abstracted GUI to use jalview.ws.params objects (JAL-591, JAL-633). User defined...

diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java
index 2528308..eccbdaf 100644 (file)
--- a/src/jalview/ws/jws2/Jws2Discoverer.java
+++ b/src/jalview/ws/jws2/Jws2Discoverer.java
@@ -15,6 +15,8 @@ import java.util.Vector;
 
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
 
 import org.apache.log4j.Level;
 
@@ -22,6 +24,7 @@ import jalview.bin.Cache;
 import jalview.datamodel.AlignmentView;
 import jalview.gui.AlignFrame;
 import jalview.ws.WSMenuEntryProviderI;
+import jalview.ws.params.ParamDatastoreI;
 import compbio.data.msa.MsaWS;
 import compbio.metadata.Option;
 import compbio.metadata.Preset;
@@ -179,6 +182,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
 
     PresetManager presets = null;
 
+    public JabaParamStore paramStore=null;
+
     /**
      * non thread safe - gets the presets for this service (blocks whilst it
      * calls the service to get the preset set)
@@ -250,6 +255,19 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       }
       super.finalize();
     }
+
+    public ParamDatastoreI getParamStore()
+    {
+      if (paramStore == null)
+      {
+        try {
+        paramStore = new JabaParamStore(this);
+        } catch (Exception ex)
+        {}
+        
+      }
+      return paramStore;
+    }
   };
 
   /**
@@ -287,6 +305,35 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
 
   public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
   {
+    // dynamically regenerate service list.
+    final JMenu jws2al = new JMenu("JABA Alignment");
+    jws2al.addMenuListener(new MenuListener() {
+      // TODO: future: add menu listener to parent menu - so submenus are populated *before* they are selected.
+      @Override
+      public void menuSelected(MenuEvent e)
+      {
+        populateWSMenuEntry(jws2al, alignFrame);
+      }
+
+      @Override
+      public void menuDeselected(MenuEvent e)
+      {
+        // TODO Auto-generated method stub
+        
+      }
+
+      @Override
+      public void menuCanceled(MenuEvent e)
+      {
+        // TODO Auto-generated method stub
+        
+      }
+      
+    });
+    wsmenu.add(jws2al);
+  }
+  private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame)
+  {
     if (running || services == null || services.size() == 0)
     {
       return;
@@ -297,9 +344,10 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
      * eventually, JWS2 services will appear under the same align/etc submenus.
      * for moment we keep them separate.
      */
-    JMenu atpoint, jws2al = new JMenu("JABA Alignment");
+    JMenu atpoint;
     MsaWSClient msacl = new MsaWSClient();
     Vector hostLabels = new Vector();
+    jws2al.removeAll();
     for (final Jws2Instance service : services)
     {
       atpoint = jws2al;
@@ -345,11 +393,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
        * alignFrame); } });
        */
     }
-    if (services.size() > 0)
-    {
-      wsmenu.add(jws2al);
-    }
-
   }
 
   public static void main(String[] args)

diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java
index 820dfb4..e025df6 100644 (file)
--- a/src/jalview/ws/jws2/MsaWSClient.java
+++ b/src/jalview/ws/jws2/MsaWSClient.java
@@ -19,6 +19,7 @@ package jalview.ws.jws2;
 
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.util.ArrayList;
 import java.util.List;
 
 import javax.swing.*;
@@ -27,9 +28,12 @@ import jalview.datamodel.*;
 import jalview.gui.*;
 import compbio.data.msa.MsaWS;
 import compbio.metadata.Argument;
+import compbio.metadata.Option;
 import compbio.metadata.Preset;
 import compbio.metadata.PresetManager;
 import jalview.ws.jws2.Jws2Discoverer.Jws2Instance;
+import jalview.ws.jws2.dm.JabaWsParamSet;
+import jalview.ws.params.WsParamSetI;
 
 /**
  * DOCUMENT ME!
@@ -60,7 +64,7 @@ public class MsaWSClient extends Jws2Client
     // TODO Auto-generated constructor stub
   }
 
-  public MsaWSClient(Jws2Discoverer.Jws2Instance sh, Preset preset,
+  public MsaWSClient(Jws2Discoverer.Jws2Instance sh, WsParamSetI preset,
           String altitle, jalview.datamodel.AlignmentView msa,
           boolean submitGaps, boolean preserveOrder, Alignment seqdataset,
           AlignFrame _alignFrame)
@@ -86,7 +90,7 @@ public class MsaWSClient extends Jws2Client
    *          DOCUMENT ME!
    */
 
-  public MsaWSClient(Jws2Discoverer.Jws2Instance sh, Preset preset,
+  public MsaWSClient(Jws2Discoverer.Jws2Instance sh, WsParamSetI preset,
           List<Argument> arguments, boolean editParams, String altitle,
           jalview.datamodel.AlignmentView msa, boolean submitGaps,
           boolean preserveOrder, Alignment seqdataset,
@@ -108,19 +112,48 @@ public class MsaWSClient extends Jws2Client
       return;
     }
     server = sh.service;
-    this.preset = preset;
+    if (preset!=null) {
+      if (preset instanceof JabaPreset){
+        this.preset = ((JabaPreset)preset).p;
+      }  else
+        if (preset instanceof JabaWsParamSet) {
+          JabaWsParamSet pset = ((JabaWsParamSet)preset);
+          if (arguments!=null && arguments.size()>0)
+          {
+            // merge arguments with preset's own arguments.
+            List<Argument> oldargs = arguments;
+            arguments = new ArrayList<Argument>();
+            for (Option opt : pset.getjabaArguments()) {
+              arguments.add(opt);
+            }
+            for (Argument opt: oldargs)
+            {
+              arguments.add(opt);
+            }
+          }
+        
+      }else{
+        throw new Error("Implementation error: Can only instantiate Jaba parameter sets.");
+      }
+    }
     this.paramset = arguments;
     if (editParams)
     {
+      if (sh.paramStore==null)
+      {
+        sh.paramStore = new JabaParamStore(sh);
+      }
       WsJobParameters jobParams = new WsJobParameters(sh, preset);
       if (!jobParams.showRunDialog())
       {
         return;
       }
-      if ((this.preset = jobParams.getPreset())==null)
+      WsParamSetI prset = jobParams.getPreset();
+      if (prset==null)
       {
-        paramset = jobParams.getJobParams();
+        paramset = JabaParamStore.getJabafromJwsArgs(jobParams.getJobParams());
       } else {
+        this.preset = ((JabaPreset)prset).p;
         paramset = null; // no user supplied parameters.
       }
     }
@@ -215,7 +248,7 @@ public class MsaWSClient extends Jws2Client
     String svcname = WebServiceName;
     if (svcname.endsWith("WS"))
     {
-      svcname = svcname.substring(0,svcname.length()-2);
+      svcname = svcname.substring(0, svcname.length() - 2);
     }
     String calcName = svcname + " ";
     if (canSubmitGaps())
@@ -263,15 +296,18 @@ public class MsaWSClient extends Jws2Client
         }
       });
       msawsmenu.add(method);
-      PresetManager presets = service.getPresets();
-      if (presets != null && presets.getPresets().size() > 0)
+      List<WsParamSetI> presets = service.getParamStore().getPresets();
+      if (presets != null && presets.size() > 0)
       {
         JMenu presetlist = new JMenu(calcName + "Presets");
 
-        for (final Preset preset : (List<Preset>) presets.getPresets())
+        for (final WsParamSetI preset : presets)
         {
           final JMenuItem methodR = new JMenuItem(preset.getName());
-          methodR.setToolTipText("<html><p>"+preset.getDescription()+"</p></html>");
+          methodR.setToolTipText("<html><p><strong>"
+                  + (preset.isModifiable() ? "User Preset"
+                          : "Service Preset") + "</strong><br/>"
+                  + preset.getDescription() + "</p></html>");
           methodR.addActionListener(new ActionListener()
           {
             public void actionPerformed(ActionEvent e)

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index 686f516..dabe368 100644 (file)
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -456,9 +456,11 @@ class MsaWSThread extends AWS2Thread implements WSClientI
           {
             boolean cancelledJob = server
                     .cancelJob(jobs[job].getJobId());
-            if (cancelledJob)
+            if (cancelledJob || true)
             {
               // CANCELLED_JOB
+              // if the Jaba server indicates the job can't be cancelled, its because its running on the server's local execution engine
+              // so we just close the window anyway.
               cancelledMessage = "Job cancelled.";
               ((MsaWSJob) jobs[job]).cancel(); // TODO: refactor to avoid this ugliness - 
               wsInfo.setStatus(jobs[job].getJobnum(),