X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSClient.java;h=e4817807f2cf05d855973ab89e33f7172781ff93;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=8a352bf052c5fb9f9272ef5a7ec32ae35ac49b06;hpb=bf16f469383285628cdae9743c008095f9662605;p=jalview.git

diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java
index 8a352bf..e481780 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 2.6)
- * 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 WsParamSetI 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)
@@ -64,9 +58,9 @@ public class MsaWSClient extends Jws2Client
     // TODO Auto-generated constructor stub
   }
 
-  public MsaWSClient(Jws2Discoverer.Jws2Instance sh, WsParamSetI preset,
-          String altitle, jalview.datamodel.AlignmentView msa,
-          boolean submitGaps, boolean preserveOrder, Alignment seqdataset,
+  public MsaWSClient(Jws2Instance sh, WsParamSetI preset, String altitle,
+          jalview.datamodel.AlignmentView msa, boolean submitGaps,
+          boolean preserveOrder, Alignment seqdataset,
           AlignFrame _alignFrame)
   {
     this(sh, preset, null, false, altitle, msa, submitGaps, preserveOrder,
@@ -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
@@ -111,68 +109,7 @@ public class MsaWSClient extends Jws2Client
 
       return;
     }
-    server = sh.service;
-    this.preset=preset;
-    if (preset != null)
-    {
-      if (!((preset instanceof JabaPreset) || preset instanceof JabaWsParamSet)) {
-      /*{
-        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 = prset; // ((JabaPreset) prset).p;
-        paramset = null; // no user supplied parameters.
-      }
-    }
-
+    server = (MsaWS) sh.service;
     if ((wsInfo = setWebService(sh, false)) == null)
     {
       JOptionPane.showMessageDialog(Desktop.desktop,
@@ -323,7 +260,7 @@ public class MsaWSClient extends Jws2Client
         List<WsParamSetI> presets = service.getParamStore().getPresets();
         if (presets != null && presets.size() > 0)
         {
-          JMenu presetlist = new JMenu("Run "+calcName + "with preset");
+          JMenu presetlist = new JMenu("Run " + calcName + "with preset");
 
           for (final WsParamSetI preset : presets)
           {