JAL-591

[jalview.git] / src / jalview / ws / jws2 / MsaWSClient.java

diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java
index 1d9a89c..d7b968d 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,
@@ -108,17 +112,63 @@ public class MsaWSClient extends Jws2Client
       return;
     }
     server = sh.service;
-    this.preset = preset;
-    this.paramset = arguments;
+    if (preset != null)
+    {
+      if (preset instanceof JabaPreset)
+      {
+        this.preset = ((JabaPreset) preset).p;
+      }
+      else if (preset instanceof JabaWsParamSet)
+      {
+        List<Argument> newargs = new ArrayList<Argument>();
+        JabaWsParamSet pset = ((JabaWsParamSet) preset);
+        for (Option opt : pset.getjabaArguments())
+        {
+          newargs.add(opt);
+        }
+        if (arguments != null && arguments.size() > 0)
+        {
+          // merge arguments with preset's own arguments.
+          for (Argument opt : arguments)
+          {
+            newargs.add(opt);
+          }
+        }
+        paramset = newargs;
+      }
+      else
+      {
+        throw new Error(
+                "Implementation error: Can only instantiate Jaba parameter sets.");
+      }
+    }
+    else
+    {
+      // just provided with a bunch of arguments
+      this.paramset = arguments;
+    }
     if (editParams)
     {
+      if (sh.paramStore == null)
+      {
+        sh.paramStore = new JabaParamStore(sh, Desktop.getUserParameterStore());
+      }
       WsJobParameters jobParams = new WsJobParameters(sh, preset);
       if (!jobParams.showRunDialog())
       {
         return;
       }
-      preset = null;
-      paramset = jobParams.getJobParams();
+      WsParamSetI prset = jobParams.getPreset();
+      if (prset == null)
+      {
+        paramset = JabaParamStore.getJabafromJwsArgs(jobParams
+                .getJobParams());
+      }
+      else
+      {
+        this.preset = ((JabaPreset) prset).p;
+        paramset = null; // no user supplied parameters.
+      }
     }
 
     if ((wsInfo = setWebService(sh, false)) == null)
@@ -211,7 +261,7 @@ 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())
@@ -259,15 +309,18 @@ 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)