X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSClient.java;h=49a34129deaec8dec44acaf0934fb5c84730cb8e;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=a557cf79a1ef4080aad567348406b22d185be9d4;hpb=39c0b5e5d2ff4352d36bb6705121dc5ed14ba81b;p=jalview.git

diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java
index a557cf7..49a3412 100644
--- a/src/jalview/ws/jws2/MsaWSClient.java
+++ b/src/jalview/ws/jws2/MsaWSClient.java
@@ -1,31 +1,47 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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.
- * 
+ * 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/>.
+ * 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.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvSwingUtils;
+import jalview.util.MessageManager;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.WsParamSetI;
+
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.List;
 
-import javax.swing.*;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.ToolTipManager;
 
-import jalview.datamodel.*;
-import jalview.gui.*;
 import compbio.data.msa.MsaWS;
-import jalview.ws.jws2.Jws2Discoverer.Jws2Instance;
+import compbio.metadata.Argument;
 
 /**
  * DOCUMENT ME!
@@ -39,7 +55,26 @@ public class MsaWSClient extends Jws2Client
    * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
    */
   MsaWS server;
-  AlignFrame alignFrame;
+
+  public MsaWSClient(Jws2Instance sh, String altitle,
+          jalview.datamodel.AlignmentView msa, boolean submitGaps,
+          boolean preserveOrder, Alignment seqdataset,
+          AlignFrame _alignFrame)
+  {
+    this(sh, null, null, false, altitle, msa, submitGaps, preserveOrder,
+            seqdataset, _alignFrame);
+    // TODO Auto-generated constructor stub
+  }
+
+  public MsaWSClient(Jws2Instance sh, WsParamSetI preset, String altitle,
+          jalview.datamodel.AlignmentView msa, boolean submitGaps,
+          boolean preserveOrder, Alignment seqdataset,
+          AlignFrame _alignFrame)
+  {
+    this(sh, preset, null, false, altitle, msa, submitGaps, preserveOrder,
+            seqdataset, _alignFrame);
+    // TODO Auto-generated constructor stub
+  }
 
   /**
    * Creates a new MsaWSClient object that uses a service given by an externally
@@ -57,38 +92,45 @@ public class MsaWSClient extends Jws2Client
    *          DOCUMENT ME!
    */
 
-  public MsaWSClient(Jws2Discoverer.Jws2Instance sh, String altitle,
+  public MsaWSClient(Jws2Instance sh, WsParamSetI preset,
+          List<Argument> arguments, boolean editParams, String altitle,
           jalview.datamodel.AlignmentView msa, boolean submitGaps,
           boolean preserveOrder, Alignment seqdataset,
           AlignFrame _alignFrame)
   {
-    super();
-    alignFrame = _alignFrame;
+    super(_alignFrame, preset, arguments);
+    if (!processParams(sh, editParams))
+    {
+      return;
+    }
+
     if (!(sh.service instanceof MsaWS))
     {
       // redundant at mo - but may change
-      JOptionPane
-              .showMessageDialog(
-                      Desktop.desktop,
-                      "The Service called \n"
-                              + sh.serviceType
-                              + "\nis not a \nMultiple Sequence Alignment Service !",
-                      "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
+      JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+              .formatMessage("label.service_called_is_not_msa_service",
+                      new String[]
+                      { sh.serviceType }), MessageManager
+              .getString("label.internal_jalview_error"),
+              JOptionPane.WARNING_MESSAGE);
 
       return;
     }
-    server = sh.service;
+    server = (MsaWS) sh.service;
     if ((wsInfo = setWebService(sh, false)) == null)
     {
-      JOptionPane.showMessageDialog(Desktop.desktop,
-              "The Multiple Sequence Alignment Service named "
-                      + sh.serviceType + " is unknown",
-              "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
+      JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+              .formatMessage("label.msa_service_is_unknown", new String[]
+              { sh.serviceType }), MessageManager
+              .getString("label.internal_jalview_error"),
+              JOptionPane.WARNING_MESSAGE);
 
       return;
     }
+
     startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);
 
+
   }
 
   public MsaWSClient()
@@ -100,10 +142,10 @@ public class MsaWSClient extends Jws2Client
   private void startMsaWSClient(String altitle, AlignmentView msa,
           boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
   {
-    //if (!locateWebService())
-   // {
-   //   return;
-   // }
+    // if (!locateWebService())
+    // {
+    // return;
+    // }
 
     wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")
             + " of " + altitle + "\nJob details\n");
@@ -129,13 +171,32 @@ public class MsaWSClient extends Jws2Client
               + "alignment of " + altitle;
     }
 
-    MsaWSThread msathread = new MsaWSThread(server, WsURL, wsInfo,
-            alignFrame, WebServiceName, jobtitle, msa, submitGaps,
-            preserveOrder, seqdataset);
-    wsInfo.setthisService(msathread);
-    msathread.start();
+    MsaWSThread msathread = new MsaWSThread(server, preset, paramset,
+            WsURL, wsInfo, alignFrame, WebServiceName, jobtitle, msa,
+            submitGaps, preserveOrder, seqdataset);
+    if (msathread.hasValidInput())
+    {
+      wsInfo.setthisService(msathread);
+      wsInfo.setVisible(true);
+      msathread.start();
+    }
+    else
+    {
+      JOptionPane.showMessageDialog(alignFrame,
+              MessageManager.getString("info.invalid_msa_input_mininfo"),
+              MessageManager.getString("info.invalid_msa_notenough"),
+              JOptionPane.INFORMATION_MESSAGE);
+      wsInfo.setVisible(false);
+    }
+  }
+
+  public static void main(String[] args)
+  {
+    System.out.println("A".matches("(-*[a-zA-Z]-*){1}[a-zA-Z-]*"));
   }
 
+
+
   protected String getServiceActionKey()
   {
     return "MsaWS";
@@ -159,47 +220,164 @@ public class MsaWSClient extends Jws2Client
     return (WebServiceName.indexOf("lustal") > -1); // cheat!
   }
 
-  public void attachWSMenuEntry(JMenu msawsmenu,
+  public void attachWSMenuEntry(JMenu rmsawsmenu,
           final Jws2Instance service, final AlignFrame alignFrame)
   {
+    if (registerAAConWSInstance(rmsawsmenu, service, alignFrame))
+    {
+      // Alignment dependent analysis calculation WS gui
+      return;
+    }
     setWebService(service, true); // headless
-    JMenuItem method = new JMenuItem(WebServiceName);
-    method.setToolTipText(WsURL);
-    method.addActionListener(new ActionListener()
+    boolean finished = true, submitGaps = false;
+    JMenu msawsmenu = rmsawsmenu;
+    String svcname = WebServiceName;
+    if (svcname.endsWith("WS"))
+    {
+      svcname = svcname.substring(0, svcname.length() - 2);
+    }
+    String calcName = svcname + " ";
+    if (canSubmitGaps())
+    {
+      msawsmenu = new JMenu(svcname);
+      rmsawsmenu.add(msawsmenu);
+      calcName = "";
+    }
+    boolean hasparams = service.hasParameters();
+    do
     {
-      public void actionPerformed(ActionEvent e)
+      String action = "Align ";
+      if (submitGaps == true)
       {
-        AlignmentView msa = alignFrame.gatherSequencesForAlignment();
-        new MsaWSClient(service, alignFrame.getTitle(),
-                msa, false, true, alignFrame.getViewport().getAlignment()
-                        .getDataset(), alignFrame);
-
+        action = "Realign ";
+        msawsmenu = new JMenu(MessageManager.formatMessage(
+                "label.realign_with_params", new String[]
+                { svcname }));
+        msawsmenu.setToolTipText(MessageManager
+                .getString("label.align_sequences_to_existing_alignment"));
+        rmsawsmenu.add(msawsmenu);
       }
+      final boolean withGaps = submitGaps;
 
-    });
-    msawsmenu.add(method);
-    if (canSubmitGaps())
-    {
-      // We know that ClustalWS can accept partial alignments for refinement.
-      final JMenuItem methodR = new JMenuItem(WebServiceName 
-              + " (With Gaps)");
-      methodR.setToolTipText(WsURL);
-      methodR.addActionListener(new ActionListener()
+      JMenuItem method = new JMenuItem(MessageManager.formatMessage(
+              "label.calcname_with_default_settings", new String[]
+              { calcName }));
+      method.setToolTipText(MessageManager.formatMessage(
+              "label.action_with_default_settings", new String[]
+              { action }));
+
+      method.addActionListener(new ActionListener()
       {
         public void actionPerformed(ActionEvent e)
         {
           AlignmentView msa = alignFrame.gatherSequencesForAlignment();
-          new MsaWSClient(service, alignFrame.getTitle(),
-                  msa, true, true, alignFrame.getViewport().getAlignment()
+
+          if (msa != null)
+          {
+          new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
+                  true, alignFrame.getViewport().getAlignment()
                           .getDataset(), alignFrame);
+          }
 
         }
-
       });
-      msawsmenu.add(methodR);
+      msawsmenu.add(method);
+      if (hasparams)
+      {
+        // only add these menu options if the service has user-modifiable
+        // arguments
+        method = new JMenuItem(
+                MessageManager.getString("label.edit_settings_and_run"));
+        method.setToolTipText(MessageManager
+                .getString("label.view_and_change_parameters_before_alignment"));
 
-    }
+        method.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            AlignmentView msa = alignFrame.gatherSequencesForAlignment();
+            if (msa != null)
+            {
+              new MsaWSClient(service, null, null, true, alignFrame
+                    .getTitle(), msa, withGaps, true, alignFrame
+                    .getViewport().getAlignment().getDataset(), alignFrame);
+            }
 
-  }
+          }
+        });
+        msawsmenu.add(method);
+        List<WsParamSetI> presets = service.getParamStore().getPresets();
+        if (presets != null && presets.size() > 0)
+        {
+          JMenu presetlist = new JMenu(MessageManager.formatMessage(
+                  "label.run_with_preset_params", new String[]
+                  { calcName }));
+
+          final int showToolTipFor = ToolTipManager.sharedInstance()
+                  .getDismissDelay();
+          for (final WsParamSetI preset : presets)
+          {
+            final JMenuItem methodR = new JMenuItem(preset.getName());
+            final int QUICK_TOOLTIP = 1500;
+            // JAL-1582 shorten tooltip display time in these menu items as
+            // they can obscure other options
+            methodR.addMouseListener(new MouseAdapter()
+            {
+              @Override
+              public void mouseEntered(MouseEvent e)
+              {
+                ToolTipManager.sharedInstance().setDismissDelay(
+                        QUICK_TOOLTIP);
+              }
+
+              @Override
+              public void mouseExited(MouseEvent e)
+              {
+                ToolTipManager.sharedInstance().setDismissDelay(showToolTipFor);
+              }
 
+            });
+            methodR.setToolTipText(JvSwingUtils.wrapTooltip(
+                    true,
+                    "<p><strong>"
+                            + (preset.isModifiable() ? MessageManager
+                                    .getString("label.user_preset")
+                                    : MessageManager
+                                            .getString("label.service_preset"))
+                            + "</strong><br/>" + preset.getDescription()
+                            + "</p>"));
+            methodR.addActionListener(new ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                AlignmentView msa = alignFrame
+                        .gatherSequencesForAlignment();
+
+                if (msa != null)
+                {
+                  MsaWSClient msac = new MsaWSClient(service, preset,
+                          alignFrame.getTitle(),
+                        msa, false, true, alignFrame.getViewport()
+                                .getAlignment().getDataset(), alignFrame);
+                }
+
+              }
+
+            });
+            presetlist.add(methodR);
+          }
+          msawsmenu.add(presetlist);
+        }
+      }
+      if (!submitGaps && canSubmitGaps())
+      {
+        submitGaps = true;
+        finished = false;
+      }
+      else
+      {
+        finished = true;
+      }
+    } while (!finished);
+  }
 }