X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FSequenceAnnotationWSClient.java;h=45bddace0aee01d66aafd74ed3e4d40c4e12999d;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=e3f3674928cc5568af8842cddfcfc93c6ec79afe;hpb=eb2a8a80d7e785f58b2e11edb8507a555affbdf0;p=jalview.git

diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
index e3f3674..45bddac 100644
--- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
+++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
@@ -1,34 +1,48 @@
-/**
+/*
+ * 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.
+ *  
+ * 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;
 
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.List;
-
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-
-import compbio.metadata.Argument;
-
 import jalview.api.AlignCalcWorkerI;
-import jalview.datamodel.AlignmentView;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
-import jalview.gui.JalviewDialog;
 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.JMenu;
+import javax.swing.JMenuItem;
 
 /**
- * @author jimp
+ * @author jprocter
  * 
  */
 public class SequenceAnnotationWSClient extends Jws2Client
 {
-
   /**
    * initialise a client so its attachWSMenuEntry method can be called.
    */
@@ -41,39 +55,63 @@ public class SequenceAnnotationWSClient extends Jws2Client
           AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
   {
     super(alignFrame, preset, null);
-    if (alignFrame.getViewport().getAlignment().isNucleotide())
-    {
-      JOptionPane
-              .showMessageDialog(
-                      Desktop.desktop,
-                      sh.serviceType+" can only be used\nfor amino acid alignments.",
-                      "Wrong type of sequences!",
-                      JOptionPane.WARNING_MESSAGE);
-      return;
+    initSequenceAnnotationWSClient(sh, alignFrame, preset, editParams);
+  }
 
-    }
-    if (sh.action.toLowerCase().contains("conservation"))
+  // 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)
+  {
+    // 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)
     {
-      // Build an AACons style client - take alignment, return annotation for columns
+      Class clientClass = aaui.getClient();
+
+      // Build an AACon style client - take alignment, return annotation for
+      // columns
 
       List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
-              .getCalcManager()
-              .getRegisteredWorkersOfClass(AAConsClient.class);
+              .getCalcManager().getRegisteredWorkersOfClass(clientClass);
+      AbstractJabaCalcWorker worker;
       if (clnts == null || clnts.size() == 0)
       {
         if (!processParams(sh, editParams))
         {
           return;
         }
-        alignFrame
-                .getViewport()
-                .getCalcManager()
-                .registerWorker(
-                        new AAConsClient(sh, alignFrame, 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
       {
-        AAConsClient worker = (AAConsClient) clnts.get(0);
+        worker = (AbstractJabaCalcWorker) clnts.get(0);
         if (editParams)
         {
           paramset = worker.getArguments();
@@ -81,29 +119,35 @@ public class SequenceAnnotationWSClient extends Jws2Client
         }
 
         if (!processParams(sh, editParams, true))
+        {
           return;
+        }
         // reinstate worker if it was blacklisted (might have happened due to
         // invalid parameters)
-        alignFrame.getViewport().getCalcManager().workerMayRun(worker);
-        worker.updateParameters(preset, paramset);
-
+        alignFrame.getViewport().getCalcManager().enableWorker(worker);
+        worker.updateParameters(this.preset, paramset);
       }
     }
     if (sh.action.toLowerCase().contains("disorder"))
     {
-      // build IUPred style client. take sequences, returns annotation per sequence.
+      // build IUPred style client. take sequences, returns annotation per
+      // sequence.
       if (!processParams(sh, editParams))
       {
         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());
+    initSequenceAnnotationWSClient(fave.getService(), alignFrame,
+            fave.getPreset(), b);
   }
 
   /*
@@ -115,12 +159,20 @@ public class SequenceAnnotationWSClient extends Jws2Client
   public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
           final AlignFrame alignFrame)
   {
+    if (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.serviceType.substring(0,
+            service.serviceType.length() - 2);
 
-    JMenuItem aacons = new JMenuItem(calcName + " Defaults");
-    aacons.addActionListener(new ActionListener()
+    JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage(
+            "label.calcname_with_default_settings", new String[]
+            { calcName }));
+    annotservice.addActionListener(new ActionListener()
     {
 
       @Override
@@ -129,35 +181,40 @@ public class SequenceAnnotationWSClient extends Jws2Client
         new SequenceAnnotationWSClient(service, alignFrame, null, false);
       }
     });
-    wsmenu.add(aacons);
+    wsmenu.add(annotservice);
     if (hasparams)
     {
       // only add these menu options if the service has user-modifiable
       // arguments
-      aacons = new JMenuItem("Edit settings and run ...");
-      aacons.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"));
 
-      aacons.addActionListener(new ActionListener()
+      annotservice.addActionListener(new ActionListener()
       {
         public void actionPerformed(ActionEvent e)
         {
           new SequenceAnnotationWSClient(service, alignFrame, null, true);
         }
       });
-      wsmenu.add(aacons);
+      wsmenu.add(annotservice);
       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()
           {
             public void actionPerformed(ActionEvent e)
@@ -173,5 +230,27 @@ public class SequenceAnnotationWSClient extends Jws2Client
       }
 
     }
+    else
+    {
+      annotservice = new JMenuItem(
+              MessageManager.getString("label.view_documentation"));
+      if (service.docUrl != null)
+      {
+        annotservice.addActionListener(new ActionListener()
+        {
+
+          @Override
+          public void actionPerformed(ActionEvent arg0)
+          {
+            Desktop.instance.showUrl(service.docUrl);
+          }
+        });
+        annotservice.setToolTipText(
+                JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage(
+                        "label.view_service_doc_url", new String[]
+                        { service.docUrl, service.docUrl })));
+        wsmenu.add(annotservice);
+      }
+    }
   }
 }