apply version 2.7 copyright

[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 fce5178..4f6ce09 100644 (file)
--- 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, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -50,7 +50,7 @@ public class MsaWSClient extends Jws2Client
 
   AlignFrame alignFrame;
 
-  private Preset preset;
+  private WsParamSetI preset;
 
   private List<Argument> paramset;
 
@@ -112,10 +112,11 @@ public class MsaWSClient extends Jws2Client
       return;
     }
     server = sh.service;
+    this.preset=preset;
     if (preset != null)
     {
-      if (preset instanceof JabaPreset)
-      {
+      if (!((preset instanceof JabaPreset) || preset instanceof JabaWsParamSet)) {
+      /*{
         this.preset = ((JabaPreset) preset).p;
       }
       else if (preset instanceof JabaWsParamSet)
@@ -137,7 +138,7 @@ public class MsaWSClient extends Jws2Client
         paramset = newargs;
       }
       else
-      {
+      {*/
         throw new Error(
                 "Implementation error: Can only instantiate Jaba parameter sets.");
       }
@@ -151,7 +152,8 @@ public class MsaWSClient extends Jws2Client
     {
       if (sh.paramStore == null)
       {
-        sh.paramStore = new JabaParamStore(sh, Desktop.getUserParameterStore());
+        sh.paramStore = new JabaParamStore(sh,
+                Desktop.getUserParameterStore());
       }
       WsJobParameters jobParams = new WsJobParameters(sh, preset);
       if (!jobParams.showRunDialog())
@@ -166,7 +168,7 @@ public class MsaWSClient extends Jws2Client
       }
       else
       {
-        this.preset = ((JabaPreset) prset).p;
+        this.preset = prset; // ((JabaPreset) prset).p;
         paramset = null; // no user supplied parameters.
       }
     }
@@ -270,17 +272,22 @@ 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 +301,55 @@ 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())
       {