X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FMsaWSClient.java;h=03a801effca126e07a36adc80db6a33eb08f599f;hb=83f6c6309e9705037a0853a26da74821c9d4fd12;hp=324f49596ca2c2478e94e83bbee9c22269ba99c0;hpb=1317ecb3c6b047999fa852b2ff28c3370aa84624;p=jalview.git

diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java
index 324f495..03a801e 100755
--- a/src/jalview/ws/MsaWSClient.java
+++ b/src/jalview/ws/MsaWSClient.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -18,14 +18,12 @@
  */
 package jalview.ws;
 
-import ext.vamsas.*;
+import javax.swing.*;
 
+import ext.vamsas.*;
 import jalview.datamodel.*;
-
 import jalview.gui.*;
 
-import javax.swing.*;
-
 /**
  * DOCUMENT ME!
  *
@@ -41,7 +39,6 @@ public class MsaWSClient
   ext.vamsas.MuscleWS server;
   AlignFrame alignFrame;
 
-
   /**
    * Creates a new MsaWSClient object that uses a service
    * given by an externally retrieved ServiceHandle
@@ -65,30 +62,30 @@ public class MsaWSClient
     {
       JOptionPane.showMessageDialog(Desktop.desktop,
                                     "The Service called \n" + sh.getName() +
-          "\nis not a \nMultiple Sequence Alignment Service !",
+                                    "\nis not a \nMultiple Sequence Alignment Service !",
                                     "Internal Jalview Error",
                                     JOptionPane.WARNING_MESSAGE);
 
       return;
     }
 
-    if ((wsInfo = setWebService(sh))==null)
-     {
-       JOptionPane.showMessageDialog(Desktop.desktop,
-                                     "The Multiple Sequence Alignment Service named " +
-                                     sh.getName() +
-                                     " is unknown", "Internal Jalview Error",
-                                     JOptionPane.WARNING_MESSAGE);
+    if ( (wsInfo = setWebService(sh)) == null)
+    {
+      JOptionPane.showMessageDialog(Desktop.desktop,
+                                    "The Multiple Sequence Alignment Service named " +
+                                    sh.getName() +
+                                    " is unknown", "Internal Jalview Error",
+                                    JOptionPane.WARNING_MESSAGE);
 
-       return;
-     }
+      return;
+    }
     startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);
 
   }
 
-
   private void startMsaWSClient(String altitle, AlignmentView msa,
-                     boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
+                                boolean submitGaps, boolean preserveOrder,
+                                Alignment seqdataset)
   {
     if (!locateWebService())
     {
@@ -98,24 +95,33 @@ public class MsaWSClient
     wsInfo.setProgressText( ( (submitGaps) ? "Re-alignment" : "Alignment") +
                            " of " + altitle + "\nJob details\n");
     String jobtitle = WebServiceName.toLowerCase();
-    if (jobtitle.endsWith("alignment")) {
-        if (submitGaps 
-                && (!jobtitle.endsWith("realignment") 
-                || !jobtitle.contains("profile"))) {
-            int pos=jobtitle.indexOf("alignment");
-            jobtitle = WebServiceName.substring(0, pos) + "re-alignment of "+altitle;
-        } else {
-            jobtitle = WebServiceName+" of "+altitle;
-        }
-    } else {
-        jobtitle = WebServiceName+(submitGaps? " re" : " ") +"alignment of "+altitle;
+    if (jobtitle.endsWith("alignment"))
+    {
+      if (submitGaps
+          && (!jobtitle.endsWith("realignment")
+              || jobtitle.indexOf("profile") == -1))
+      {
+        int pos = jobtitle.indexOf("alignment");
+        jobtitle = WebServiceName.substring(0, pos) + "re-alignment of " +
+            altitle;
+      }
+      else
+      {
+        jobtitle = WebServiceName + " of " + altitle;
+      }
+    }
+    else
+    {
+      jobtitle = WebServiceName + (submitGaps ? " re" : " ") + "alignment of " +
+          altitle;
     }
-    
+
     MsaWSThread msathread = new MsaWSThread(server, WsURL, wsInfo, alignFrame,
-                                               WebServiceName,
-                                               jobtitle,
-                                               msa,
-                                               submitGaps, preserveOrder, seqdataset);
+                                            WebServiceName,
+                                            jobtitle,
+                                            msa,
+                                            submitGaps, preserveOrder,
+                                            seqdataset);
     wsInfo.setthisService(msathread);
     msathread.start();
   }