JAL-3690 separate startup and poll code in SeqAnnotationCalcWorker

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

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 088d83d..e9bf09f 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -59,8 +59,11 @@ import java.util.Hashtable;
 import java.util.List;
 import java.util.ListIterator;
 import java.util.Vector;
+import java.util.concurrent.ExecutionException;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
+import java.util.concurrent.FutureTask;
 import java.util.concurrent.Semaphore;
 
 import javax.swing.AbstractAction;
@@ -120,6 +123,7 @@ import jalview.util.Platform;
 import jalview.util.ShortcutKeyMaskExWrapper;
 import jalview.util.UrlConstants;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.WSDiscovererI;
 import jalview.ws.params.ParamManager;
 import jalview.ws.utils.UrlDownloadClient;
 
@@ -157,6 +161,7 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   public static HashMap<String, FileWriter> savingFiles = new HashMap<String, FileWriter>();
 
+  @SuppressWarnings("deprecation")
   private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
 
   /**
@@ -170,6 +175,7 @@ public class Desktop extends jalview.jbgui.GDesktop
    * @param listener
    * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener)
    */
+  @Deprecated
   public void addJalviewPropertyChangeListener(
           PropertyChangeListener listener)
   {
@@ -182,6 +188,7 @@ public class Desktop extends jalview.jbgui.GDesktop
    * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.lang.String,
    *      java.beans.PropertyChangeListener)
    */
+  @Deprecated
   public void addJalviewPropertyChangeListener(String propertyName,
           PropertyChangeListener listener)
   {
@@ -194,6 +201,7 @@ public class Desktop extends jalview.jbgui.GDesktop
    * @see jalview.gui.JalviewChangeSupport#removeJalviewPropertyChangeListener(java.lang.String,
    *      java.beans.PropertyChangeListener)
    */
+  @Deprecated
   public void removeJalviewPropertyChangeListener(String propertyName,
           PropertyChangeListener listener)
   {
@@ -1547,7 +1555,8 @@ public class Desktop extends jalview.jbgui.GDesktop
       return;
     }
 
-    AlignmentViewport source = null, target = null;
+    AlignViewportI source = null;
+    AlignViewportI target = null;
     if (frames[0] instanceof AlignFrame)
     {
       source = ((AlignFrame) frames[0]).getCurrentView();
@@ -1767,7 +1776,7 @@ public class Desktop extends jalview.jbgui.GDesktop
           {
                try 
             {
-              new Jalview2XML().loadJalviewAlign(choice);
+              new Jalview2XML().loadJalviewAlign(selectedFile);
             } catch (OutOfMemoryError oom)
                {
                  new OOMWarning("Whilst loading project from " + choice, oom);
@@ -2511,6 +2520,13 @@ public class Desktop extends jalview.jbgui.GDesktop
       progressBars.put(Long.valueOf(id), addProgressPanel(message));
     }
   }
+  
+  @Override
+  public void removeProgressBar(long id)
+  {
+    //TODO
+    throw new UnsupportedOperationException("not implemented");
+  }
 
   /*
    * (non-Javadoc)
@@ -2629,10 +2645,9 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   public void startServiceDiscovery(boolean blocking)
   {
-    boolean alive = true;
-    Thread t0 = null, t1 = null, t2 = null;
+    var tasks = new ArrayList<Future<?>>();
     // JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release
-    if (true)
+
     {
       // todo: changesupport handlers need to be transferred
       if (discoverer == null)
@@ -2643,31 +2658,30 @@ public class Desktop extends jalview.jbgui.GDesktop
       }
       // JAL-940 - disabled JWS1 service configuration - always start discoverer
       // until we phase out completely
-      (t0 = new Thread(discoverer)).start();
+      var f = new FutureTask<Void>(discoverer, null);
+      new Thread(f).start();
+      tasks.add(f);
     }
 
     if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
     {
-      t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
-              .startDiscoverer(changeSupport);
+      tasks.add(jalview.ws.jws2.Jws2Discoverer.getDiscoverer().startDiscoverer());
     }
-    Thread t3 = null;
+    if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true))
     {
-      // TODO: do rest service discovery
+      tasks.add(jalview.ws.slivkaws.SlivkaWSDiscoverer.getInstance().startDiscoverer());
     }
     if (blocking)
     {
-      while (alive)
-      {
+      for (Future<?> task : tasks) {
         try
         {
-          Thread.sleep(15);
+          // block until all discovery tasks are done
+          task.get();
         } catch (Exception e)
         {
+          e.printStackTrace();
         }
-        alive = (t1 != null && t1.isAlive()) || (t2 != null && t2.isAlive())
-                || (t3 != null && t3.isAlive())
-                || (t0 != null && t0.isAlive());
       }
     }
   }
@@ -2681,8 +2695,9 @@ public class Desktop extends jalview.jbgui.GDesktop
   {
     if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector)
     {
-      final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
-              .getErrorMessages();
+      final WSDiscovererI discoverer = jalview.ws.jws2.Jws2Discoverer
+          .getDiscoverer();
+      final String ermsg = discoverer.getErrorMessages();
       if (ermsg != null)
       {
         if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true))