X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FSequenceAnnotationWSClient.java;h=29343f2bf66f7ed6e2c1ad1e6d831a720c938537;hb=ab58313e7bb31264ddb2715a1c548cdc789d7fa6;hp=fea8f2a72e74c3236e6d4c4759061a5a986f5a84;hpb=b2c4d6c467255b5e30caf4cac1be372b89db0eea;p=jalview.git

diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
index fea8f2a..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.
    */
@@ -37,58 +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 (sh.serviceType.toLowerCase().contains("aaconws"))
+    initSequenceAnnotationWSClient(sh, alignFrame, preset, editParams);
+  }
+
+  // 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 client
-      if (alignFrame.getViewport().getAlignment().isNucleotide())
-      {
-        JOptionPane
-                .showMessageDialog(
-                        Desktop.desktop,
-                        "AACons can only be used\nfor amino acid alignments.\nSorry about that!",
-                        "Wrong type of sequences!",
-                        JOptionPane.WARNING_MESSAGE);
-        return;
+      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);
+          }
+        });
       }
     }
-    
+    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.
+      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);
   }
 
   /*
@@ -97,67 +188,113 @@ 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 (service.serviceType.toLowerCase().contains("aaconws"))
+    if (Jws2ClientFactory.registerAAConWSInstance(wsmenu,
+            service, alignFrame))
+    {
+      // Alignment dependent analysis calculation WS gui
+      return;
+    }
+    boolean hasparams = service.hasParameters();
+    String calcName = service.getName();
+    if (calcName.endsWith("WS"))
     {
-      boolean hasparams = service.hasParameters();
-      String calcName = "AACons";
-      JMenuItem aacons = new JMenuItem("AACons Defaults");
-      aacons.addActionListener(new ActionListener()
+      // Remove "WS" suffix
+      calcName = calcName.substring(0, calcName.length() - 2);
+    }
+
+    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);
+      }
+    });
+    wsmenu.add(annotservice);
+    if (hasparams)
+    {
+      // only add these menu options if the service has user-modifiable
+      // arguments
+      annotservice = new JMenuItem(
+              MessageManager.getString("label.edit_settings_and_run"));
+      annotservice.setToolTipText(MessageManager.getString(
+              "label.view_and_change_parameters_before_running_calculation"));
 
+      annotservice.addActionListener(new ActionListener()
+      {
         @Override
         public void actionPerformed(ActionEvent e)
         {
-          new SequenceAnnotationWSClient(service, alignFrame, null, false);
+          new SequenceAnnotationWSClient(service, alignFrame,
+                  null, true);
         }
       });
-      wsmenu.add(aacons);
-      if (hasparams)
+      wsmenu.add(annotservice);
+      List<WsParamSetI> presets = service.getParamStore().getPresets();
+      if (presets != null && presets.size() > 0)
       {
-        // only add these menu options if the service has user-modifiable
-        // arguments
-        aacons = new JMenuItem("Edit settings and run ...");
-        aacons.setToolTipText("View and change the parameters before alignment.");
+        JMenu presetlist = new JMenu(MessageManager
+                .formatMessage("label.run_with_preset", new String[]
+                { calcName }));
 
-        aacons.addActionListener(new ActionListener()
+        for (final WsParamSetI preset : presets)
         {
-          public void actionPerformed(ActionEvent e)
+          final JMenuItem methodR = new JMenuItem(preset.getName());
+          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()
           {
-            new SequenceAnnotationWSClient(service, alignFrame, null, true);
-          }
-        });
-        wsmenu.add(aacons);
-        List<WsParamSetI> presets = service.getParamStore().getPresets();
-        if (presets != null && presets.size() > 0)
+            @Override
+            public void actionPerformed(ActionEvent e)
+            {
+              new SequenceAnnotationWSClient(service,
+                      alignFrame, preset,
+                      false);
+            }
+
+          });
+          presetlist.add(methodR);
+        }
+        wsmenu.add(presetlist);
+      }
+
+    }
+    else
+    {
+      annotservice = new JMenuItem(
+              MessageManager.getString("label.view_documentation"));
+      if (service != null && service.hasDocumentationUrl())
+      {
+        annotservice.addActionListener(new ActionListener()
         {
-          JMenu presetlist = new JMenu("Run " + calcName + "with preset");
 
-          for (final WsParamSetI preset : presets)
+          @Override
+          public void actionPerformed(ActionEvent arg0)
           {
-            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.addActionListener(new ActionListener()
-            {
-              public void actionPerformed(ActionEvent e)
-              {
-                new SequenceAnnotationWSClient(service, alignFrame, preset,
-                        false);
-              }
-
-            });
-            presetlist.add(methodR);
+            Desktop.getInstance().showUrl(service.getDocumentationUrl());
           }
-          wsmenu.add(presetlist);
-        }
+        });
+        annotservice.setToolTipText(
+                JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage(
+                        "label.view_service_doc_url", new String[]
+                        { service.getDocumentationUrl(),
+                            service.getDocumentationUrl() })));
+        wsmenu.add(annotservice);
       }
-
     }
   }
 }