X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FSequenceAnnotationWSClient.java;h=29343f2bf66f7ed6e2c1ad1e6d831a720c938537;hb=c41398473f1493a06f28da53be50630a0f6e6f6d;hp=078803c19e0e6164fa0dee8b116262ebd43ef76c;hpb=3ccc8045265bf23335df3c4b7448e0d91cb7c4df;p=jalview.git

diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
index 078803c..29343f2 100644
--- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
+++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
@@ -1,34 +1,50 @@
-/**
+/*
+ * 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 jalview.api.AlignCalcWorkerI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvSwingUtils;
+import jalview.util.MessageManager;
+import jalview.ws.api.ServiceWithParameters;
+import jalview.ws.params.AutoCalcSetting;
+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 java.util.Locale;
+
 
 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;
 
 /**
- * @author jimp
+ * @author jprocter
  * 
  */
 public class SequenceAnnotationWSClient extends Jws2Client
 {
-
   /**
    * initialise a client so its attachWSMenuEntry method can be called.
    */
@@ -37,72 +53,133 @@ 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);
-    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
+
+  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())
+    // {
+    // 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
+      Class clientClass = aaui.getClient();
+
+      // Build an AACon style client - take alignment, return annotation for
       // columns
 
       List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
-              .getCalcManager()
-              .getRegisteredWorkersOfClass(AAConsClient.class);
-      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;
         }
-        alignFrame
-                .getViewport()
-                .getCalcManager()
-                .registerWorker(
-                        new AAConsClient(sh, alignFrame, preset, paramset));
+      }
+      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_);
+                // also starts the worker
+            startSeqAnnotationWorker(sh, alignFrame, preset, editParams);
+          }
+        });
+
       }
       else
       {
-        AAConsClient worker = (AAConsClient) clnts.get(0);
+        WsParamSetI preset_;
         if (editParams)
         {
           paramset = worker.getArguments();
-          preset = worker.getPreset();
+          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(preset, paramset);
-
+        else
+        {
+          preset_ = preset;
+        }
+        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.action.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(AutoCalcSetting fave,
+          AlignFrame alignFrame, boolean b)
+  {
+    super(alignFrame, fave.getPreset(), fave.getArgumentSet());
+    initSequenceAnnotationWSClient(fave.getService(), alignFrame,
+            fave.getPreset(), b);
   }
 
   /*
@@ -111,58 +188,81 @@ public class SequenceAnnotationWSClient extends Jws2Client
    * @see jalview.ws.jws2.Jws2Client#attachWSMenuEntry(javax.swing.JMenu,
    * jalview.ws.jws2.jabaws2.Jws2Instance, jalview.gui.AlignFrame)
    */
-  public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
+  @Override
+  public void attachWSMenuEntry(JMenu wsmenu,
+          final ServiceWithParameters service,
           final AlignFrame 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.serviceType.substring(0,
-            service.serviceType.length() - 2);
+    String calcName = service.getName();
+    if (calcName.endsWith("WS"))
+    {
+      // Remove "WS" suffix
+      calcName = calcName.substring(0, calcName.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
       public void actionPerformed(ActionEvent e)
       {
-        new SequenceAnnotationWSClient(service, alignFrame, null, false);
+        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()
       {
+        @Override
         public void actionPerformed(ActionEvent e)
         {
-          new SequenceAnnotationWSClient(service, alignFrame, null, true);
+          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()
           {
+            @Override
             public void actionPerformed(ActionEvent e)
             {
-              new SequenceAnnotationWSClient(service, alignFrame, preset,
+              new SequenceAnnotationWSClient(service,
+                      alignFrame, preset,
                       false);
             }
 
@@ -173,5 +273,28 @@ public class SequenceAnnotationWSClient extends Jws2Client
       }
 
     }
+    else
+    {
+      annotservice = new JMenuItem(
+              MessageManager.getString("label.view_documentation"));
+      if (service != null && service.hasDocumentationUrl())
+      {
+        annotservice.addActionListener(new ActionListener()
+        {
+
+          @Override
+          public void actionPerformed(ActionEvent arg0)
+          {
+            Desktop.getInstance().showUrl(service.getDocumentationUrl());
+          }
+        });
+        annotservice.setToolTipText(
+                JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage(
+                        "label.view_service_doc_url", new String[]
+                        { service.getDocumentationUrl(),
+                            service.getDocumentationUrl() })));
+        wsmenu.add(annotservice);
+      }
+    }
   }
 }