X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FSequenceAnnotationWSClient.java;h=eb0884870c2ff2da8508936d9c5733683bc3029e;hb=54ee3e95ec4f21a301e458f8b7f22876ae70a017;hp=d57eae40b5d1c38721a3fbaf90204a19cd49f8c0;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
index d57eae4..eb08848 100644
--- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
+++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
@@ -1,41 +1,41 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ * 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/>.
+ * 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;
 
 import jalview.api.AlignCalcWorkerI;
-import jalview.bin.Cache;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.JvSwingUtils;
+import jalview.util.MessageManager;
 import jalview.ws.jws2.dm.AAConSettings;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.WsParamSetI;
+import jalview.ws.uimodel.AlignAnalysisUIText;
 
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.util.List;
 
-import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.event.MenuEvent;
-import javax.swing.event.MenuListener;
 
 /**
  * @author jprocter
@@ -43,9 +43,6 @@ import javax.swing.event.MenuListener;
  */
 public class SequenceAnnotationWSClient extends Jws2Client
 {
-
-  public static final String AAConCalcId = "jabaws2.AACon";
-
   /**
    * initialise a client so its attachWSMenuEntry method can be called.
    */
@@ -61,44 +58,60 @@ public class SequenceAnnotationWSClient extends Jws2Client
     initSequenceAnnotationWSClient(sh, alignFrame, preset, editParams);
   }
 
+  // dan think. Do I need to change this method to run RNAalifold through the
+  // GUI
+
   public void initSequenceAnnotationWSClient(final Jws2Instance sh,
           AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
   {
-    if (alignFrame.getViewport().getAlignment().isNucleotide())
+    // dan changed! dan test. comment out if conditional
+    // if (alignFrame.getViewport().getAlignment().isNucleotide())
+    // {
+    // JvOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
+    // + " can only be used\nfor amino acid alignments.",
+    // "Wrong type of sequences!", JvOptionPane.WARNING_MESSAGE);
+    // return;
+    //
+    // }
+    AlignAnalysisUIText aaui = sh.getAlignAnalysisUI();
+    if (aaui != null)
     {
-      JOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
-              + " can only be used\nfor amino acid alignments.",
-              "Wrong type of sequences!", JOptionPane.WARNING_MESSAGE);
-      return;
+      Class clientClass = aaui.getClient();
 
-    }
-    if (sh.action.toLowerCase().contains("conservation"))
-    {
       // Build an AACon style client - take alignment, return annotation for
       // columns
 
       List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
-              .getCalcManager()
-              .getRegisteredWorkersOfClass(AAConClient.class);
+              .getCalcManager().getRegisteredWorkersOfClass(clientClass);
+      AbstractJabaCalcWorker worker;
       if (clnts == null || clnts.size() == 0)
       {
         if (!processParams(sh, editParams))
         {
           return;
         }
-        AAConClient worker;
-        alignFrame
-                .getViewport()
-                .getCalcManager()
-                .registerWorker(
-                        worker = new AAConClient(sh, alignFrame,
-                                this.preset, paramset));
+        try
+        {
+          worker = (AbstractJabaCalcWorker) (clientClass
+                  .getConstructor(new Class[]
+                  { Jws2Instance.class, AlignFrame.class, WsParamSetI.class,
+                      List.class })
+                  .newInstance(new Object[]
+                  { sh, alignFrame, this.preset, paramset }));
+        } catch (Exception x)
+        {
+          x.printStackTrace();
+          throw new Error(
+                  MessageManager.getString("error.implementation_error"),
+                  x);
+        }
+        alignFrame.getViewport().getCalcManager().registerWorker(worker);
         alignFrame.getViewport().getCalcManager().startWorker(worker);
 
       }
       else
       {
-        AAConClient worker = (AAConClient) clnts.get(0);
+        worker = (AbstractJabaCalcWorker) clnts.get(0);
         if (editParams)
         {
           paramset = worker.getArguments();
@@ -111,12 +124,11 @@ 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.
@@ -125,19 +137,15 @@ public class SequenceAnnotationWSClient extends Jws2Client
         return;
       }
 
-      alignFrame
-              .getViewport()
-              .getCalcManager()
-              .startWorker(
-                      new AADisorderClient(sh, alignFrame, preset, paramset));
+      alignFrame.getViewport().getCalcManager().startWorker(
+              new AADisorderClient(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);
   }
@@ -148,21 +156,23 @@ public class SequenceAnnotationWSClient extends Jws2Client
    * @see jalview.ws.jws2.Jws2Client#attachWSMenuEntry(javax.swing.JMenu,
    * jalview.ws.jws2.jabaws2.Jws2Instance, jalview.gui.AlignFrame)
    */
+  @Override
   public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
           final AlignFrame alignFrame)
   {
-    if (service.serviceType.equals(compbio.ws.client.Services.AAConWS
-            .toString()))
+    if (registerAAConWSInstance(wsmenu, service, alignFrame))
     {
-      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(calcName + " Defaults");
+    JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage(
+            "label.calcname_with_default_settings", new String[]
+            { calcName }));
     annotservice.addActionListener(new ActionListener()
     {
 
@@ -177,12 +187,14 @@ public class SequenceAnnotationWSClient extends Jws2Client
     {
       // only add these menu options if the service has user-modifiable
       // arguments
-      annotservice = new JMenuItem("Edit settings and run ...");
-      annotservice
-              .setToolTipText("View and change parameters before running calculation");
+      annotservice = new JMenuItem(
+              MessageManager.getString("label.edit_settings_and_run"));
+      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);
@@ -192,18 +204,22 @@ public class SequenceAnnotationWSClient 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(MessageManager
+                .formatMessage("label.run_with_preset", new String[]
+                { calcName }));
 
         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.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,
@@ -219,7 +235,8 @@ public class SequenceAnnotationWSClient extends Jws2Client
     }
     else
     {
-      annotservice = new JMenuItem("View documentation");
+      annotservice = new JMenuItem(
+              MessageManager.getString("label.view_documentation"));
       if (service.docUrl != null)
       {
         annotservice.addActionListener(new ActionListener()
@@ -231,236 +248,12 @@ public class SequenceAnnotationWSClient extends Jws2Client
             Desktop.instance.showUrl(service.docUrl);
           }
         });
-        annotservice.setToolTipText("<html>"
-                + JvSwingUtils.wrapTooltip("View <a href=\""
-                        + service.docUrl + "\">" + service.docUrl + "</a>")
-                + "</html>");
+        annotservice.setToolTipText(
+                JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage(
+                        "label.view_service_doc_url", new String[]
+                        { service.docUrl, service.docUrl })));
         wsmenu.add(annotservice);
       }
     }
   }
-
-  private final String AAconToggle = "AACon Calculations",
-          AAconToggleTooltip = "When checked, AACon calculations are updated automatically.",
-          AAeditSettings = "Change AACon Settings...",
-          AAeditSettingsTooltip = "Modify settings for AACon calculations.";
-
-  private void registerAAConWSInstance(final JMenu wsmenu,
-          final Jws2Instance service, final AlignFrame alignFrame)
-  {
-    // register this in the AACon settings set
-    JCheckBoxMenuItem _aaConEnabled = null;
-    for (int i = 0; i < wsmenu.getItemCount(); i++)
-    {
-      JMenuItem item = wsmenu.getItem(i);
-      if (item instanceof JCheckBoxMenuItem
-              && item.getText().equals(AAconToggle))
-      {
-        _aaConEnabled = (JCheckBoxMenuItem) item;
-      }
-    }
-    // is there an aaCon worker already present - if so, set it to use the
-    // given service handle
-    {
-      List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
-              .getCalcManager()
-              .getRegisteredWorkersOfClass(AAConClient.class);
-      if (aaconClient != null && aaconClient.size() > 0)
-      {
-        AAConClient worker = (AAConClient) aaconClient.get(0);
-        if (!worker.service.hosturl.equals(service.hosturl))
-        {
-          // javax.swing.SwingUtilities.invokeLater(new Runnable()
-          {
-            // @Override
-            // public void run()
-            {
-              removeCurrentAAConWorkerFor(alignFrame);
-              buildCurrentAAConWorkerFor(alignFrame, service);
-            }
-          }// );
-        }
-      }
-    }
-
-    // is there a service already registered ? there shouldn't be if we are
-    // being called correctly
-    if (_aaConEnabled == null)
-    {
-      final JCheckBoxMenuItem aaConEnabled = new JCheckBoxMenuItem(
-              AAconToggle);
-      wsmenu.addMenuListener(new MenuListener()
-      {
-
-        @Override
-        public void menuSelected(MenuEvent arg0)
-        {
-          wsmenu.setEnabled(!alignFrame.getViewport().getAlignment()
-                  .isNucleotide());
-          List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
-                  .getCalcManager()
-                  .getRegisteredWorkersOfClass(AAConClient.class);
-          if (aaconClient != null && aaconClient.size() > 0)
-          {
-            aaConEnabled.setSelected(true);
-          }
-          else
-          {
-            aaConEnabled.setSelected(false);
-          }
-        }
-
-        @Override
-        public void menuDeselected(MenuEvent arg0)
-        {
-          // TODO Auto-generated method stub
-
-        }
-
-        @Override
-        public void menuCanceled(MenuEvent arg0)
-        {
-          // TODO Auto-generated method stub
-
-        }
-      });
-      aaConEnabled.setToolTipText("<html><p>"
-              + JvSwingUtils.wrapTooltip(AAconToggleTooltip + "</p>")
-              + "</html>");
-      aaConEnabled.addActionListener(new ActionListener()
-      {
-        @Override
-        public void actionPerformed(ActionEvent arg0)
-        {
-          List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
-                  .getCalcManager()
-                  .getRegisteredWorkersOfClass(AAConClient.class);
-          if (aaconClient != null && aaconClient.size() > 0)
-          {
-            removeCurrentAAConWorkerFor(alignFrame);
-          }
-          else
-          {
-            buildCurrentAAConWorkerFor(alignFrame);
-
-          }
-        }
-
-      });
-      wsmenu.add(aaConEnabled);
-      JMenuItem modifyParams = new JMenuItem(AAeditSettings);
-      modifyParams.setToolTipText("<html><p>"
-              + JvSwingUtils.wrapTooltip(AAeditSettingsTooltip + "</p>")
-              + "</html>");
-      modifyParams.addActionListener(new ActionListener()
-      {
-
-        @Override
-        public void actionPerformed(ActionEvent arg0)
-        {
-          showAAConAnnotationSettingsFor(alignFrame);
-        }
-      });
-      wsmenu.add(modifyParams);
-
-    }
-  }
-
-  private static void showAAConAnnotationSettingsFor(AlignFrame alignFrame)
-  {
-    /*
-     * preferred settings Whether AACon is automatically recalculated Which
-     * AACon server to use What parameters to use
-     */
-    // could actually do a class search for this too
-    AAConSettings fave = (AAConSettings) alignFrame.getViewport()
-            .getCalcIdSettingsFor(AAConCalcId);
-    if (fave == null)
-    {
-      fave = createDefaultAAConSettings();
-    }
-    new SequenceAnnotationWSClient(fave, alignFrame, true);
-
-  }
-
-  private static void buildCurrentAAConWorkerFor(AlignFrame alignFrame)
-  {
-    buildCurrentAAConWorkerFor(alignFrame, null);
-  }
-
-  private static void buildCurrentAAConWorkerFor(AlignFrame alignFrame,
-          Jws2Instance service)
-  {
-    /*
-     * preferred settings Whether AACon is automatically recalculated Which
-     * AACon server to use What parameters to use
-     */
-    AAConSettings fave = (AAConSettings) alignFrame.getViewport()
-            .getCalcIdSettingsFor(AAConCalcId);
-    if (fave == null)
-    {
-      fave = createDefaultAAConSettings(service);
-    }
-    else
-    {
-      if (service != null
-              && !fave.getService().hosturl.equals(service.hosturl))
-      {
-        Cache.log.debug("Changing AACon service to " + service.hosturl
-                + " from " + fave.getService().hosturl);
-        fave.setService(service);
-      }
-    }
-    new SequenceAnnotationWSClient(fave, alignFrame, false);
-  }
-
-  private static AAConSettings createDefaultAAConSettings()
-  {
-    return createDefaultAAConSettings(null);
-  }
-
-  private static AAConSettings createDefaultAAConSettings(
-          Jws2Instance service)
-  {
-    if (service != null)
-    {
-      if (!service.serviceType.toString().equals(
-              compbio.ws.client.Services.AAConWS.toString()))
-      {
-        Cache.log
-                .warn("Ignoring invalid preferred service for AACon calculations (service type was "
-                        + service.serviceType + ")");
-        service = null;
-      }
-      else
-      {
-        // check service is actually in the list of currently avaialable
-        // services
-        if (!Jws2Discoverer.getDiscoverer().getServices().contains(service))
-        {
-          // it isn't ..
-          service = null;
-        }
-      }
-    }
-    if (service == null)
-    {
-      // get the default service for AACon
-      service = Jws2Discoverer.getDiscoverer().getPreferredServiceFor(null,
-              compbio.ws.client.Services.AAConWS.toString());
-    }
-    if (service == null)
-    {
-      // TODO raise dialog box explaining error, and/or open the JABA
-      // preferences menu.
-      throw new Error("No AACon service found.");
-    }
-    return new AAConSettings(true, service, null, null);
-  }
-
-  private static void removeCurrentAAConWorkerFor(AlignFrame alignFrame)
-  {
-    alignFrame.getViewport().getCalcManager()
-            .removeRegisteredWorkersOfClass(AAConClient.class);
-  }
 }