X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FSequenceAnnotationWSClient.java;h=aae6f7954858a6245bf70a44f3ceeabb94bf6964;hb=66a0dd08260a7ded38e4437f6d75af9fc6189f1c;hp=eb0884870c2ff2da8508936d9c5733683bc3029e;hpb=54ee3e95ec4f21a301e458f8b7f22876ae70a017;p=jalview.git

diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
index eb08848..aae6f79 100644
--- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
+++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
@@ -25,8 +25,8 @@ 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.api.ServiceWithParameters;
+import jalview.ws.params.AutoCalcSetting;
 import jalview.ws.params.WsParamSetI;
 import jalview.ws.uimodel.AlignAnalysisUIText;
 
@@ -51,7 +51,7 @@ public class SequenceAnnotationWSClient extends Jws2Client
     // TODO Auto-generated constructor stub
   }
 
-  public SequenceAnnotationWSClient(final Jws2Instance sh,
+  public SequenceAnnotationWSClient(final ServiceWithParameters sh,
           AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
   {
     super(alignFrame, preset, null);
@@ -61,8 +61,8 @@ public class SequenceAnnotationWSClient extends Jws2Client
   // 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)
+  private void initSequenceAnnotationWSClient(final ServiceWithParameters sh,
+      AlignFrame alignFrame, final WsParamSetI preset, boolean editParams)
   {
     // dan changed! dan test. comment out if conditional
     // if (alignFrame.getViewport().getAlignment().isNucleotide())
@@ -82,67 +82,96 @@ public class SequenceAnnotationWSClient extends Jws2Client
       // columns
 
       List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
-              .getCalcManager().getRegisteredWorkersOfClass(clientClass);
-      AbstractJabaCalcWorker worker;
-      if (clnts == null || clnts.size() == 0)
+          .getCalcManager()
+          .getWorkersOfClass(SeqAnnotationServiceCalcWorker.class);
+
+      SeqAnnotationServiceCalcWorker tmpworker = null;
+      if (clnts != null)
       {
-        if (!processParams(sh, editParams))
+        for (AlignCalcWorkerI _worker : clnts)
         {
-          return;
+          tmpworker = (SeqAnnotationServiceCalcWorker) _worker;
+          if (tmpworker.hasService()
+              && tmpworker.getService().getClass().equals(clientClass))
+          {
+            break;
+          }
+          tmpworker = null;
         }
-        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(
+      }
+      final var worker = tmpworker;
+      if (worker == null)
+      {
+        processParams(sh, editParams).thenAccept((startJob) -> {
+          if (startJob)
+          {
+            final SeqAnnotationServiceCalcWorker worker_;
+            try
+            {
+              worker_ = new SeqAnnotationServiceCalcWorker(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);
-
+            }
+            alignFrame.getViewport().getCalcManager().registerWorker(worker_);
+                // also starts the worker
+            startSeqAnnotationWorker(sh, alignFrame, preset, editParams);
+          }
+        });
       }
       else
       {
-        worker = (AbstractJabaCalcWorker) clnts.get(0);
+        WsParamSetI preset_;
         if (editParams)
         {
           paramset = worker.getArguments();
-          preset = worker.getPreset();
+          preset_ = worker.getPreset();
         }
-
-        if (!processParams(sh, editParams, true))
+        else
         {
-          return;
+          preset_ = preset;
         }
-        // reinstate worker if it was blacklisted (might have happened due to
-        // invalid parameters)
-        alignFrame.getViewport().getCalcManager().enableWorker(worker);
-        worker.updateParameters(this.preset, paramset);
+        processParams(sh, editParams, true).thenAccept((startJob) -> {
+          if (startJob)
+          {
+            // reinstate worker if it was blacklisted (might have happened due
+            // to
+            // invalid parameters)
+            alignFrame.getViewport().getCalcManager().enableWorker(worker);
+            worker.updateParameters(this.preset, paramset);
+            startSeqAnnotationWorker(sh, alignFrame, preset_, editParams);
+          }
+        });
       }
     }
-    if (sh.getAction().toLowerCase().contains("disorder"))
+    else
+    {
+      startSeqAnnotationWorker(sh, alignFrame, preset, editParams);
+    }
+  }
+
+  private void startSeqAnnotationWorker(ServiceWithParameters sh,
+      AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
+  {
+    if (!sh.isInteractiveUpdate())
     {
       // 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));
+      processParams(sh, editParams).thenAccept((startJob) -> {
+        if (startJob)
+        {
+          alignFrame.getViewport().getCalcManager().startWorker(
+              new SeqAnnotationServiceCalcWorker(sh, alignFrame, preset, paramset));
+        }
+      });
     }
   }
 
-  public SequenceAnnotationWSClient(AAConSettings fave,
+  public SequenceAnnotationWSClient(AutoCalcSetting fave,
           AlignFrame alignFrame, boolean b)
   {
     super(alignFrame, fave.getPreset(), fave.getArgumentSet());
@@ -157,18 +186,23 @@ public class SequenceAnnotationWSClient extends Jws2Client
    * jalview.ws.jws2.jabaws2.Jws2Instance, jalview.gui.AlignFrame)
    */
   @Override
-  public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
+  public void attachWSMenuEntry(JMenu wsmenu,
+          final ServiceWithParameters service,
           final AlignFrame alignFrame)
   {
-    if (registerAAConWSInstance(wsmenu, service, alignFrame))
+    if (Jws2ClientFactory.registerAAConWSInstance(wsmenu,
+            service, alignFrame))
     {
       // Alignment dependent analysis calculation WS gui
       return;
     }
     boolean hasparams = service.hasParameters();
-    // Assume name ends in WS
-    String calcName = service.getName().substring(0,
-            service.getName().length() - 2);
+    String calcName = service.getName();
+    if (calcName.endsWith("WS"))
+    {
+      // Remove "WS" suffix
+      calcName = calcName.substring(0, calcName.length() - 2);
+    }
 
     JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage(
             "label.calcname_with_default_settings", new String[]
@@ -179,7 +213,8 @@ public class SequenceAnnotationWSClient extends Jws2Client
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        new SequenceAnnotationWSClient(service, alignFrame, null, false);
+        new SequenceAnnotationWSClient(service, alignFrame,
+                null, false);
       }
     });
     wsmenu.add(annotservice);
@@ -197,7 +232,8 @@ public class SequenceAnnotationWSClient extends Jws2Client
         @Override
         public void actionPerformed(ActionEvent e)
         {
-          new SequenceAnnotationWSClient(service, alignFrame, null, true);
+          new SequenceAnnotationWSClient(service, alignFrame,
+                  null, true);
         }
       });
       wsmenu.add(annotservice);
@@ -222,7 +258,8 @@ public class SequenceAnnotationWSClient extends Jws2Client
             @Override
             public void actionPerformed(ActionEvent e)
             {
-              new SequenceAnnotationWSClient(service, alignFrame, preset,
+              new SequenceAnnotationWSClient(service,
+                      alignFrame, preset,
                       false);
             }
 
@@ -237,7 +274,7 @@ public class SequenceAnnotationWSClient extends Jws2Client
     {
       annotservice = new JMenuItem(
               MessageManager.getString("label.view_documentation"));
-      if (service.docUrl != null)
+      if (service != null && service.hasDocumentationUrl())
       {
         annotservice.addActionListener(new ActionListener()
         {
@@ -245,13 +282,14 @@ public class SequenceAnnotationWSClient extends Jws2Client
           @Override
           public void actionPerformed(ActionEvent arg0)
           {
-            Desktop.instance.showUrl(service.docUrl);
+            Desktop.getInstance().showUrl(service.getDocumentationUrl());
           }
         });
         annotservice.setToolTipText(
                 JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage(
                         "label.view_service_doc_url", new String[]
-                        { service.docUrl, service.docUrl })));
+                        { service.getDocumentationUrl(),
+                            service.getDocumentationUrl() })));
         wsmenu.add(annotservice);
       }
     }