X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FSequenceAnnotationWSClient.java;h=d57eae40b5d1c38721a3fbaf90204a19cd49f8c0;hb=e1476d3c4ebb1c8f6b3ec7d46bb824b23987960e;hp=e62950383a26c91896310c784c664ddff8056e57;hpb=b2290fc7943376b99d2528c233d941d4394d261b;p=jalview.git

diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
index e629503..d57eae4 100644
--- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
+++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
@@ -1,8 +1,31 @@
-/**
+/*
+ * 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;
@@ -11,31 +34,17 @@ import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
 import javax.swing.JOptionPane;
-import javax.swing.event.AncestorEvent;
-import javax.swing.event.AncestorListener;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
-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.dm.AAConsSettings;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.WsParamSetI;
-
 /**
- * @author jimp
+ * @author jprocter
  * 
  */
 public class SequenceAnnotationWSClient extends Jws2Client
 {
 
-  public static final String AAConsCalcId = "jabaws2.AACons";
+  public static final String AAConCalcId = "jabaws2.AACon";
 
   /**
    * initialise a client so its attachWSMenuEntry method can be called.
@@ -51,7 +60,7 @@ public class SequenceAnnotationWSClient extends Jws2Client
     super(alignFrame, preset, null);
     initSequenceAnnotationWSClient(sh, alignFrame, preset, editParams);
   }
-  
+
   public void initSequenceAnnotationWSClient(final Jws2Instance sh,
           AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
   {
@@ -65,31 +74,31 @@ public class SequenceAnnotationWSClient extends Jws2Client
     }
     if (sh.action.toLowerCase().contains("conservation"))
     {
-      // Build an AACons style client - take alignment, return annotation for
+      // 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;
         }
-        AAConsClient worker;
+        AAConClient worker;
         alignFrame
                 .getViewport()
                 .getCalcManager()
                 .registerWorker(
-                        worker = new AAConsClient(sh, alignFrame, this.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();
@@ -125,11 +134,12 @@ public class SequenceAnnotationWSClient extends Jws2Client
 
   }
 
-  public SequenceAnnotationWSClient(AAConsSettings fave,
+  public SequenceAnnotationWSClient(AAConSettings fave,
           AlignFrame alignFrame, boolean b)
   {
     super(alignFrame, fave.getPreset(), fave.getJobArgset());
-    initSequenceAnnotationWSClient(fave.getService(), alignFrame, fave.getPreset(), b);
+    initSequenceAnnotationWSClient(fave.getService(), alignFrame,
+            fave.getPreset(), b);
   }
 
   /*
@@ -144,7 +154,7 @@ public class SequenceAnnotationWSClient extends Jws2Client
     if (service.serviceType.equals(compbio.ws.client.Services.AAConWS
             .toString()))
     {
-      registerAAConsWSInstance(wsmenu, service, alignFrame);
+      registerAAConWSInstance(wsmenu, service, alignFrame);
       return;
     }
     boolean hasparams = service.hasParameters();
@@ -152,8 +162,8 @@ public class SequenceAnnotationWSClient extends Jws2Client
     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
@@ -162,22 +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)
       {
@@ -206,36 +217,78 @@ public class SequenceAnnotationWSClient extends Jws2Client
       }
 
     }
-  }
+    else
+    {
+      annotservice = new JMenuItem("View documentation");
+      if (service.docUrl != null)
+      {
+        annotservice.addActionListener(new ActionListener()
+        {
 
-  private final String AAconsToggle = "AACons Calculations",
-          AAconsToggleTooltip = "When checked, AACons calculations are updated automatically.",
-          AAeditSettings = "Change AACons Settings...",
-          AAeditSettingsTooltip = "Modify settings for AACons calculations.";
+          @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 SequenceAnnotationWSClient preferredAAConsClient = null;
+  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 final enableAAConsCalculation(final AlignFrame alignFrame, )
-  private void registerAAConsWSInstance(final JMenu wsmenu,
+  private void registerAAConWSInstance(final JMenu wsmenu,
           final Jws2Instance service, final AlignFrame alignFrame)
   {
-    // register this in the AACons settings set
-    JCheckBoxMenuItem _aaConsEnabled = null;
+    // 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(AAconsToggle))
+              && item.getText().equals(AAconToggle))
       {
-        _aaConsEnabled = (JCheckBoxMenuItem) item;
+        _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 ?
-    if (_aaConsEnabled == null)
+    // is there a service already registered ? there shouldn't be if we are
+    // being called correctly
+    if (_aaConEnabled == null)
     {
-      final JCheckBoxMenuItem aaConsEnabled = new JCheckBoxMenuItem(
-              AAconsToggle);
+      final JCheckBoxMenuItem aaConEnabled = new JCheckBoxMenuItem(
+              AAconToggle);
       wsmenu.addMenuListener(new MenuListener()
       {
 
@@ -244,16 +297,16 @@ public class SequenceAnnotationWSClient extends Jws2Client
         {
           wsmenu.setEnabled(!alignFrame.getViewport().getAlignment()
                   .isNucleotide());
-          List<AlignCalcWorkerI> aaconsClient = alignFrame.getViewport()
+          List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
                   .getCalcManager()
-                  .getRegisteredWorkersOfClass(AAConsClient.class);
-          if (aaconsClient != null && aaconsClient.size() > 0)
+                  .getRegisteredWorkersOfClass(AAConClient.class);
+          if (aaconClient != null && aaconClient.size() > 0)
           {
-            aaConsEnabled.setSelected(true);
+            aaConEnabled.setSelected(true);
           }
           else
           {
-            aaConsEnabled.setSelected(false);
+            aaConEnabled.setSelected(false);
           }
         }
 
@@ -271,31 +324,30 @@ public class SequenceAnnotationWSClient extends Jws2Client
 
         }
       });
-      aaConsEnabled.setToolTipText("<html><p>"
-              + JvSwingUtils.wrapTooltip(AAconsToggleTooltip + "</p>")
+      aaConEnabled.setToolTipText("<html><p>"
+              + JvSwingUtils.wrapTooltip(AAconToggleTooltip + "</p>")
               + "</html>");
-      aaConsEnabled.addActionListener(new ActionListener()
+      aaConEnabled.addActionListener(new ActionListener()
       {
         @Override
         public void actionPerformed(ActionEvent arg0)
         {
-          // aaConsEnabled.setSelected(!aaConsEnabled.isSelected());
-          List<AlignCalcWorkerI> aaconsClient = alignFrame.getViewport()
+          List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
                   .getCalcManager()
-                  .getRegisteredWorkersOfClass(AAConsClient.class);
-          if (aaconsClient != null && aaconsClient.size() > 0)
+                  .getRegisteredWorkersOfClass(AAConClient.class);
+          if (aaconClient != null && aaconClient.size() > 0)
           {
-            removeCurrentAAConsWorkerFor(alignFrame);
+            removeCurrentAAConWorkerFor(alignFrame);
           }
           else
           {
-            buildCurrentAAConsWorkerFor(alignFrame);
+            buildCurrentAAConWorkerFor(alignFrame);
 
           }
         }
 
       });
-      wsmenu.add(aaConsEnabled);
+      wsmenu.add(aaConEnabled);
       JMenuItem modifyParams = new JMenuItem(AAeditSettings);
       modifyParams.setToolTipText("<html><p>"
               + JvSwingUtils.wrapTooltip(AAeditSettingsTooltip + "</p>")
@@ -306,72 +358,109 @@ public class SequenceAnnotationWSClient extends Jws2Client
         @Override
         public void actionPerformed(ActionEvent arg0)
         {
-          showAAConsAnnotationSettingsFor(alignFrame);
+          showAAConAnnotationSettingsFor(alignFrame);
         }
       });
       wsmenu.add(modifyParams);
 
     }
-
   }
 
-  private static void showAAConsAnnotationSettingsFor(AlignFrame alignFrame)
+  private static void showAAConAnnotationSettingsFor(AlignFrame alignFrame)
   {
     /*
-     * preferred settings
-     * Whether AACons is automatically recalculated
-     * Which AACons server to use
-     * What parameters to use
+     * 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
-    AAConsSettings fave= (AAConsSettings) alignFrame.getViewport().getCalcIdSettingsFor(AAConsCalcId);
-    if (fave==null)
+    AAConSettings fave = (AAConSettings) alignFrame.getViewport()
+            .getCalcIdSettingsFor(AAConCalcId);
+    if (fave == null)
     {
-      fave = createDefaultAAConsSettings();
+      fave = createDefaultAAConSettings();
     }
     new SequenceAnnotationWSClient(fave, alignFrame, true);
 
   }
-  private static void buildCurrentAAConsWorkerFor(AlignFrame alignFrame)
+
+  private static void buildCurrentAAConWorkerFor(AlignFrame alignFrame)
+  {
+    buildCurrentAAConWorkerFor(alignFrame, null);
+  }
+
+  private static void buildCurrentAAConWorkerFor(AlignFrame alignFrame,
+          Jws2Instance service)
   {
     /*
-     * preferred settings
-     * Whether AACons is automatically recalculated
-     * Which AACons server to use
-     * What parameters to use
+     * preferred settings Whether AACon is automatically recalculated Which
+     * AACon server to use What parameters to use
      */
-    AAConsSettings fave= (AAConsSettings) alignFrame.getViewport().getCalcIdSettingsFor(AAConsCalcId);
-    if (fave==null)
+    AAConSettings fave = (AAConSettings) alignFrame.getViewport()
+            .getCalcIdSettingsFor(AAConCalcId);
+    if (fave == null)
     {
-      fave = createDefaultAAConsSettings();
+      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 AAConsSettings createDefaultAAConsSettings()
+  private static AAConSettings createDefaultAAConSettings()
   {
-    Jws2Instance service=null;
-    // set sensible defaults
-    for (Jws2Instance sv: Jws2Discoverer.getDiscoverer().getServices()) {
-      if (sv.serviceType.toString().equals(compbio.ws.client.Services.AAConWS.toString()))
+    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
       {
-        service = sv;
-        break;
+        // 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)
+    if (service == null)
     {
-      // TODO raise dialog box explaining error, and/or open the JABA preferences menu.
-      throw new Error("No AACons service found.");
+      // get the default service for AACon
+      service = Jws2Discoverer.getDiscoverer().getPreferredServiceFor(null,
+              compbio.ws.client.Services.AAConWS.toString());
     }
-    return new AAConsSettings(true, service, null, null);
+    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 removeCurrentAAConsWorkerFor(AlignFrame alignFrame)
+  private static void removeCurrentAAConWorkerFor(AlignFrame alignFrame)
   {
     alignFrame.getViewport().getCalcManager()
-            .removeRegisteredWorkersOfClass(AAConsClient.class);
-    // AAConsClient.removeAAConsAnnotation(alignFrame.alignPanel);
-
+            .removeRegisteredWorkersOfClass(AAConClient.class);
   }
 }