
@@ -133,7 +136,12 @@ public class VamsasApplication implements SelectionSource
    *          null or a valid vamsas document file
    * @return false if no vamsas connection was made
    */
-  private boolean initClientSession(String sess, File vamsasDocument)
+  private void initClientSession(String sess, File vamsasDocument)
+  {
+    initClientSession(sess,vamsasDocument,null);
+  }
+
+  private boolean initClientSession(String sess, File vamsasDocument, String newDocSessionName)
   {
     try
     {
@@ -149,8 +157,14 @@ public class VamsasApplication implements SelectionSource
         }
         try
         {
-          vclient = clientfactory.openAsNewSessionIClient(app,
+          if (newDocSessionName!=null)
+          {
+            vclient = clientfactory.openAsNewSessionIClient(app,
+                    vamsasDocument,newDocSessionName);
+          } else {
+            vclient = clientfactory.openAsNewSessionIClient(app,
                   vamsasDocument);
+          }
         } catch (InvalidSessionDocumentException e)
         {
           JOptionPane
@@ -252,9 +266,11 @@ public class VamsasApplication implements SelectionSource
     addDocumentUpdateHandler();
     addStoreDocumentHandler();
     startSession();
+    inInitialUpdate = true;
     Cache.log
             .debug("Jalview loading the Vamsas Session for the first time.");
     dealWithDocumentUpdate(false); // we don't push an update out to the
+    inInitialUpdate = false;
     // document yet.
     Cache.log.debug("... finished update for the first time.");
   }
@@ -302,6 +318,7 @@ public class VamsasApplication implements SelectionSource
       {
         Cache.log.info("Jalview updating to the Vamsas Session.");
 
+        
         dealWithDocumentUpdate(true);
         Cache.log.info("Jalview finished updating to the Vamsas Session.");
       }
@@ -420,9 +437,11 @@ public class VamsasApplication implements SelectionSource
    * bindings is made.
    * 
    * @param doc
+   * @return number of views stored in document (updated and new views)
    */
-  public void updateVamsasDocument(IClientDocument doc)
+  public int updateVamsasDocument(IClientDocument doc)
   {
+    int storedviews=0;
     ensureJvVamsas();
     errorsDuringUpdate = false;
     errorsDuringAppUpdate = false;
@@ -434,7 +453,7 @@ public class VamsasApplication implements SelectionSource
 
     if (frames == null)
     {
-      return;
+      return 0;
     }
     Hashtable skipList = new Hashtable();
     Hashtable viewset = new Hashtable();
@@ -471,6 +490,7 @@ public class VamsasApplication implements SelectionSource
             }
             else
             {
+              storedviews++;
               // could try to eliminate sequenceSetId from skiplist ..
               // (skipList.containsKey(af.getViewport().getSequenceSetId()))
               // remember sequenceSetId so we can skip all the other views on
@@ -516,6 +536,7 @@ public class VamsasApplication implements SelectionSource
       errorsDuringAppUpdate = true;
     }
     vds.clearSkipList();
+    return storedviews;
   }
 
   private Entry baseProvEntry()
@@ -533,9 +554,11 @@ public class VamsasApplication implements SelectionSource
    * 
    * @param fromJalview
    *          true to update from jalview to the vamsas document
+   *          @return total number of stored alignments in the document after the update 
    */
-  protected void dealWithDocumentUpdate(boolean fromJalview)
+  protected int dealWithDocumentUpdate(boolean fromJalview)
   {
+    int storedviews = 0;
     // called by update handler for document update.
     Cache.log.debug("Updating jalview from changed vamsas document.");
     disableGui(true);
@@ -551,7 +574,7 @@ public class VamsasApplication implements SelectionSource
       }
       if (fromJalview)
       {
-        this.updateVamsasDocument(cdoc);
+        storedviews+=updateVamsasDocument(cdoc);
         if (Cache.log.isDebugEnabled())
         {
           Cache.log
@@ -593,10 +616,12 @@ public class VamsasApplication implements SelectionSource
       ee.printStackTrace(System.err);
       // recover object map backup, since its probably corrupted with references
       // to Vobjects that don't exist anymore.
-      this.recover_objectMappingBackup();
+      recover_objectMappingBackup();
+      storedviews=0;
     }
     Cache.log.debug("Finished updating from document change.");
     disableGui(false);
+    return storedviews;
   }
 
   private void addDocumentUpdateHandler()
@@ -684,6 +709,11 @@ public class VamsasApplication implements SelectionSource
   {
     if (_backup_vobj2jv == null)
     {
+      if (inInitialUpdate) {
+        // nothing to recover so just
+        return;
+      }
+      
       throw new Error(
               "IMPLEMENTATION ERROR: Cannot recover vamsas object mappings - no backup was made.");
     }
@@ -786,7 +816,7 @@ public class VamsasApplication implements SelectionSource
                 if (jvobjs[o] == null)
                 {
                   // can't cope with selections for unmapped objects
-                  // continue;
+                  continue;
                 }
                 if (type == null)
                 {
@@ -872,26 +902,14 @@ public class VamsasApplication implements SelectionSource
                   {
                     int[] prange = uk.ac.vamsas.objects.utils.Range
                             .getBounds(sm.getRanges());
-                    boolean rangeset = false;
-                    colsel = new ColumnSelection();
+                    jselection.setStartRes(prange[0] - 1);
+                    jselection.setEndRes(prange[1] - 1);
                     prange = uk.ac.vamsas.objects.utils.Range
                             .getIntervals(sm.getRanges());
+                    colsel = new ColumnSelection();
                     for (int p = 0; p < prange.length; p += 2)
                     {
                       int d = (prange[p] <= prange[p + 1]) ? 1 : -1;
-                      if (!rangeset)
-                      {
-                        if (jselection != null)
-                        {
-                          // set the bounds of the selected area using the first
-                          // interval.
-                          jselection.setStartRes(prange[p] - 1);
-                          jselection.setEndRes(prange[p + 1] - 1);
-                          rangeset = true;
-                        }
-                      }
-                      else
-                      {
                         // try to join up adjacent columns to make a larger
                         // selection
                         // lower and upper bounds
@@ -909,7 +927,6 @@ public class VamsasApplication implements SelectionSource
                         {
                           jselection.setEndRes(prange[p + u] - 1);
                         }
-                      }
                       // mark all the columns in the range.
                       for (int sr = prange[p], er = prange[p + 1], de = er
                               + d; sr != de; sr += d)