X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSClient.java;h=39be45402abc399ef36df90a7d371276a58612ce;hb=38d52319e75f1882278928184066da1033aef332;hp=4e3f81c137e8438ec73a51952e4627add3ccfaad;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git

diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java
index 4e3f81c..39be454 100644
--- a/src/jalview/ws/jws2/MsaWSClient.java
+++ b/src/jalview/ws/jws2/MsaWSClient.java
@@ -1,35 +1,48 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
  * 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.datamodel.SequenceI;
+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 compbio.metadata.Argument;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.WsParamSetI;
 
 /**
  * DOCUMENT ME!
@@ -95,28 +108,30 @@ public class MsaWSClient extends Jws2Client
     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 = (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()
@@ -161,9 +176,55 @@ public class MsaWSClient extends Jws2Client
             WsURL, wsInfo, alignFrame, WebServiceName, jobtitle, msa,
             submitGaps, preserveOrder, seqdataset);
     wsInfo.setthisService(msathread);
+
     msathread.start();
+
   }
 
+  private boolean isValidAlignment(AlignmentView av)
+  {
+    int validSeqCount = 0;
+    List<SequenceI> seqs = av.getVisibleAlignment('c').getSequences(); // .getSequences();
+    if (seqs.size() < 2)
+    {
+      JOptionPane
+              .showMessageDialog(
+                      alignFrame,
+                      "A minimum of two sequences is required to perform this operation",
+                      "Invalid selection", JOptionPane.INFORMATION_MESSAGE);
+
+      return false;
+    }
+
+    for (SequenceI seq : seqs)
+    {
+
+      if (seq.getSequenceAsString().matches("(-*[a-zA-Z]-*){3}[a-zA-Z-]*"))
+      {
+        ++validSeqCount;
+      }
+      if (validSeqCount > 1)
+      {
+        return true;
+      }
+    }
+
+    JOptionPane
+            .showMessageDialog(
+                    alignFrame,
+                    "All selected sequence for this job must have a  minimum of \nthree non-gap character to perform this operation",
+                    "Invalid selection", JOptionPane.INFORMATION_MESSAGE);
+
+    return false;
+  }
+
+  public static void main(String[] args)
+  {
+    System.out.println("A".matches("(-*[a-zA-Z]-*){1}[a-zA-Z-]*"));
+  }
+
+
+
   protected String getServiceActionKey()
   {
     return "MsaWS";
@@ -190,6 +251,11 @@ public class MsaWSClient extends Jws2Client
   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
     boolean finished = true, submitGaps = false;
     JMenu msawsmenu = rmsawsmenu;
@@ -212,24 +278,34 @@ public class MsaWSClient extends Jws2Client
       if (submitGaps == true)
       {
         action = "Realign ";
-        msawsmenu = new JMenu("Realign with " + svcname);
-        msawsmenu
-                .setToolTipText("Align sequences to an existing alignment");
+        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;
 
-      JMenuItem method = new JMenuItem(calcName + "with Defaults");
-      method.setToolTipText(action + "with default settings");
+      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();
+
+          if (msa != null && isValidAlignment(msa))
+          {
           new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
                   true, alignFrame.getViewport().getAlignment()
                           .getDataset(), alignFrame);
+          }
 
         }
       });
@@ -238,17 +314,23 @@ public class MsaWSClient extends Jws2Client
       {
         // only add these menu options if the service has user-modifiable
         // arguments
-        method = new JMenuItem("Edit settings and run ...");
-        method.setToolTipText("View and change the parameters before alignment.");
+        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 && isValidAlignment(msa))
+            {
             new MsaWSClient(service, null, null, true, alignFrame
                     .getTitle(), msa, withGaps, true, alignFrame
                     .getViewport().getAlignment().getDataset(), alignFrame);
+            }
 
           }
         });
@@ -256,25 +338,56 @@ public class MsaWSClient extends Jws2Client
         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_params", new String[]
+                  { calcName }));
 
+          final int showToolTipFor = ToolTipManager.sharedInstance()
+                  .getDismissDelay();
           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>");
+            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 && isValidAlignment(msa))
+                {
                 new MsaWSClient(service, preset, alignFrame.getTitle(),
                         msa, false, true, alignFrame.getViewport()
                                 .getAlignment().getDataset(), alignFrame);
+                }
 
               }