X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSClient.java;h=b7230595f95f80244f812ae1b318d3f382932bf0;hb=0935f3c68446aa5cd3a928295a0c5ea78f303648;hp=eee55ad1c9f4c5f48c2471356e77eeb8eac67f83;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git

diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java
index eee55ad..b723059 100644
--- a/src/jalview/ws/jws2/MsaWSClient.java
+++ b/src/jalview/ws/jws2/MsaWSClient.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,10 +20,11 @@
  */
 package jalview.ws.jws2;
 
-import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
 import jalview.gui.JvSwingUtils;
 import jalview.util.MessageManager;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
@@ -37,7 +38,6 @@ import java.util.List;
 
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
 import javax.swing.ToolTipManager;
 
 import compbio.data.msa.MsaWS;
@@ -58,7 +58,7 @@ public class MsaWSClient extends Jws2Client
 
   public MsaWSClient(Jws2Instance sh, String altitle,
           jalview.datamodel.AlignmentView msa, boolean submitGaps,
-          boolean preserveOrder, Alignment seqdataset,
+          boolean preserveOrder, AlignmentI seqdataset,
           AlignFrame _alignFrame)
   {
     this(sh, null, null, false, altitle, msa, submitGaps, preserveOrder,
@@ -68,7 +68,7 @@ public class MsaWSClient extends Jws2Client
 
   public MsaWSClient(Jws2Instance sh, WsParamSetI preset, String altitle,
           jalview.datamodel.AlignmentView msa, boolean submitGaps,
-          boolean preserveOrder, Alignment seqdataset,
+          boolean preserveOrder, AlignmentI seqdataset,
           AlignFrame _alignFrame)
   {
     this(sh, preset, null, false, altitle, msa, submitGaps, preserveOrder,
@@ -95,7 +95,7 @@ public class MsaWSClient extends Jws2Client
   public MsaWSClient(Jws2Instance sh, WsParamSetI preset,
           List<Argument> arguments, boolean editParams, String altitle,
           jalview.datamodel.AlignmentView msa, boolean submitGaps,
-          boolean preserveOrder, Alignment seqdataset,
+          boolean preserveOrder, AlignmentI seqdataset,
           AlignFrame _alignFrame)
   {
     super(_alignFrame, preset, arguments);
@@ -107,22 +107,22 @@ public class MsaWSClient extends Jws2Client
     if (!(sh.service instanceof MsaWS))
     {
       // redundant at mo - but may change
-      JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+      JvOptionPane.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);
+              JvOptionPane.WARNING_MESSAGE);
 
       return;
     }
     server = (MsaWS) sh.service;
     if ((wsInfo = setWebService(sh, false)) == null)
     {
-      JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+      JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
               .formatMessage("label.msa_service_is_unknown",
                       new String[] { sh.serviceType }), MessageManager
               .getString("label.internal_jalview_error"),
-              JOptionPane.WARNING_MESSAGE);
+              JvOptionPane.WARNING_MESSAGE);
 
       return;
     }
@@ -138,7 +138,7 @@ public class MsaWSClient extends Jws2Client
   }
 
   private void startMsaWSClient(String altitle, AlignmentView msa,
-          boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
+          boolean submitGaps, boolean preserveOrder, AlignmentI seqdataset)
   {
     // if (!locateWebService())
     // {
@@ -180,10 +180,10 @@ public class MsaWSClient extends Jws2Client
     }
     else
     {
-      JOptionPane.showMessageDialog(alignFrame,
+      JvOptionPane.showMessageDialog(alignFrame,
               MessageManager.getString("info.invalid_msa_input_mininfo"),
               MessageManager.getString("info.invalid_msa_notenough"),
-              JOptionPane.INFORMATION_MESSAGE);
+              JvOptionPane.INFORMATION_MESSAGE);
       wsInfo.setVisible(false);
     }
   }
@@ -216,6 +216,7 @@ public class MsaWSClient extends Jws2Client
     return (WebServiceName.indexOf("lustal") > -1); // cheat!
   }
 
+  @Override
   public void attachWSMenuEntry(JMenu rmsawsmenu,
           final Jws2Instance service, final AlignFrame alignFrame)
   {
@@ -263,6 +264,7 @@ public class MsaWSClient extends Jws2Client
 
       method.addActionListener(new ActionListener()
       {
+        @Override
         public void actionPerformed(ActionEvent e)
         {
           AlignmentView msa = alignFrame.gatherSequencesForAlignment();
@@ -288,6 +290,7 @@ public class MsaWSClient extends Jws2Client
 
         method.addActionListener(new ActionListener()
         {
+          @Override
           public void actionPerformed(ActionEvent e)
           {
             AlignmentView msa = alignFrame.gatherSequencesForAlignment();
@@ -335,17 +338,20 @@ public class MsaWSClient extends Jws2Client
               }
 
             });
-            methodR.setToolTipText(JvSwingUtils.wrapTooltip(
-                    true,
-                    "<p><strong>"
-                            + (preset.isModifiable() ? MessageManager
-                                    .getString("label.user_preset")
-                                    : MessageManager
-                                            .getString("label.service_preset"))
-                            + "</strong><br/>" + preset.getDescription()
-                            + "</p>"));
+            String tooltip = JvSwingUtils
+                    .wrapTooltip(
+                            true,
+                            "<strong>"
+                                    + (preset.isModifiable() ? MessageManager
+                                            .getString("label.user_preset")
+                                            : MessageManager
+                                                    .getString("label.service_preset"))
+                                    + "</strong><br/>"
+                                    + preset.getDescription());
+            methodR.setToolTipText(tooltip);
             methodR.addActionListener(new ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 AlignmentView msa = alignFrame