X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSClient.java;h=66ef9a64d926c60880a9c77f39f83ecc707b7278;hb=2a5cbe264ec842c1a0f93e6bd78294607a94e686;hp=fce5178ce4196b8eb852967a3f63966bc6d10237;hpb=e027f5e68a48d24b62ee86eb840aa186144edd65;p=jalview.git

diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java
index fce5178..66ef9a6 100644
--- a/src/jalview/ws/jws2/MsaWSClient.java
+++ b/src/jalview/ws/jws2/MsaWSClient.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -31,8 +31,8 @@ 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.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.WsParamSetI;
 
 /**
@@ -48,13 +48,7 @@ public class MsaWSClient extends Jws2Client
    */
   MsaWS server;
 
-  AlignFrame alignFrame;
-
-  private Preset preset;
-
-  private List<Argument> paramset;
-
-  public MsaWSClient(Jws2Discoverer.Jws2Instance sh, String altitle,
+  public MsaWSClient(Jws2Instance sh, String altitle,
           jalview.datamodel.AlignmentView msa, boolean submitGaps,
           boolean preserveOrder, Alignment seqdataset,
           AlignFrame _alignFrame)
@@ -64,7 +58,7 @@ public class MsaWSClient extends Jws2Client
     // TODO Auto-generated constructor stub
   }
 
-  public MsaWSClient(Jws2Discoverer.Jws2Instance sh, WsParamSetI preset,
+  public MsaWSClient(Jws2Instance sh, WsParamSetI preset,
           String altitle, jalview.datamodel.AlignmentView msa,
           boolean submitGaps, boolean preserveOrder, Alignment seqdataset,
           AlignFrame _alignFrame)
@@ -90,14 +84,18 @@ public class MsaWSClient extends Jws2Client
    *          DOCUMENT ME!
    */
 
-  public MsaWSClient(Jws2Discoverer.Jws2Instance sh, WsParamSetI preset,
+  public MsaWSClient(Jws2Instance sh, WsParamSetI preset,
           List<Argument> arguments, boolean editParams, String altitle,
           jalview.datamodel.AlignmentView msa, boolean submitGaps,
           boolean preserveOrder, Alignment seqdataset,
           AlignFrame _alignFrame)
   {
-    super();
-    alignFrame = _alignFrame;
+    super(_alignFrame, preset, arguments);
+    if (!processParams(sh, editParams))
+    {
+      return;
+    }
+
     if (!(sh.service instanceof MsaWS))
     {
       // redundant at mo - but may change
@@ -111,66 +109,7 @@ public class MsaWSClient extends Jws2Client
 
       return;
     }
-    server = sh.service;
-    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;
-      }
-      WsParamSetI prset = jobParams.getPreset();
-      if (prset == null)
-      {
-        paramset = JabaParamStore.getJabafromJwsArgs(jobParams
-                .getJobParams());
-      }
-      else
-      {
-        this.preset = ((JabaPreset) prset).p;
-        paramset = null; // no user supplied parameters.
-      }
-    }
-
+    server = (MsaWS) sh.service;
     if ((wsInfo = setWebService(sh, false)) == null)
     {
       JOptionPane.showMessageDialog(Desktop.desktop,
@@ -252,6 +191,7 @@ public class MsaWSClient extends Jws2Client
     return (WebServiceName.indexOf("lustal") > -1); // cheat!
   }
 
+  
   public void attachWSMenuEntry(JMenu rmsawsmenu,
           final Jws2Instance service, final AlignFrame alignFrame)
   {
@@ -270,17 +210,22 @@ public class MsaWSClient extends Jws2Client
       rmsawsmenu.add(msawsmenu);
       calcName = "";
     }
-
+    boolean hasparams = service.hasParameters();
     do
     {
+      String action = "Align ";
       if (submitGaps == true)
       {
-        msawsmenu = new JMenu("profile " + svcname);
+        action = "Realign ";
+        msawsmenu = new JMenu("Realign with " + svcname);
+        msawsmenu
+                .setToolTipText("Align sequences to an existing alignment");
         rmsawsmenu.add(msawsmenu);
       }
       final boolean withGaps = submitGaps;
-      JMenuItem method = new JMenuItem(calcName + "Defaults");
-      method.setToolTipText("Align with default settings");
+
+      JMenuItem method = new JMenuItem(calcName + "with Defaults");
+      method.setToolTipText(action + "with default settings");
 
       method.addActionListener(new ActionListener()
       {
@@ -294,48 +239,55 @@ public class MsaWSClient extends Jws2Client
         }
       });
       msawsmenu.add(method);
-      method = new JMenuItem(calcName + "Edit and run ...");
-      method.setToolTipText("View and change the parameters before alignment.");
-
-      method.addActionListener(new ActionListener()
+      if (hasparams)
       {
-        public void actionPerformed(ActionEvent e)
-        {
-          AlignmentView msa = alignFrame.gatherSequencesForAlignment();
-          new MsaWSClient(service, null, null, true, alignFrame.getTitle(),
-                  msa, withGaps, true, alignFrame.getViewport()
-                          .getAlignment().getDataset(), alignFrame);
+        // only add these menu options if the service has user-modifiable
+        // arguments
+        method = new JMenuItem("Edit settings and run ...");
+        method.setToolTipText("View and change the parameters before alignment.");
 
-        }
-      });
-      msawsmenu.add(method);
-      List<WsParamSetI> presets = service.getParamStore().getPresets();
-      if (presets != null && presets.size() > 0)
-      {
-        JMenu presetlist = new JMenu(calcName + "Presets");
+        method.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            AlignmentView msa = alignFrame.gatherSequencesForAlignment();
+            new MsaWSClient(service, null, null, true, alignFrame
+                    .getTitle(), msa, withGaps, true, alignFrame
+                    .getViewport().getAlignment().getDataset(), alignFrame);
 
-        for (final WsParamSetI preset : presets)
+          }
+        });
+        msawsmenu.add(method);
+        List<WsParamSetI> presets = service.getParamStore().getPresets();
+        if (presets != null && presets.size() > 0)
         {
-          final JMenuItem methodR = new JMenuItem(preset.getName());
-          methodR.setToolTipText("<html><p>"+JvSwingUtils.wrapTooltip("<strong>"
-                  + (preset.isModifiable() ? "User Preset"
-                          : "Service Preset") + "</strong><br/>"
-                  + preset.getDescription() + "</p>")+"</html>");
-          methodR.addActionListener(new ActionListener()
+          JMenu presetlist = new JMenu("Run "+calcName + "with preset");
+
+          for (final WsParamSetI preset : presets)
           {
-            public void actionPerformed(ActionEvent e)
+            final JMenuItem methodR = new JMenuItem(preset.getName());
+            methodR.setToolTipText("<html><p>"
+                    + JvSwingUtils.wrapTooltip("<strong>"
+                            + (preset.isModifiable() ? "User Preset"
+                                    : "Service Preset") + "</strong><br/>"
+                            + preset.getDescription() + "</p>") + "</html>");
+            methodR.addActionListener(new ActionListener()
             {
-              AlignmentView msa = alignFrame.gatherSequencesForAlignment();
-              new MsaWSClient(service, preset, alignFrame.getTitle(), msa,
-                      false, true, alignFrame.getViewport().getAlignment()
-                              .getDataset(), alignFrame);
+              public void actionPerformed(ActionEvent e)
+              {
+                AlignmentView msa = alignFrame
+                        .gatherSequencesForAlignment();
+                new MsaWSClient(service, preset, alignFrame.getTitle(),
+                        msa, false, true, alignFrame.getViewport()
+                                .getAlignment().getDataset(), alignFrame);
 
-            }
+              }
 
-          });
-          presetlist.add(methodR);
+            });
+            presetlist.add(methodR);
+          }
+          msawsmenu.add(presetlist);
         }
-        msawsmenu.add(presetlist);
       }
       if (!submitGaps && canSubmitGaps())
       {