JAL-1365 unified GUI building for AACon and RNAAliFold service clients

diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
index eecefd9..cca6af3 100644 (file)
--- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
+++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
@@ -25,6 +25,7 @@ import jalview.gui.JvSwingUtils;
 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;
@@ -43,9 +44,6 @@ 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.
    */
@@ -75,33 +73,45 @@ public class SequenceAnnotationWSClient extends Jws2Client
 //      return;
 //
 //    }
-    if (sh.action.toLowerCase().contains("conservation"))
+    AlignAnalysisUIText aaui = sh.getAlignAnalysisUI();
+    if (aaui!=null)
     {
+      Class clientClass = aaui.getClient();
+      
       // Build an AACon style client - take alignment, return annotation for
       // columns
 
       List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
               .getCalcManager()
-              .getRegisteredWorkersOfClass(AAConClient.class);
+              .getRegisteredWorkersOfClass(clientClass);
+      JabawsAlignCalcWorker worker;
       if (clnts == null || clnts.size() == 0)
       {
         if (!processParams(sh, editParams))
         {
           return;
         }
-        AAConClient worker;
+        try {
+          worker = (JabawsAlignCalcWorker) (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("Implementation error",x);
+        }
         alignFrame
                 .getViewport()
                 .getCalcManager()
                 .registerWorker(
-                        worker = new AAConClient(sh, alignFrame,
-                                this.preset, paramset));
+                        worker);
         alignFrame.getViewport().getCalcManager().startWorker(worker);
 
       }
       else
       {
-        AAConClient worker = (AAConClient) clnts.get(0);
+        worker = (JabawsAlignCalcWorker) clnts.get(0);
         if (editParams)
         {
           paramset = worker.getArguments();
@@ -116,7 +126,6 @@ public class SequenceAnnotationWSClient extends Jws2Client
         // invalid parameters)
         alignFrame.getViewport().getCalcManager().workerMayRun(worker);
         worker.updateParameters(this.preset, paramset);
-
       }
     }
     if (sh.action.toLowerCase().contains("disorder"))
@@ -134,51 +143,6 @@ public class SequenceAnnotationWSClient extends Jws2Client
               .startWorker(
                       new AADisorderClient(sh, alignFrame, preset, paramset));
     }
-    
-    
-    // dan test dan changed!
-    if (sh.action.toLowerCase().contains("rna structure prediction"))
-    {
-
-       List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
-                       .getCalcManager()
-                       .getRegisteredWorkersOfClass(RNAalifoldClient.class);
-       if (clnts == null || clnts.size() == 0)
-       {
-               if (!processParams(sh, editParams))
-               {
-                       return;
-               }
-               RNAalifoldClient worker;
-               alignFrame
-                                               .getViewport()
-                                               .getCalcManager()
-                                               .registerWorker(
-                                                                       worker = new RNAalifoldClient(sh, alignFrame,
-                                                                                                       this.preset, paramset));
-               alignFrame.getViewport().getCalcManager().startWorker(worker);
-       }
-       else 
-       {
-               RNAalifoldClient worker = (RNAalifoldClient) clnts.get(0);
-               if (editParams)
-               {
-                       paramset = worker.getArguments();
-                       preset = worker.getPreset();
-               }
-               
-               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(this.preset, paramset);
-       }
-       
-    }
   }
 
   public SequenceAnnotationWSClient(AAConSettings fave,
@@ -198,10 +162,8 @@ 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);
+    if (registerAAConWSInstance(wsmenu, service, alignFrame)) {
+      // Alignment dependent analysis calculation WS gui
       return;
     }
     boolean hasparams = service.hasParameters();
@@ -287,21 +249,24 @@ public class SequenceAnnotationWSClient extends Jws2Client
     }
   }
 
-  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,
+  
+  private boolean registerAAConWSInstance(final JMenu wsmenu,
           final Jws2Instance service, final AlignFrame alignFrame)
   {
-    // register this in the AACon settings set
+    final AlignAnalysisUIText aaui = service.getAlignAnalysisUI(); // null ; // AlignAnalysisUIText.aaConGUI.get(service.serviceType.toString());
+    if (aaui==null)
+    {
+      // not an instantaneous calculation GUI type service
+      return false;
+    }
+    // create the instaneous calculation GUI bits and update state if existing GUI elements already present
+    
     JCheckBoxMenuItem _aaConEnabled = null;
     for (int i = 0; i < wsmenu.getItemCount(); i++)
     {
       JMenuItem item = wsmenu.getItem(i);
       if (item instanceof JCheckBoxMenuItem
-              && item.getText().equals(AAconToggle))
+              && item.getText().equals(aaui.getAAconToggle()))
       {
         _aaConEnabled = (JCheckBoxMenuItem) item;
       }
@@ -311,10 +276,10 @@ public class SequenceAnnotationWSClient extends Jws2Client
     {
       List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
               .getCalcManager()
-              .getRegisteredWorkersOfClass(AAConClient.class);
+              .getRegisteredWorkersOfClass(aaui.getClient());
       if (aaconClient != null && aaconClient.size() > 0)
       {
-        AAConClient worker = (AAConClient) aaconClient.get(0);
+        JabawsAlignCalcWorker worker = (JabawsAlignCalcWorker) aaconClient.get(0);
         if (!worker.service.hosturl.equals(service.hosturl))
         {
           // javax.swing.SwingUtilities.invokeLater(new Runnable()
@@ -322,8 +287,8 @@ public class SequenceAnnotationWSClient extends Jws2Client
             // @Override
             // public void run()
             {
-              removeCurrentAAConWorkerFor(alignFrame);
-              buildCurrentAAConWorkerFor(alignFrame, service);
+              removeCurrentAAConWorkerFor(aaui, alignFrame);
+              buildCurrentAAConWorkerFor(aaui, alignFrame, service);
             }
           }// );
         }
@@ -335,18 +300,19 @@ public class SequenceAnnotationWSClient extends Jws2Client
     if (_aaConEnabled == null)
     {
       final JCheckBoxMenuItem aaConEnabled = new JCheckBoxMenuItem(
-              AAconToggle);
+              aaui.getAAconToggle());
       wsmenu.addMenuListener(new MenuListener()
       {
 
         @Override
         public void menuSelected(MenuEvent arg0)
         {
-          wsmenu.setEnabled(!alignFrame.getViewport().getAlignment()
-                  .isNucleotide());
+          // TODO: refactor to the implementing class.
+          wsmenu.setEnabled((alignFrame.getViewport().getAlignment()
+                  .isNucleotide() ? aaui.isNa() : aaui.isPr()));
           List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
                   .getCalcManager()
-                  .getRegisteredWorkersOfClass(AAConClient.class);
+                  .getRegisteredWorkersOfClass(aaui.getClient());
           if (aaconClient != null && aaconClient.size() > 0)
           {
             aaConEnabled.setSelected(true);
@@ -372,7 +338,7 @@ public class SequenceAnnotationWSClient extends Jws2Client
         }
       });
       aaConEnabled.setToolTipText("<html><p>"
-              + JvSwingUtils.wrapTooltip(AAconToggleTooltip + "</p>")
+              + JvSwingUtils.wrapTooltip(aaui.getAAconToggleTooltip() + "</p>")
               + "</html>");
       aaConEnabled.addActionListener(new ActionListener()
       {
@@ -381,23 +347,23 @@ public class SequenceAnnotationWSClient extends Jws2Client
         {
           List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
                   .getCalcManager()
-                  .getRegisteredWorkersOfClass(AAConClient.class);
+                  .getRegisteredWorkersOfClass(aaui.getClient());
           if (aaconClient != null && aaconClient.size() > 0)
           {
-            removeCurrentAAConWorkerFor(alignFrame);
+            removeCurrentAAConWorkerFor(aaui, alignFrame);
           }
           else
           {
-            buildCurrentAAConWorkerFor(alignFrame);
+            buildCurrentAAConWorkerFor(aaui, alignFrame);
 
           }
         }
 
       });
       wsmenu.add(aaConEnabled);
-      JMenuItem modifyParams = new JMenuItem(AAeditSettings);
+      JMenuItem modifyParams = new JMenuItem(aaui.getAAeditSettings());
       modifyParams.setToolTipText("<html><p>"
-              + JvSwingUtils.wrapTooltip(AAeditSettingsTooltip + "</p>")
+              + JvSwingUtils.wrapTooltip(aaui.getAAeditSettingsTooltip() + "</p>")
               + "</html>");
       modifyParams.addActionListener(new ActionListener()
       {
@@ -405,15 +371,16 @@ public class SequenceAnnotationWSClient extends Jws2Client
         @Override
         public void actionPerformed(ActionEvent arg0)
         {
-          showAAConAnnotationSettingsFor(alignFrame);
+          showAAConAnnotationSettingsFor(aaui, alignFrame);
         }
       });
       wsmenu.add(modifyParams);
 
     }
+    return true;
   }
 
-  private static void showAAConAnnotationSettingsFor(AlignFrame alignFrame)
+  private static void showAAConAnnotationSettingsFor(final AlignAnalysisUIText aaui, AlignFrame alignFrame)
   {
     /*
      * preferred settings Whether AACon is automatically recalculated Which
@@ -421,21 +388,21 @@ public class SequenceAnnotationWSClient extends Jws2Client
      */
     // could actually do a class search for this too
     AAConSettings fave = (AAConSettings) alignFrame.getViewport()
-            .getCalcIdSettingsFor(AAConCalcId);
+            .getCalcIdSettingsFor(aaui.getCalcId());
     if (fave == null)
     {
-      fave = createDefaultAAConSettings();
+      fave = createDefaultAAConSettings(aaui);
     }
     new SequenceAnnotationWSClient(fave, alignFrame, true);
 
   }
 
-  private static void buildCurrentAAConWorkerFor(AlignFrame alignFrame)
+  private static void buildCurrentAAConWorkerFor(final AlignAnalysisUIText aaui, AlignFrame alignFrame)
   {
-    buildCurrentAAConWorkerFor(alignFrame, null);
+    buildCurrentAAConWorkerFor(aaui, alignFrame, null);
   }
 
-  private static void buildCurrentAAConWorkerFor(AlignFrame alignFrame,
+  private static void buildCurrentAAConWorkerFor(final AlignAnalysisUIText aaui, AlignFrame alignFrame,
           Jws2Instance service)
   {
     /*
@@ -443,10 +410,10 @@ public class SequenceAnnotationWSClient extends Jws2Client
      * AACon server to use What parameters to use
      */
     AAConSettings fave = (AAConSettings) alignFrame.getViewport()
-            .getCalcIdSettingsFor(AAConCalcId);
+            .getCalcIdSettingsFor(aaui.getCalcId());
     if (fave == null)
     {
-      fave = createDefaultAAConSettings(service);
+      fave = createDefaultAAConSettings(aaui, service);
     }
     else
     {
@@ -461,12 +428,12 @@ public class SequenceAnnotationWSClient extends Jws2Client
     new SequenceAnnotationWSClient(fave, alignFrame, false);
   }
 
-  private static AAConSettings createDefaultAAConSettings()
+  private static AAConSettings createDefaultAAConSettings(AlignAnalysisUIText aaui)
   {
-    return createDefaultAAConSettings(null);
+    return createDefaultAAConSettings(aaui, null);
   }
 
-  private static AAConSettings createDefaultAAConSettings(
+  private static AAConSettings createDefaultAAConSettings(AlignAnalysisUIText aaui,
           Jws2Instance service)
   {
     if (service != null)
@@ -494,7 +461,7 @@ public class SequenceAnnotationWSClient extends Jws2Client
     {
       // get the default service for AACon
       service = Jws2Discoverer.getDiscoverer().getPreferredServiceFor(null,
-              compbio.ws.client.Services.AAConWS.toString());
+              aaui.getServiceType());
     }
     if (service == null)
     {
@@ -505,9 +472,9 @@ public class SequenceAnnotationWSClient extends Jws2Client
     return new AAConSettings(true, service, null, null);
   }
 
-  private static void removeCurrentAAConWorkerFor(AlignFrame alignFrame)
+  private static void removeCurrentAAConWorkerFor(AlignAnalysisUIText aaui, AlignFrame alignFrame)
   {
     alignFrame.getViewport().getCalcManager()
-            .removeRegisteredWorkersOfClass(AAConClient.class);
+            .removeRegisteredWorkersOfClass(aaui.getClient());
   }
 }