X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FSequenceAnnotationWSClient.java;h=bf5dc2342340f1639c6a456b8bafd6ce29f774e1;hb=47b802c67970e1d0d90ad1b2200d905225bcb5c3;hp=e7e5a6f575a0d2c73c19bfb63ad8afe621c24caa;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git

diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
index e7e5a6f..bf5dc23 100644
--- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
+++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -25,6 +25,7 @@ import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.JvSwingUtils;
 import jalview.util.MessageManager;
+import jalview.ws.api.ServiceWithParameters;
 import jalview.ws.jws2.dm.AAConSettings;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.WsParamSetI;
@@ -67,9 +68,9 @@ public class SequenceAnnotationWSClient extends Jws2Client
     // dan changed! dan test. comment out if conditional
     // if (alignFrame.getViewport().getAlignment().isNucleotide())
     // {
-    // JOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
+    // JvOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
     // + " can only be used\nfor amino acid alignments.",
-    // "Wrong type of sequences!", JOptionPane.WARNING_MESSAGE);
+    // "Wrong type of sequences!", JvOptionPane.WARNING_MESSAGE);
     // return;
     //
     // }
@@ -82,9 +83,24 @@ public class SequenceAnnotationWSClient extends Jws2Client
       // columns
 
       List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
-              .getCalcManager().getRegisteredWorkersOfClass(clientClass);
-      AbstractJabaCalcWorker worker;
-      if (clnts == null || clnts.size() == 0)
+              .getCalcManager()
+              .getRegisteredWorkersOfClass(SeqAnnotationServiceCalcWorker.class);
+
+      SeqAnnotationServiceCalcWorker worker = null;
+      if (clnts != null)
+      {
+        for (AlignCalcWorkerI _worker : clnts)
+        {
+          worker = (SeqAnnotationServiceCalcWorker) _worker;
+          if (worker.hasService()
+                  && worker.getService().getClass().equals(clientClass))
+          {
+            break;
+          }
+          worker = null;
+        }
+      }
+      if (worker == null)
       {
         if (!processParams(sh, editParams))
         {
@@ -92,16 +108,14 @@ public class SequenceAnnotationWSClient extends Jws2Client
         }
         try
         {
-          worker = (AbstractJabaCalcWorker) (clientClass
-                  .getConstructor(new Class[] { Jws2Instance.class,
-                      AlignFrame.class, WsParamSetI.class, List.class })
-                  .newInstance(new Object[] { sh, alignFrame, this.preset,
-                      paramset }));
+          worker = new SeqAnnotationServiceCalcWorker(sh, alignFrame, this.preset,
+                  paramset);
         } catch (Exception x)
         {
           x.printStackTrace();
           throw new Error(
-                  MessageManager.getString("error.implementation_error"), x);
+                  MessageManager.getString("error.implementation_error"),
+                  x);
         }
         alignFrame.getViewport().getCalcManager().registerWorker(worker);
         alignFrame.getViewport().getCalcManager().startWorker(worker);
@@ -109,7 +123,6 @@ public class SequenceAnnotationWSClient extends Jws2Client
       }
       else
       {
-        worker = (AbstractJabaCalcWorker) clnts.get(0);
         if (editParams)
         {
           paramset = worker.getArguments();
@@ -122,11 +135,11 @@ public class SequenceAnnotationWSClient extends Jws2Client
         }
         // reinstate worker if it was blacklisted (might have happened due to
         // invalid parameters)
-        alignFrame.getViewport().getCalcManager().workerMayRun(worker);
+        alignFrame.getViewport().getCalcManager().enableWorker(worker);
         worker.updateParameters(this.preset, paramset);
       }
     }
-    if (sh.action.toLowerCase().contains("disorder"))
+    if (sh.getAction().toLowerCase().contains("disorder"))
     {
       // build IUPred style client. take sequences, returns annotation per
       // sequence.
@@ -135,18 +148,15 @@ public class SequenceAnnotationWSClient extends Jws2Client
         return;
       }
 
-      alignFrame
-              .getViewport()
-              .getCalcManager()
-              .startWorker(
-                      new AADisorderClient(sh, alignFrame, preset, paramset));
+      alignFrame.getViewport().getCalcManager().startWorker(
+              new SeqAnnotationServiceCalcWorker(sh, alignFrame, preset, paramset));
     }
   }
 
   public SequenceAnnotationWSClient(AAConSettings fave,
           AlignFrame alignFrame, boolean b)
   {
-    super(alignFrame, fave.getPreset(), fave.getJobArgset());
+    super(alignFrame, fave.getPreset(), fave.getArgumentSet());
     initSequenceAnnotationWSClient(fave.getService(), alignFrame,
             fave.getPreset(), b);
   }
@@ -157,29 +167,33 @@ public class SequenceAnnotationWSClient extends Jws2Client
    * @see jalview.ws.jws2.Jws2Client#attachWSMenuEntry(javax.swing.JMenu,
    * jalview.ws.jws2.jabaws2.Jws2Instance, jalview.gui.AlignFrame)
    */
-  public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
+  @Override
+  public void attachWSMenuEntry(JMenu wsmenu,
+          final ServiceWithParameters service,
           final AlignFrame alignFrame)
   {
-    if (registerAAConWSInstance(wsmenu, service, alignFrame))
+    if (Jws2ClientFactory.registerAAConWSInstance(wsmenu, service,
+            alignFrame))
     {
       // Alignment dependent analysis calculation WS gui
       return;
     }
     boolean hasparams = service.hasParameters();
     // Assume name ends in WS
-    String calcName = service.serviceType.substring(0,
-            service.serviceType.length() - 2);
+    String calcName = service.getName().substring(0,
+            service.getName().length() - 2);
 
     JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage(
-            "label.calcname_with_default_settings",
-            new String[] { calcName }));
+            "label.calcname_with_default_settings", new String[]
+            { calcName }));
     annotservice.addActionListener(new ActionListener()
     {
 
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        new SequenceAnnotationWSClient(service, alignFrame, null, false);
+        new SequenceAnnotationWSClient((Jws2Instance) service, alignFrame,
+                null, false);
       }
     });
     wsmenu.add(annotservice);
@@ -189,40 +203,42 @@ public class SequenceAnnotationWSClient extends Jws2Client
       // arguments
       annotservice = new JMenuItem(
               MessageManager.getString("label.edit_settings_and_run"));
-      annotservice
-              .setToolTipText(MessageManager
-                      .getString("label.view_and_change_parameters_before_running_calculation"));
+      annotservice.setToolTipText(MessageManager.getString(
+              "label.view_and_change_parameters_before_running_calculation"));
 
       annotservice.addActionListener(new ActionListener()
       {
+        @Override
         public void actionPerformed(ActionEvent e)
         {
-          new SequenceAnnotationWSClient(service, alignFrame, null, true);
+          new SequenceAnnotationWSClient((Jws2Instance) service, alignFrame,
+                  null, true);
         }
       });
       wsmenu.add(annotservice);
       List<WsParamSetI> presets = service.getParamStore().getPresets();
       if (presets != null && presets.size() > 0)
       {
-        JMenu presetlist = new JMenu(MessageManager.formatMessage(
-                "label.run_with_preset", new String[] { calcName }));
+        JMenu presetlist = new JMenu(MessageManager
+                .formatMessage("label.run_with_preset", new String[]
+                { calcName }));
 
         for (final WsParamSetI preset : presets)
         {
           final JMenuItem methodR = new JMenuItem(preset.getName());
-          methodR.setToolTipText(JvSwingUtils.wrapTooltip(
-                  true,
-                  "<strong>"
-                          + (preset.isModifiable() ? MessageManager
-                                  .getString("label.user_preset")
-                                  : MessageManager
-                                          .getString("label.service_preset"))
-                          + "</strong><br/>" + preset.getDescription()));
+          methodR.setToolTipText(JvSwingUtils.wrapTooltip(true, "<strong>"
+                  + (preset.isModifiable()
+                          ? MessageManager.getString("label.user_preset")
+                          : MessageManager
+                                  .getString("label.service_preset"))
+                  + "</strong><br/>" + preset.getDescription()));
           methodR.addActionListener(new ActionListener()
           {
+            @Override
             public void actionPerformed(ActionEvent e)
             {
-              new SequenceAnnotationWSClient(service, alignFrame, preset,
+              new SequenceAnnotationWSClient((Jws2Instance) service,
+                      alignFrame, preset,
                       false);
             }
 
@@ -237,7 +253,7 @@ public class SequenceAnnotationWSClient extends Jws2Client
     {
       annotservice = new JMenuItem(
               MessageManager.getString("label.view_documentation"));
-      if (service.docUrl != null)
+      if (service != null && service.hasDocumentationUrl())
       {
         annotservice.addActionListener(new ActionListener()
         {
@@ -245,12 +261,14 @@ public class SequenceAnnotationWSClient extends Jws2Client
           @Override
           public void actionPerformed(ActionEvent arg0)
           {
-            Desktop.instance.showUrl(service.docUrl);
+            Desktop.instance.showUrl(service.getDocumentationUrl());
           }
         });
-        annotservice.setToolTipText(JvSwingUtils.wrapTooltip(true,
-                MessageManager.formatMessage("label.view_service_doc_url",
-                        new String[] { service.docUrl, service.docUrl })));
+        annotservice.setToolTipText(
+                JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage(
+                        "label.view_service_doc_url", new String[]
+                        { service.getDocumentationUrl(),
+                            service.getDocumentationUrl() })));
         wsmenu.add(annotservice);
       }
     }