implemented @SilentNotification

This makes it possible with just an a manager method annotation to make any BioclipseUIJobs to be run not when the job i done but after the job is done and the user has clicked in the Progress view on the actual job. Fixes bug: #1611.

plugins/net.bioclipse.core/META-INF/MANIFEST.MF

@@ -22,7 +22,8 @@ Require-Bundle: org.eclipse.core.runtime,
  org.springframework.bundle.spring.aop;bundle-version="2.5.1",
  org.springframework.osgi.aopalliance.osgi;bundle-version="1.0.0",
  org.springframework.bundle.spring.core;bundle-version="2.5.1",
- net.sf.cglib;bundle-version="2.1.3"
+ net.sf.cglib;bundle-version="2.1.3",
+ org.eclipse.jface
 Bundle-ClassPath: libs/js.jar,
  .,
  libs/groovy-1.0.jar,

plugins/net.bioclipse.core/src/net/bioclipse/core/SilentNotification.java

@@ -0,0 +1,28 @@
+/*******************************************************************************
+ * Copyright (c) 2009  Jonathan Alvarsson <jonalv@users.sourceforge.net>
+ *
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * www.eclipse.orgÑepl-v10.html <http://www.eclipse.org/legal/epl-v10.html>
+ *
+ * Contact: http://www.bioclipse.net/
+ ******************************************************************************/
+package net.bioclipse.core;
+
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
+
+/**
+ * @author jonalv
+ *
+ */
+@Retention(RetentionPolicy.RUNTIME)
+@Target(ElementType.METHOD)
+public @interface SilentNotification {
+
+    String message() default "Job completed, results available!";
+
+}

plugins/net.bioclipse.core/src/net/bioclipse/jobs/BioclipseJob.java

@@ -7,6 +7,7 @@
 import java.util.List;
 
 import net.bioclipse.core.ResourcePathTransformer;
+import net.bioclipse.core.SilentNotification;
 import net.bioclipse.core.business.BioclipseException;
 import net.bioclipse.core.util.LogUtils;
 import net.bioclipse.managers.business.IBioclipseManager;
@@ -19,7 +20,9 @@
 import org.eclipse.core.runtime.OperationCanceledException;
 import org.eclipse.core.runtime.Status;
 import org.eclipse.core.runtime.jobs.Job;
+import org.eclipse.jface.action.Action;
 import org.eclipse.swt.widgets.Display;
+import org.eclipse.ui.progress.IProgressConstants;
 import org.eclipse.ui.progress.WorkbenchJob;
 
 
@@ -274,11 +277,28 @@ public void partialReturn( Object o ) {
 
             if ( uiJob != null ) {
                 uiJob.setReturnValue( returnValue );
-                Display.getDefault().asyncExec( new Runnable() {
-                    public void run() {
-                        uiJob.runInUI();
-                    }
-                });
+                SilentNotification a 
+                    = this.methodCalled
+                          .getAnnotation( SilentNotification.class );
+                if ( a != null ) {
+                    setProperty(IProgressConstants.KEEP_PROPERTY, Boolean.TRUE);
+                   monitor.subTask( a.message() );
+
+                   setProperty( IProgressConstants.ACTION_PROPERTY, 
+                                 new Action( a.message() ) {
+                                    public void run() {
+                                        uiJob.runInUI();
+                                    }
+                                 }
+                    );
+                }
+                else {
+                    Display.getDefault().asyncExec( new Runnable() {
+                        public void run() {
+                            uiJob.runInUI();
+                        }
+                    });
+                }
             }
         } 
         catch ( Exception e ) {