X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FMsaWSClient.java;h=bb0e43d3dc23e56ef8bb7baab6c4c03bc2ed0364;hb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;hp=5d84286b62b77c5adc238f692e75a161f3e89113;hpb=2b34ad8d6c224117ca2a3199c237fd74d8137da6;p=jalview.git

diff --git a/src/jalview/ws/jws1/MsaWSClient.java b/src/jalview/ws/jws1/MsaWSClient.java
index 5d84286..bb0e43d 100644
--- a/src/jalview/ws/jws1/MsaWSClient.java
+++ b/src/jalview/ws/jws1/MsaWSClient.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 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.
  * 
@@ -20,15 +20,25 @@
  */
 package jalview.ws.jws1;
 
+import java.util.Locale;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.gui.WebserviceInfo;
+import jalview.util.MessageManager;
+
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 
-import javax.swing.*;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
 
-import ext.vamsas.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.util.MessageManager;
+import ext.vamsas.MuscleWSServiceLocator;
+import ext.vamsas.MuscleWSSoapBindingStub;
+import ext.vamsas.ServiceHandle;
 
 /**
  * DOCUMENT ME!
@@ -43,8 +53,6 @@ public class MsaWSClient extends WS1Client
    */
   ext.vamsas.MuscleWS server;
 
-  AlignFrame alignFrame;
-
   /**
    * Creates a new MsaWSClient object that uses a service given by an externally
    * retrieved ServiceHandle
@@ -63,28 +71,31 @@ public class MsaWSClient extends WS1Client
 
   public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle,
           jalview.datamodel.AlignmentView msa, boolean submitGaps,
-          boolean preserveOrder, Alignment seqdataset,
+          boolean preserveOrder, AlignmentI seqdataset,
           AlignFrame _alignFrame)
   {
     super();
     alignFrame = _alignFrame;
     if (!sh.getAbstractName().equals("MsaWS"))
     {
-      JOptionPane
-              .showMessageDialog(
-                      Desktop.desktop,
-                      MessageManager.formatMessage("label.service_called_is_not_msa_service", new String[]{sh.getName()}),
-                      MessageManager.getString("label.internal_jalview_error"), JOptionPane.WARNING_MESSAGE);
+      JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
+              MessageManager.formatMessage(
+                      "label.service_called_is_not_msa_service",
+                      new String[]
+                      { sh.getName() }),
+              MessageManager.getString("label.internal_jalview_error"),
+              JvOptionPane.WARNING_MESSAGE);
 
       return;
     }
 
     if ((wsInfo = setWebService(sh)) == null)
     {
-      JOptionPane.showMessageDialog(
-              Desktop.desktop,
-              MessageManager.formatMessage("label.msa_service_is_unknown", new String[]{sh.getName()}),
-              MessageManager.getString("label.internal_jalview_error"), JOptionPane.WARNING_MESSAGE);
+      JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), MessageManager
+              .formatMessage("label.msa_service_is_unknown", new String[]
+              { sh.getName() }),
+              MessageManager.getString("label.internal_jalview_error"),
+              JvOptionPane.WARNING_MESSAGE);
 
       return;
     }
@@ -99,7 +110,7 @@ public class MsaWSClient extends WS1Client
   }
 
   private void startMsaWSClient(String altitle, AlignmentView msa,
-          boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
+          boolean submitGaps, boolean preserveOrder, AlignmentI seqdataset)
   {
     if (!locateWebService())
     {
@@ -108,12 +119,11 @@ public class MsaWSClient extends WS1Client
 
     wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")
             + " of " + altitle + "\nJob details\n");
-    String jobtitle = WebServiceName.toLowerCase();
+    String jobtitle = WebServiceName.toLowerCase(Locale.ROOT);
     if (jobtitle.endsWith("alignment"))
     {
-      if (submitGaps
-              && (!jobtitle.endsWith("realignment") || jobtitle
-                      .indexOf("profile") == -1))
+      if (submitGaps && (!jobtitle.endsWith("realignment")
+              || jobtitle.indexOf("profile") == -1))
       {
         int pos = jobtitle.indexOf("alignment");
         jobtitle = WebServiceName.substring(0, pos) + "re-alignment of "
@@ -149,7 +159,7 @@ public class MsaWSClient extends WS1Client
 
     try
     {
-      this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));
+      this.server = loc.getMuscleWS(new java.net.URL(WsURL));
       ((MuscleWSSoapBindingStub) this.server).setTimeout(60000); // One minute
       // timeout
     } catch (Exception ex)
@@ -191,6 +201,7 @@ public class MsaWSClient extends WS1Client
     return (WebServiceName.indexOf("lustal") > -1); // cheat!
   }
 
+  @Override
   public void attachWSMenuEntry(JMenu msawsmenu,
           final ServiceHandle serviceHandle, final AlignFrame alignFrame)
   {
@@ -199,12 +210,14 @@ public class MsaWSClient extends WS1Client
     method.setToolTipText(WsURL);
     method.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         AlignmentView msa = alignFrame.gatherSequencesForAlignment();
-        new jalview.ws.jws1.MsaWSClient(serviceHandle, alignFrame
-                .getTitle(), msa, false, true, alignFrame.getViewport()
-                .getAlignment().getDataset(), alignFrame);
+        new jalview.ws.jws1.MsaWSClient(serviceHandle,
+                alignFrame.getTitle(), msa, false, true,
+                alignFrame.getViewport().getAlignment().getDataset(),
+                alignFrame);
 
       }
 
@@ -213,17 +226,19 @@ public class MsaWSClient extends WS1Client
     if (canSubmitGaps())
     {
       // We know that ClustalWS can accept partial alignments for refinement.
-      final JMenuItem methodR = new JMenuItem(serviceHandle.getName()
-              + " Realign");
+      final JMenuItem methodR = new JMenuItem(
+              serviceHandle.getName() + " Realign");
       methodR.setToolTipText(WsURL);
       methodR.addActionListener(new ActionListener()
       {
+        @Override
         public void actionPerformed(ActionEvent e)
         {
           AlignmentView msa = alignFrame.gatherSequencesForAlignment();
-          new jalview.ws.jws1.MsaWSClient(serviceHandle, alignFrame
-                  .getTitle(), msa, true, true, alignFrame.getViewport()
-                  .getAlignment().getDataset(), alignFrame);
+          new jalview.ws.jws1.MsaWSClient(serviceHandle,
+                  alignFrame.getTitle(), msa, true, true,
+                  alignFrame.getViewport().getAlignment().getDataset(),
+                  alignFrame);
 
         }