-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 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.analysis.AlignSeq;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import jalview.gui.*;\r
-\r
-import java.util.*;\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) 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
+ * 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 javax.swing.*;
+
+import ext.vamsas.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
+
+/**
+ * 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.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);
+ 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";
+ }
+}