X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FSequenceAnnotationWSClient.java;h=d57eae40b5d1c38721a3fbaf90204a19cd49f8c0;hb=17142caeaf7d7ce17da0a77b1e36b125b4f447a9;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..d57eae4 100644
--- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
+++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
@@ -1,34 +1,51 @@
-/**
+/*
+ * 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
+ * 
+ * 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/>.
  */
 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.ws.jws2.dm.AAConSettings;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.WsParamSetI;
+
 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 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.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.WsParamSetI;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
 
 /**
- * @author jimp
+ * @author jprocter
  * 
  */
 public class SequenceAnnotationWSClient extends Jws2Client
 {
 
+  public static final String AAConCalcId = "jabaws2.AACon";
+
   /**
    * initialise a client so its attachWSMenuEntry method can be called.
    */
@@ -41,39 +58,47 @@ public class SequenceAnnotationWSClient extends Jws2Client
           AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
   {
     super(alignFrame, preset, null);
+    initSequenceAnnotationWSClient(sh, alignFrame, preset, editParams);
+  }
+
+  public void initSequenceAnnotationWSClient(final Jws2Instance sh,
+          AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
+  {
     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);
+      JOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
+              + " can only be used\nfor amino acid alignments.",
+              "Wrong type of sequences!", JOptionPane.WARNING_MESSAGE);
       return;
 
     }
     if (sh.action.toLowerCase().contains("conservation"))
     {
-      // Build an AACons style client - take alignment, return annotation for columns
+      // Build an AACon style client - take alignment, return annotation for
+      // columns
 
       List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
               .getCalcManager()
-              .getRegisteredWorkersOfClass(AAConsClient.class);
+              .getRegisteredWorkersOfClass(AAConClient.class);
       if (clnts == null || clnts.size() == 0)
       {
         if (!processParams(sh, editParams))
         {
           return;
         }
+        AAConClient worker;
         alignFrame
                 .getViewport()
                 .getCalcManager()
                 .registerWorker(
-                        new AAConsClient(sh, alignFrame, preset, paramset));
+                        worker = new AAConClient(sh, alignFrame,
+                                this.preset, paramset));
+        alignFrame.getViewport().getCalcManager().startWorker(worker);
+
       }
       else
       {
-        AAConsClient worker = (AAConsClient) clnts.get(0);
+        AAConClient worker = (AAConClient) clnts.get(0);
         if (editParams)
         {
           paramset = worker.getArguments();
@@ -81,17 +106,20 @@ 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);
+        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;
@@ -106,6 +134,14 @@ public class SequenceAnnotationWSClient extends Jws2Client
 
   }
 
+  public SequenceAnnotationWSClient(AAConSettings fave,
+          AlignFrame alignFrame, boolean b)
+  {
+    super(alignFrame, fave.getPreset(), fave.getJobArgset());
+    initSequenceAnnotationWSClient(fave.getService(), alignFrame,
+            fave.getPreset(), b);
+  }
+
   /*
    * (non-Javadoc)
    * 
@@ -115,12 +151,19 @@ public class SequenceAnnotationWSClient extends Jws2Client
   public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
           final AlignFrame alignFrame)
   {
+    if (service.serviceType.equals(compbio.ws.client.Services.AAConWS
+            .toString()))
+    {
+      registerAAConWSInstance(wsmenu, service, alignFrame);
+      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(calcName + " Defaults");
+    annotservice.addActionListener(new ActionListener()
     {
 
       @Override
@@ -129,22 +172,23 @@ 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("Edit settings and run ...");
+      annotservice
+              .setToolTipText("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)
       {
@@ -173,5 +217,250 @@ public class SequenceAnnotationWSClient extends Jws2Client
       }
 
     }
+    else
+    {
+      annotservice = new JMenuItem("View documentation");
+      if (service.docUrl != null)
+      {
+        annotservice.addActionListener(new ActionListener()
+        {
+
+          @Override
+          public void actionPerformed(ActionEvent arg0)
+          {
+            Desktop.instance.showUrl(service.docUrl);
+          }
+        });
+        annotservice.setToolTipText("<html>"
+                + JvSwingUtils.wrapTooltip("View <a href=\""
+                        + service.docUrl + "\">" + service.docUrl + "</a>")
+                + "</html>");
+        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);
   }
 }