fix bad grammar in new alignment title

diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java
index 8a1a499..324f495 100755 (executable)
--- a/src/jalview/ws/MsaWSClient.java
+++ b/src/jalview/ws/MsaWSClient.java
@@ -1,151 +1,164 @@
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
- */\r
-package jalview.ws;\r
-\r
-import ext.vamsas.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import jalview.gui.*;\r
-\r
-import javax.swing.*;\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class MsaWSClient\r
-    extends WSClient\r
-{\r
-  /**\r
-   * server is a WSDL2Java generated stub for an archetypal MsaWSI service.\r
-   */\r
-  ext.vamsas.MuscleWS server;\r
-  AlignFrame alignFrame;\r
-\r
-\r
-  /**\r
-   * Creates a new MsaWSClient object that uses a service\r
-   * given by an externally retrieved ServiceHandle\r
-   *\r
-   * @param sh service handle of type AbstractName(MsaWS)\r
-   * @param altitle DOCUMENT ME!\r
-   * @param msa DOCUMENT ME!\r
-   * @param submitGaps DOCUMENT ME!\r
-   * @param preserveOrder DOCUMENT ME!\r
-   */\r
-\r
-  public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle,\r
-                     jalview.datamodel.AlignmentView msa,\r
-                     boolean submitGaps, boolean preserveOrder,\r
-                     Alignment seqdataset,\r
-                     AlignFrame _alignFrame)\r
-  {\r
-    super();\r
-    alignFrame = _alignFrame;\r
-    if (!sh.getAbstractName().equals("MsaWS"))\r
-    {\r
-      JOptionPane.showMessageDialog(Desktop.desktop,\r
-                                    "The Service called \n" + sh.getName() +\r
-          "\nis not a \nMultiple Sequence Alignment Service !",\r
-                                    "Internal Jalview Error",\r
-                                    JOptionPane.WARNING_MESSAGE);\r
-\r
-      return;\r
-    }\r
-\r
-    if ((wsInfo = setWebService(sh))==null)\r
-     {\r
-       JOptionPane.showMessageDialog(Desktop.desktop,\r
-                                     "The Multiple Sequence Alignment Service named " +\r
-                                     sh.getName() +\r
-                                     " is unknown", "Internal Jalview Error",\r
-                                     JOptionPane.WARNING_MESSAGE);\r
-\r
-       return;\r
-     }\r
-    startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);\r
-\r
-  }\r
-\r
-\r
-  private void startMsaWSClient(String altitle, AlignmentView msa,\r
-                     boolean submitGaps, boolean preserveOrder, Alignment seqdataset)\r
-  {\r
-    if (!locateWebService())\r
-    {\r
-      return;\r
-    }\r
-\r
-    wsInfo.setProgressText( ( (submitGaps) ? "Re-alignment" : "Alignment") +\r
-                           " of " + altitle + "\nJob details\n");\r
-\r
-    MsaWSThread musclethread = new MsaWSThread(server, WsURL, wsInfo, alignFrame,\r
-                                               WebServiceName,\r
-                                               WebServiceName+" alignment of " + altitle,\r
-                                               msa,\r
-                                               submitGaps, preserveOrder, seqdataset);\r
-    wsInfo.setthisService(musclethread);\r
-    musclethread.start();\r
-  }\r
-\r
-  /**\r
-   * Initializes the server field with a valid service implementation.\r
-   *\r
-   * @return true if service was located.\r
-   */\r
-  private boolean locateWebService()\r
-  {\r
-    // TODO: MuscleWS transmuted to generic MsaWS client\r
-    MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default\r
-\r
-    try\r
-    {\r
-      this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));\r
-      ( (MuscleWSSoapBindingStub)this.server).setTimeout(60000); // One minute timeout\r
-    }\r
-    catch (Exception ex)\r
-    {\r
-      wsInfo.setProgressText("Serious! " + WebServiceName +\r
-                             " Service location failed\nfor URL :" + WsURL +\r
-                             "\n" +\r
-                             ex.getMessage());\r
-      wsInfo.setStatus(WebserviceInfo.ERROR);\r
-      ex.printStackTrace();\r
-\r
-      return false;\r
-    }\r
-\r
-    loc.getEngine().setOption("axis", "1");\r
-\r
-    return true;\r
-  }\r
-\r
-  protected String getServiceActionKey()\r
-  {\r
-    return "MsaWS";\r
-  }\r
-\r
-  protected String getServiceActionDescription()\r
-  {\r
-    return "Multiple Sequence Alignment";\r
-  }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.ws;
+
+import ext.vamsas.*;
+
+import jalview.datamodel.*;
+
+import jalview.gui.*;
+
+import javax.swing.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class MsaWSClient
+    extends WSClient
+{
+  /**
+   * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
+   */
+  ext.vamsas.MuscleWS server;
+  AlignFrame alignFrame;
+
+
+  /**
+   * Creates a new MsaWSClient object that uses a service
+   * given by an externally retrieved ServiceHandle
+   *
+   * @param sh service handle of type AbstractName(MsaWS)
+   * @param altitle DOCUMENT ME!
+   * @param msa DOCUMENT ME!
+   * @param submitGaps DOCUMENT ME!
+   * @param preserveOrder DOCUMENT ME!
+   */
+
+  public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle,
+                     jalview.datamodel.AlignmentView msa,
+                     boolean submitGaps, boolean preserveOrder,
+                     Alignment seqdataset,
+                     AlignFrame _alignFrame)
+  {
+    super();
+    alignFrame = _alignFrame;
+    if (!sh.getAbstractName().equals("MsaWS"))
+    {
+      JOptionPane.showMessageDialog(Desktop.desktop,
+                                    "The Service called \n" + sh.getName() +
+          "\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);
+
+       return;
+     }
+    startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);
+
+  }
+
+
+  private void startMsaWSClient(String altitle, AlignmentView msa,
+                     boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
+  {
+    if (!locateWebService())
+    {
+      return;
+    }
+
+    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;
+    }
+    
+    MsaWSThread msathread = new MsaWSThread(server, WsURL, wsInfo, alignFrame,
+                                               WebServiceName,
+                                               jobtitle,
+                                               msa,
+                                               submitGaps, preserveOrder, seqdataset);
+    wsInfo.setthisService(msathread);
+    msathread.start();
+  }
+
+  /**
+   * Initializes the server field with a valid service implementation.
+   *
+   * @return true if service was located.
+   */
+  private boolean locateWebService()
+  {
+    // TODO: MuscleWS transmuted to generic MsaWS client
+    MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default
+
+    try
+    {
+      this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));
+      ( (MuscleWSSoapBindingStub)this.server).setTimeout(60000); // One minute timeout
+    }
+    catch (Exception ex)
+    {
+      wsInfo.setProgressText("Serious! " + WebServiceName +
+                             " Service location failed\nfor URL :" + WsURL +
+                             "\n" +
+                             ex.getMessage());
+      wsInfo.setStatus(WebserviceInfo.ERROR);
+      ex.printStackTrace();
+
+      return false;
+    }
+
+    loc.getEngine().setOption("axis", "1");
+
+    return true;
+  }
+
+  protected String getServiceActionKey()
+  {
+    return "MsaWS";
+  }
+
+  protected String getServiceActionDescription()
+  {
+    return "Multiple Sequence Alignment";
+  }
+}