edit jws2 job parameters before running job

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 2d1fc1e..ca4a48b 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -30,6 +30,7 @@ import javax.swing.*;
 import javax.swing.event.MenuEvent;
 
 import jalview.analysis.*;
+import jalview.bin.Cache;
 import jalview.commands.*;
 import jalview.datamodel.*;
 import jalview.io.*;
@@ -514,16 +515,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /* Set up intrinsic listeners for dynamically generated GUI bits. */
   private void addServiceListeners()
   {
-    final java.beans.PropertyChangeListener thisListener, thatListener;
-    // Do this once to get current state
-    BuildWebServiceMenu();
-    Desktop.discoverer
-            .addPropertyChangeListener(thisListener = new java.beans.PropertyChangeListener()
+    final java.beans.PropertyChangeListener thisListener;
+    Desktop.instance.addJalviewPropertyChangeListener("services",
+            thisListener = new java.beans.PropertyChangeListener()
             {
               public void propertyChange(PropertyChangeEvent evt)
               {
-                // System.out.println("Discoverer property change.");
-                if (evt.getPropertyName().equals("services"))
+                // // System.out.println("Discoverer property change.");
+                // if (evt.getPropertyName().equals("services"))
                 {
                   SwingUtilities.invokeLater(new Runnable()
                   {
@@ -532,7 +531,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     public void run()
                     {
                       System.err
-                              .println("Change support JWS1: build services again.");
+                              .println("Rebuild WS Menu for service change");
                       BuildWebServiceMenu();
                     }
 
@@ -540,29 +539,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 }
               }
             });
-    jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
-            .addPropertyChangeListener(
-                    thatListener = new java.beans.PropertyChangeListener()
-                    {
-                      public void propertyChange(PropertyChangeEvent evt)
-                      {
-                        System.err
-                                .println("Change support JWS2: build services again.");
-                        BuildWebServiceMenu();
-                      }
-                    });
     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
     {
       public void internalFrameClosed(
               javax.swing.event.InternalFrameEvent evt)
       {
-        // System.out.println("deregistering discoverer listener");
-        Desktop.discoverer.removePropertyChangeListener(thisListener);
-        jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
-                .removePropertyChangeListener(thatListener);
+        System.out.println("deregistering discoverer listener");
+        Desktop.instance.removeJalviewPropertyChangeListener("services",
+                thisListener);
         closeMenuItem_actionPerformed(true);
       };
     });
+    // Finally, build the menu once to get current service state
+    BuildWebServiceMenu();
   }
 
   public void setGUINucleotide(boolean nucleotide)
@@ -3843,7 +3832,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // object broker mechanism.
       Vector wsmenu = new Vector();
       final IProgressIndicator af = this;
-      if ((Discoverer.services != null) && (Discoverer.services.size() > 0))
+      if (Cache.getDefault("SHOW_JWS1_SERVICES", true)
+              && Discoverer.services != null
+              && (Discoverer.services.size() > 0))
       {
         // TODO: refactor to allow list of AbstractName/Handler bindings to be
         // stored or retrieved from elsewhere
@@ -3901,6 +3892,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
 
       // TODO: move into separate menu builder class.
+      if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
       {
         Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
         if (jws2servs != null)
@@ -3909,13 +3901,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           {
             JMenu jws2men = new JMenu("Jalview 2 Services");
             jws2servs.attachWSMenuEntry(jws2men, this);
-            wsmenu.add(jws2men);
-          }
-          else
-          {
-            if (!jws2servs.isRunning())
+            for (int i = 0, iSize = jws2men.getMenuComponentCount(); i < iSize; i++)
             {
-              new Thread(jws2servs).start();
+              wsmenu.add(jws2men.getMenuComponent(i));
             }
           }
         }
@@ -3959,8 +3947,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   private void build_urlServiceMenu(JMenu webService)
   {
-    jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
-            webService, this);
+    if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
+    {
+      jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
+              webService, this);
+    }
   }
 
   /*
@@ -4714,8 +4705,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       for (int g = 0; g < gps.length; g++)
       {
         gps[g].setShowNonconserved(viewport.getShowUnconserved());
-        gps[g].setIncludeAllConsSymbols(viewport
-                .isIncludeAllConsensusSymbols());
+        gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
         viewport.alignment.addGroup(gps[g]);
         Color col = new Color((int) (Math.random() * 255), (int) (Math
                 .random() * 255), (int) (Math.random() * 255));