X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSClient.java;h=4e3f81c137e8438ec73a51952e4627add3ccfaad;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=b65242fd5d2e84ea34e9f0b8430299daf3b7f9ca;hpb=fee7b75bff69e58669a3b42f31e1c7a4c3607518;p=jalview.git

diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java
index b65242f..4e3f81c 100644
--- a/src/jalview/ws/jws2/MsaWSClient.java
+++ b/src/jalview/ws/jws2/MsaWSClient.java
@@ -1,19 +1,20 @@
 /*
- * 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 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.ws.jws2;
 
@@ -27,9 +28,8 @@ import jalview.datamodel.*;
 import jalview.gui.*;
 import compbio.data.msa.MsaWS;
 import compbio.metadata.Argument;
-import compbio.metadata.Preset;
-import compbio.metadata.PresetManager;
-import jalview.ws.jws2.Jws2Discoverer.Jws2Instance;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.WsParamSetI;
 
 /**
  * DOCUMENT ME!
@@ -43,28 +43,27 @@ public class MsaWSClient extends Jws2Client
    * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
    */
   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)
   {
-    this(sh, null, null, altitle, msa, submitGaps, preserveOrder, seqdataset, _alignFrame);
+    this(sh, null, null, false, altitle, msa, submitGaps, preserveOrder,
+            seqdataset, _alignFrame);
     // TODO Auto-generated constructor stub
   }
 
-  public MsaWSClient(Jws2Discoverer.Jws2Instance sh, Preset preset, String altitle,
+  public MsaWSClient(Jws2Instance sh, WsParamSetI preset, String altitle,
           jalview.datamodel.AlignmentView msa, boolean submitGaps,
           boolean preserveOrder, Alignment seqdataset,
           AlignFrame _alignFrame)
   {
-    this(sh, preset, null, altitle, msa, submitGaps, preserveOrder, seqdataset, _alignFrame);
+    this(sh, preset, null, false, altitle, msa, submitGaps, preserveOrder,
+            seqdataset, _alignFrame);
     // TODO Auto-generated constructor stub
   }
+
   /**
    * Creates a new MsaWSClient object that uses a service given by an externally
    * retrieved ServiceHandle
@@ -81,12 +80,18 @@ public class MsaWSClient extends Jws2Client
    *          DOCUMENT ME!
    */
 
-  public MsaWSClient(Jws2Discoverer.Jws2Instance sh, Preset preset, List<Argument> arguments, String altitle,
+  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;
+          AlignFrame _alignFrame)
+  {
+    super(_alignFrame, preset, arguments);
+    if (!processParams(sh, editParams))
+    {
+      return;
+    }
+
     if (!(sh.service instanceof MsaWS))
     {
       // redundant at mo - but may change
@@ -100,9 +105,7 @@ public class MsaWSClient extends Jws2Client
 
       return;
     }
-    server = sh.service;
-    this.preset = preset;
-    this.paramset = arguments;
+    server = (MsaWS) sh.service;
     if ((wsInfo = setWebService(sh, false)) == null)
     {
       JOptionPane.showMessageDialog(Desktop.desktop,
@@ -125,10 +128,10 @@ public class MsaWSClient extends Jws2Client
   private void startMsaWSClient(String altitle, AlignmentView msa,
           boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
   {
-    //if (!locateWebService())
-   // {
-   //   return;
-   // }
+    // if (!locateWebService())
+    // {
+    // return;
+    // }
 
     wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")
             + " of " + altitle + "\nJob details\n");
@@ -154,9 +157,9 @@ public class MsaWSClient extends Jws2Client
               + "alignment of " + altitle;
     }
 
-    MsaWSThread msathread = new MsaWSThread(server, preset, paramset, WsURL, wsInfo,
-            alignFrame, WebServiceName, jobtitle, msa, submitGaps,
-            preserveOrder, seqdataset);
+    MsaWSThread msathread = new MsaWSThread(server, preset, paramset,
+            WsURL, wsInfo, alignFrame, WebServiceName, jobtitle, msa,
+            submitGaps, preserveOrder, seqdataset);
     wsInfo.setthisService(msathread);
     msathread.start();
   }
@@ -184,72 +187,112 @@ public class MsaWSClient extends Jws2Client
     return (WebServiceName.indexOf("lustal") > -1); // cheat!
   }
 
-  public void attachWSMenuEntry(JMenu msawsmenu,
+  public void attachWSMenuEntry(JMenu rmsawsmenu,
           final Jws2Instance service, final AlignFrame alignFrame)
   {
     setWebService(service, true); // headless
-    JMenuItem method = new JMenuItem(WebServiceName);
-    method.setToolTipText(WsURL);
-    method.addActionListener(new ActionListener()
+    boolean finished = true, submitGaps = false;
+    JMenu msawsmenu = rmsawsmenu;
+    String svcname = WebServiceName;
+    if (svcname.endsWith("WS"))
     {
-      public void actionPerformed(ActionEvent e)
+      svcname = svcname.substring(0, svcname.length() - 2);
+    }
+    String calcName = svcname + " ";
+    if (canSubmitGaps())
+    {
+      msawsmenu = new JMenu(svcname);
+      rmsawsmenu.add(msawsmenu);
+      calcName = "";
+    }
+    boolean hasparams = service.hasParameters();
+    do
+    {
+      String action = "Align ";
+      if (submitGaps == true)
       {
-        AlignmentView msa = alignFrame.gatherSequencesForAlignment();
-        new MsaWSClient(service, alignFrame.getTitle(),
-                msa, false, true, alignFrame.getViewport().getAlignment()
-                        .getDataset(), alignFrame);
-
+        action = "Realign ";
+        msawsmenu = new JMenu("Realign with " + svcname);
+        msawsmenu
+                .setToolTipText("Align sequences to an existing alignment");
+        rmsawsmenu.add(msawsmenu);
       }
+      final boolean withGaps = submitGaps;
 
-    });
-    msawsmenu.add(method);
-    if (canSubmitGaps())
-    {
-      // We know that ClustalWS can accept partial alignments for refinement.
-      final JMenuItem methodR = new JMenuItem(WebServiceName 
-              + " (With Gaps)");
-      methodR.setToolTipText(WsURL);
-      methodR.addActionListener(new ActionListener()
+      JMenuItem method = new JMenuItem(calcName + "with Defaults");
+      method.setToolTipText(action + "with default settings");
+
+      method.addActionListener(new ActionListener()
       {
         public void actionPerformed(ActionEvent e)
         {
           AlignmentView msa = alignFrame.gatherSequencesForAlignment();
-          new MsaWSClient(service, alignFrame.getTitle(),
-                  msa, true, true, alignFrame.getViewport().getAlignment()
+          new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
+                  true, alignFrame.getViewport().getAlignment()
                           .getDataset(), alignFrame);
 
         }
-
       });
-      msawsmenu.add(methodR);
-
-    }
-    PresetManager presets = service.getPresets();
-    if (presets!=null && presets.getPresets().size()>0)
-    {
-      JMenu presetlist = new JMenu("Presets for "+WebServiceName+"(Without gaps)");
-      
-      for (final Preset preset : (List<Preset>) presets.getPresets())
+      msawsmenu.add(method);
+      if (hasparams)
       {
-        final JMenuItem methodR = new JMenuItem(preset.getName());
-        methodR.setToolTipText(preset.getDescription());
-        methodR.addActionListener(new ActionListener()
+        // 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.");
+
+        method.addActionListener(new ActionListener()
         {
           public void actionPerformed(ActionEvent e)
           {
             AlignmentView msa = alignFrame.gatherSequencesForAlignment();
-            new MsaWSClient(service, preset, alignFrame.getTitle(),
-                    msa, false, true, alignFrame.getViewport().getAlignment()
-                            .getDataset(), alignFrame);
+            new MsaWSClient(service, null, null, true, alignFrame
+                    .getTitle(), msa, withGaps, true, alignFrame
+                    .getViewport().getAlignment().getDataset(), alignFrame);
 
           }
-
         });
-        presetlist.add(methodR);
-      }
-      msawsmenu.add(presetlist);
-    }
+        msawsmenu.add(method);
+        List<WsParamSetI> presets = service.getParamStore().getPresets();
+        if (presets != null && presets.size() > 0)
+        {
+          JMenu presetlist = new JMenu("Run " + calcName + "with preset");
 
-  }
+          for (final WsParamSetI preset : presets)
+          {
+            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()
+            {
+              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);
+          }
+          msawsmenu.add(presetlist);
+        }
+      }
+      if (!submitGaps && canSubmitGaps())
+      {
+        submitGaps = true;
+        finished = false;
+      }
+      else
+      {
+        finished = true;
+      }
+    } while (!finished);
+  }
 }