X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FSequenceAnnotationWSClient.java;h=187540c3138cb14df61c52c2f30031528861dab3;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;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..187540c 100644
--- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
+++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
@@ -1,34 +1,48 @@
-/**
+/*
+ * 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 java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.List;
-
-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.util.MessageManager;
+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;
+import java.util.List;
+
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
 
 /**
- * @author jimp
+ * @author jprocter
  * 
  */
 public class SequenceAnnotationWSClient extends Jws2Client
 {
-
   /**
    * initialise a client so its attachWSMenuEntry method can be called.
    */
@@ -41,38 +55,61 @@ public class SequenceAnnotationWSClient extends Jws2Client
           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
+
+  public void initSequenceAnnotationWSClient(final Jws2Instance sh,
+          AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
+  {
+    // dan changed! dan test. comment out if conditional
+    // 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;
+    //
+    // }
+    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);
+              .getCalcManager().getRegisteredWorkersOfClass(clientClass);
+      AbstractJabaCalcWorker worker;
       if (clnts == null || clnts.size() == 0)
       {
         if (!processParams(sh, editParams))
         {
           return;
         }
-        alignFrame
-                .getViewport()
-                .getCalcManager()
-                .registerWorker(
-                        new AAConsClient(sh, alignFrame, preset, paramset));
+        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(
+                  MessageManager.getString("error.implementation_error"), x);
+        }
+        alignFrame.getViewport().getCalcManager().registerWorker(worker);
+        alignFrame.getViewport().getCalcManager().startWorker(worker);
+
       }
       else
       {
-        AAConsClient worker = (AAConsClient) clnts.get(0);
+        worker = (AbstractJabaCalcWorker) clnts.get(0);
         if (editParams)
         {
           paramset = worker.getArguments();
@@ -80,15 +117,38 @@ public class SequenceAnnotationWSClient extends Jws2Client
         }
 
         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);
-
+        worker.updateParameters(this.preset, paramset);
       }
     }
-    
+    if (sh.action.toLowerCase().contains("disorder"))
+    {
+      // 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));
+    }
+  }
+
+  public SequenceAnnotationWSClient(AAConSettings fave,
+          AlignFrame alignFrame, boolean b)
+  {
+    super(alignFrame, fave.getPreset(), fave.getJobArgset());
+    initSequenceAnnotationWSClient(fave.getService(), alignFrame,
+            fave.getPreset(), b);
   }
 
   /*
@@ -100,64 +160,99 @@ public class SequenceAnnotationWSClient extends Jws2Client
   public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
           final AlignFrame alignFrame)
   {
-    if (service.serviceType.toLowerCase().contains("aaconws"))
+    if (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);
+
+    JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage(
+            "label.calcname_with_default_settings",
+            new String[] { calcName }));
+    annotservice.addActionListener(new ActionListener()
     {
-      boolean hasparams = service.hasParameters();
-      String calcName = "AACons";
-      JMenuItem aacons = new JMenuItem("AACons Defaults");
-      aacons.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"));
 
-        @Override
+      annotservice.addActionListener(new ActionListener()
+      {
         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)
+            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.docUrl != null)
+      {
+        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.instance.showUrl(service.docUrl);
           }
-          wsmenu.add(presetlist);
-        }
+        });
+        annotservice.setToolTipText(JvSwingUtils.wrapTooltip(true,
+                MessageManager.formatMessage("label.view_service_doc_url",
+                        new String[] { service.docUrl, service.docUrl })));
+        wsmenu.add(annotservice);
       }
-
     }
   }
 }