From f34fce2ca880ad6e0f944e3f956b47fc7c4f278d Mon Sep 17 00:00:00 2001
From: Sasha <asherstnev@main-laptop2>
Date: Fri, 26 Apr 2013 18:19:05 +0100
Subject: [PATCH] Re-formatting files

---
 WEB-INF/web.xml |  616 ++++++++++++++++++++++++++++---------------------------
 wsbuild.xml     |  236 ++++++++++-----------
 2 files changed, 425 insertions(+), 427 deletions(-)

diff --git a/WEB-INF/web.xml b/WEB-INF/web.xml
index dc5cee3..8c2fc89 100644
--- a/WEB-INF/web.xml
+++ b/WEB-INF/web.xml
@@ -1,311 +1,321 @@
 <web-app xmlns="http://java.sun.com/xml/ns/j2ee"
-    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-    xsi:schemaLocation="http://java.sun.com/xml/ns/j2ee http://java.sun.com/xml/ns/j2ee/web-app_2_4.xsd"
-    version="2.4">
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://java.sun.com/xml/ns/j2ee http://java.sun.com/xml/ns/j2ee/web-app_2_4.xsd"
+ version="2.4">
 
-    <display-name>JABAWS</display-name>
-    <description>JAva Bioinformatics Analysis Web Services (JABAWS) v.2</description>
+<display-name>JABAWS</display-name>
+<description>JAva Bioinformatics Analysis Web Services (JABAWS) v.2</description>
 
+
+	<!-- JABAWS listeners -->
 	<listener>
 		<listener-class>compbio.ws.server.ShutdownEngines</listener-class>
 	</listener>
-    <listener>
-        <listener-class>compbio.stat.servlet.StatisticCollector</listener-class>
-     </listener>
-     <listener>
-        <listener-class>compbio.ws.server.SetExecutableFlag</listener-class>
-     </listener>
-     <listener>
-        <listener-class>com.sun.xml.ws.transport.http.servlet.WSServletContextListener</listener-class>
-     </listener>
-    
- 	<!-- Session timeout in minutes -->
+	<listener>
+		<listener-class>compbio.stat.servlet.StatisticCollector</listener-class>
+	</listener>
+	<listener>
+		<listener-class>compbio.ws.server.SetExecutableFlag</listener-class>
+	</listener>
+	<listener>
+		<listener-class>com.sun.xml.ws.transport.http.servlet.WSServletContextListener</listener-class>
+	</listener>
+
+
+	<!-- Session timeout in minutes -->
 	<session-config>
-   		<session-timeout>20</session-timeout>
-    </session-config>
- 
-     <servlet>
-        <display-name>This is a standard tomcat 'default' servlet for making listings</display-name>
-        <servlet-name>listings</servlet-name>
-        <servlet-class>org.apache.catalina.servlets.DefaultServlet</servlet-class>
-        <init-param>
-            <param-name>debug</param-name>
-            <param-value>0</param-value>
-        </init-param>
-        <init-param>
-            <param-name>readonly</param-name>
-            <param-value>true</param-value>
-        </init-param>
-        <init-param>
-            <param-name>listings</param-name>
-            <param-value>true</param-value>
-        </init-param>
-        <load-on-startup>1</load-on-startup>
-    </servlet>
-
-    <servlet>
-    	<description>Display pre-calculated accounting info</description>
-    	<servlet-name>DisplayStat</servlet-name>
-    	<servlet-class>compbio.stat.servlet.DisplayStat</servlet-class>
-    </servlet>
-  
-   <servlet>
-    	<description>WebServices Status</description>
-    	<servlet-name>ServiceStatus</servlet-name>
-    	<servlet-class>compbio.stat.servlet.ServiceStatus</servlet-class>
-    </servlet>
-
-   <servlet>
-    	<servlet-name>DownloadRedirector</servlet-name>
-    	<servlet-class>compbio.stat.servlet.DownloadRedirector</servlet-class>
-    </servlet>
-   
-    <servlet>
-    	<description>WebService Status with no UI. Accepts web service name as a parameter</description>
-    	<servlet-name>HttpCodeResponseServiceStatus</servlet-name>
-    	<servlet-class>compbio.stat.servlet.HttpCodeResponseServiceStatus</servlet-class>
-    </servlet>
-    
-    <servlet>
-    	<description>Display job list</description>
-    	<servlet-name>Joblist</servlet-name>
-    	<servlet-class>compbio.stat.servlet.Joblist</servlet-class>
-    </servlet>
-    
-    <servlet>
-    	<description>Display monthly summary statistics</description>
-    	<servlet-name>AnnualStat</servlet-name>
-    	<servlet-class>compbio.stat.servlet.AnnualStat</servlet-class>
-    </servlet>
-    
-     <servlet>
-    	<description>Display monthly summary statistics with no links to details</description>
-    	<servlet-name>PublicAnnualStat</servlet-name>
-    	<servlet-class>compbio.stat.servlet.AnnualStat</servlet-class>
-    </servlet>
-    
-    <servlet>
-        <servlet-name>RegistryWS</servlet-name>
-        <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
-        <load-on-startup>1</load-on-startup>
-    </servlet>
-    
-    <servlet>
-        <servlet-name>ClustalWS</servlet-name>
-        <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
-        <load-on-startup>1</load-on-startup>
-    </servlet>
-    
-    <servlet>
-        <servlet-name>ClustalOWS</servlet-name>
-        <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
-        <load-on-startup>1</load-on-startup>
-    </servlet>
-    
-    <servlet>
-        <servlet-name>MuscleWS</servlet-name>
-        <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
-        <load-on-startup>1</load-on-startup>
-    </servlet>
-    
-    <servlet>
-        <servlet-name>MafftWS</servlet-name>
-        <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
-        <load-on-startup>1</load-on-startup>
-    </servlet>
-    
-    <servlet>
-        <servlet-name>TcoffeeWS</servlet-name>
-        <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
-        <load-on-startup>1</load-on-startup>
-    </servlet>
-     
-    <servlet>
-        <servlet-name>ProbconsWS</servlet-name>
-        <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
-        <load-on-startup>1</load-on-startup>
-    </servlet>
-    
-     <servlet>
-        <servlet-name>AAConWS</servlet-name>
-        <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
-        <load-on-startup>1</load-on-startup>
-    </servlet>
-   
-     <servlet>
-        <servlet-name>JronnWS</servlet-name>
-        <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
-        <load-on-startup>1</load-on-startup>
-    </servlet>
-
-     <servlet>
-        <servlet-name>DisemblWS</servlet-name>
-        <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+		<session-timeout>20</session-timeout>
+	</session-config>
+
+
+	<servlet>
+		<display-name>This is a standard tomcat 'default' servlet for making listings</display-name>
+		<servlet-name>listings</servlet-name>
+		<servlet-class>org.apache.catalina.servlets.DefaultServlet</servlet-class>
+		<init-param>
+			<param-name>debug</param-name>
+			<param-value>0</param-value>
+		</init-param>
+		<init-param>
+			<param-name>readonly</param-name>
+			<param-value>true</param-value>
+		</init-param>
+		<init-param>
+			<param-name>listings</param-name>
+			<param-value>true</param-value>
+		</init-param>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+
+
+	<!-- JABAWS servlets -->
+	<servlet>
+		<description>Display pre-calculated accounting info</description>
+		<servlet-name>DisplayStat</servlet-name>
+		<servlet-class>compbio.stat.servlet.DisplayStat</servlet-class>
+	</servlet>
+
+	<servlet>
+		<description>WebServices Status</description>
+		<servlet-name>ServiceStatus</servlet-name>
+		<servlet-class>compbio.stat.servlet.ServiceStatus</servlet-class>
+	</servlet>
+
+	<servlet>
+		<servlet-name>DownloadRedirector</servlet-name>
+		<servlet-class>compbio.stat.servlet.DownloadRedirector</servlet-class>
+	</servlet>
+
+	<servlet>
+		<description>WebService Status with no UI. Accepts web service name as a parameter</description>
+		<servlet-name>HttpCodeResponseServiceStatus</servlet-name>
+		<servlet-class>compbio.stat.servlet.HttpCodeResponseServiceStatus</servlet-class>
+	</servlet>
+
+	<servlet>
+		<description>Display job list</description>
+		<servlet-name>Joblist</servlet-name>
+		<servlet-class>compbio.stat.servlet.Joblist</servlet-class>
+	</servlet>
+
+	<servlet>
+		<description>Display monthly summary statistics</description>
+		<servlet-name>AnnualStat</servlet-name>
+		<servlet-class>compbio.stat.servlet.AnnualStat</servlet-class>
+	</servlet>
+
+	<servlet>
+		<description>Display monthly summary statistics with no links to details</description>
+		<servlet-name>PublicAnnualStat</servlet-name>
+		<servlet-class>compbio.stat.servlet.AnnualStat</servlet-class>
+	</servlet>
+
+	<servlet>
+		<servlet-name>RegistryWS</servlet-name>
+		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+
+	<servlet>
+		<servlet-name>ClustalWS</servlet-name>
+		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+
+	<servlet>
+		<servlet-name>ClustalOWS</servlet-name>
+		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+
+	<servlet>
+		<servlet-name>MuscleWS</servlet-name>
+		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+
+	<servlet>
+		<servlet-name>MafftWS</servlet-name>
+		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+
+	<servlet>
+		<servlet-name>TcoffeeWS</servlet-name>
+		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+
+	<servlet>
+		<servlet-name>ProbconsWS</servlet-name>
+		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+
+	<servlet>
+		<servlet-name>AAConWS</servlet-name>
+		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+
+	<servlet>
+		<servlet-name>JronnWS</servlet-name>
+		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
 		<load-on-startup>1</load-on-startup>
-    </servlet>
-    
-    <servlet>
-        <servlet-name>GlobPlotWS</servlet-name>
-        <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
-        <load-on-startup>1</load-on-startup>
-    </servlet>
-    
-     <servlet>
-        <servlet-name>IUPredWS</servlet-name>
-        <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
-        <load-on-startup>1</load-on-startup>
-    </servlet>
-   
-    <servlet-mapping>
-    	<servlet-name>listings</servlet-name>
-    	<url-pattern>/</url-pattern>
-  	</servlet-mapping>
-  	
-  	     
-    <servlet-mapping>
-    	<servlet-name>DownloadRedirector</servlet-name>
-    	<url-pattern>/download</url-pattern>
-  	</servlet-mapping>
-  	
-    <servlet-mapping>
-    	<servlet-name>DisplayStat</servlet-name>
-    	<url-pattern>/DisplayStat</url-pattern>
-  	</servlet-mapping>
-  	
-  	<servlet-mapping>
-    	<servlet-name>ServiceStatus</servlet-name>
-    	<url-pattern>/ServiceStatus</url-pattern>
-  	</servlet-mapping>
-  	
-  	<servlet-mapping>
-    	<servlet-name>HttpCodeResponseServiceStatus</servlet-name>
-    	<url-pattern>/HttpCodeResponseServiceStatus/*</url-pattern>
-  	</servlet-mapping>
-  	
-  	 <servlet-mapping>
-    	<servlet-name>AnnualStat</servlet-name>
-    	<url-pattern>/AnnualStat</url-pattern>
-  	</servlet-mapping>  
-    
-     <servlet-mapping>
-    	<servlet-name>PublicAnnualStat</servlet-name>
-    	<url-pattern>/PublicAnnualStat</url-pattern>
-  	</servlet-mapping>  
-    
-    
-    <servlet-mapping>
-    	<servlet-name>Joblist</servlet-name>
-    	<url-pattern>/Joblist</url-pattern>
-  	</servlet-mapping> 
-  	
-    <servlet-mapping>
-    	<servlet-name>RegistryWS</servlet-name>
-    	<url-pattern>/RegistryWS</url-pattern>
-    </servlet-mapping>
-    
-    <servlet-mapping>
-    	<servlet-name>ClustalWS</servlet-name>
-    	<url-pattern>/ClustalWS</url-pattern>
-    </servlet-mapping>
-    
-     <servlet-mapping>
-    	<servlet-name>ClustalOWS</servlet-name>
-    	<url-pattern>/ClustalOWS</url-pattern>
-    </servlet-mapping>
-    
-    <servlet-mapping>
-    	<servlet-name>MuscleWS</servlet-name>
-    	<url-pattern>/MuscleWS</url-pattern>
-    </servlet-mapping>
-
-   <servlet-mapping>
-    	<servlet-name>MafftWS</servlet-name>
-    	<url-pattern>/MafftWS</url-pattern>
-    </servlet-mapping>
-    
-   <servlet-mapping>
-    	<servlet-name>TcoffeeWS</servlet-name>
-    	<url-pattern>/TcoffeeWS</url-pattern>
-   </servlet-mapping>
-
-   <servlet-mapping>
-    	<servlet-name>ProbconsWS</servlet-name>
-    	<url-pattern>/ProbconsWS</url-pattern>
-   </servlet-mapping>
- 
-   <servlet-mapping>
-    	<servlet-name>AAConWS</servlet-name>
-    	<url-pattern>/AAConWS</url-pattern>
-   </servlet-mapping>
-   
-    <servlet-mapping>
-    	<servlet-name>JronnWS</servlet-name>
-    	<url-pattern>/JronnWS</url-pattern>
-   </servlet-mapping>
-   
-   <servlet-mapping>
-    	<servlet-name>DisemblWS</servlet-name>
-    	<url-pattern>/DisemblWS</url-pattern>
-   </servlet-mapping>
-   
-   <servlet-mapping>
-    	<servlet-name>GlobPlotWS</servlet-name>
-    	<url-pattern>/GlobPlotWS</url-pattern>
-   </servlet-mapping>
-   
-    <servlet-mapping>
-    	<servlet-name>IUPredWS</servlet-name>
-    	<url-pattern>/IUPredWS</url-pattern>
-   </servlet-mapping>
-   
-   <security-constraint>
-    <web-resource-collection>
-    	<web-resource-name>Administrator pages</web-resource-name>
-   		<!-- Prohibit access to any resources -->
-    	<url-pattern>/DisplayStat</url-pattern>
-    	<url-pattern>/Joblist</url-pattern>
-    	<url-pattern>/AnnualStat</url-pattern>
-    	<url-pattern>/conf/*</url-pattern>
-   		<url-pattern>/binaries/*</url-pattern>
-   		<url-pattern>/jobsout/*</url-pattern>
-   		<url-pattern>/testsrc/*</url-pattern>
-   		<url-pattern>/lib/*</url-pattern>
-   		<url-pattern>/test-output/*</url-pattern>
-   		<!-- Uncomment this to secure services status checker 
-   		<url-pattern>/HttpCodeResponseServiceStatus/*</url-pattern>
-   		<url-pattern>/ServiceStatus</url-pattern>
-   		 -->
-    	<!-- No http-method means all methods are constrained -->
-    </web-resource-collection>
-    <auth-constraint>
-      <role-name>admin</role-name>
-    </auth-constraint>
-   </security-constraint>
-
-  <!-- unsupported HTTP methods -->
-  <security-constraint>
-        <web-resource-collection>
-        <web-resource-name>unsupported HTTP methods</web-resource-name>
-        <url-pattern>/*</url-pattern>
-            <http-method>PUT</http-method>
-            <http-method>DELETE</http-method>
-            <http-method>TRACE</http-method>
-            <http-method>OPTIONS</http-method>
-        </web-resource-collection>
-        <auth-constraint/>
-  </security-constraint>
-      <!-- Define the Login Configuration for this Application -->
-  <login-config>
-   	 <auth-method>BASIC</auth-method>
-  	 <realm-name>JABAWS administrators</realm-name>
-  </login-config>
-  
-    <!-- Security roles referenced by this web application -->
-  <security-role>
-    <description>
-      The role that is required to log in and view JABAWS internals
-    </description>
-    <role-name>admin</role-name>
-  </security-role>
-  
-</web-app>
\ No newline at end of file
+	</servlet>
+
+	<servlet>
+		<servlet-name>DisemblWS</servlet-name>
+		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+
+	<servlet>
+		<servlet-name>GlobPlotWS</servlet-name>
+		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+
+	<servlet>
+		<servlet-name>IUPredWS</servlet-name>
+		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
+		<load-on-startup>1</load-on-startup>
+	</servlet>
+
+	<!-- JABAWS servlet mappings -->
+	<servlet-mapping>
+		<servlet-name>listings</servlet-name>
+		<url-pattern>/</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>DownloadRedirector</servlet-name>
+		<url-pattern>/download</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>DisplayStat</servlet-name>
+		<url-pattern>/DisplayStat</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>ServiceStatus</servlet-name>
+		<url-pattern>/ServiceStatus</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>HttpCodeResponseServiceStatus</servlet-name>
+		<url-pattern>/HttpCodeResponseServiceStatus/*</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>AnnualStat</servlet-name>
+		<url-pattern>/AnnualStat</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>PublicAnnualStat</servlet-name>
+		<url-pattern>/PublicAnnualStat</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>Joblist</servlet-name>
+		<url-pattern>/Joblist</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>RegistryWS</servlet-name>
+		<url-pattern>/RegistryWS</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>ClustalWS</servlet-name>
+		<url-pattern>/ClustalWS</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>ClustalOWS</servlet-name>
+		<url-pattern>/ClustalOWS</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>MuscleWS</servlet-name>
+		<url-pattern>/MuscleWS</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>MafftWS</servlet-name>
+		<url-pattern>/MafftWS</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>TcoffeeWS</servlet-name>
+		<url-pattern>/TcoffeeWS</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>ProbconsWS</servlet-name>
+		<url-pattern>/ProbconsWS</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>AAConWS</servlet-name>
+		<url-pattern>/AAConWS</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>JronnWS</servlet-name>
+		<url-pattern>/JronnWS</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>DisemblWS</servlet-name>
+		<url-pattern>/DisemblWS</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>GlobPlotWS</servlet-name>
+		<url-pattern>/GlobPlotWS</url-pattern>
+	</servlet-mapping>
+
+	<servlet-mapping>
+		<servlet-name>IUPredWS</servlet-name>
+		<url-pattern>/IUPredWS</url-pattern>
+	</servlet-mapping>
+
+
+
+	<!-- JABAWS security constraints -->
+	<security-constraint>
+		<web-resource-collection>
+		<web-resource-name>Administrator pages</web-resource-name>
+			<!-- Prohibit access to any resources -->
+			<url-pattern>/DisplayStat</url-pattern>
+			<url-pattern>/Joblist</url-pattern>
+			<url-pattern>/AnnualStat</url-pattern>
+			<url-pattern>/conf/*</url-pattern>
+			<url-pattern>/binaries/*</url-pattern>
+			<url-pattern>/jobsout/*</url-pattern>
+			<url-pattern>/testsrc/*</url-pattern>
+			<url-pattern>/lib/*</url-pattern>
+			<url-pattern>/test-output/*</url-pattern>
+			<!-- Uncomment this to secure services status checker 
+			<url-pattern>/HttpCodeResponseServiceStatus/*</url-pattern>
+			<url-pattern>/ServiceStatus</url-pattern>
+			-->
+			<!-- No http-method means all methods are constrained -->
+		</web-resource-collection>
+		<auth-constraint>
+			<role-name>admin</role-name>
+		</auth-constraint>
+	</security-constraint>
+
+
+	<!-- unsupported HTTP methods -->
+	<security-constraint>
+		<web-resource-collection>
+			<web-resource-name>unsupported HTTP methods</web-resource-name>
+			<url-pattern>/*</url-pattern>
+			<http-method>PUT</http-method>
+			<http-method>DELETE</http-method>
+			<http-method>TRACE</http-method>
+			<http-method>OPTIONS</http-method>
+		</web-resource-collection>
+		<auth-constraint/>
+	</security-constraint>
+
+
+	<!-- Define the Login Configuration for this Application -->
+	<login-config>
+		<auth-method>BASIC</auth-method>
+		<realm-name>JABAWS administrators</realm-name>
+	</login-config>
+
+
+	<!-- Security roles referenced by this web application -->
+	<security-role>
+		<description>The role that is required to log in and view JABAWS internals</description>
+		<role-name>admin</role-name>
+	</security-role>
+
+</web-app>
diff --git a/wsbuild.xml b/wsbuild.xml
index bd9f15b..f61ffaf 100644
--- a/wsbuild.xml
+++ b/wsbuild.xml
@@ -52,120 +52,117 @@
 			<!-- resourcedestdir - Where to put generated source files -->
 
 		<wsgen sei="compbio.ws.server.AAConWS" 
-					sourcedestdir="${basedir}/webservices" 
-					destdir="${classes}" 
-					resourcedestdir="${wsdl.dir}" 
-					keep="true" genwsdl="true" 
-					extension="false" 
-					xendorsed="true"			
-					verbose="true">
-					<classpath refid="classes.path" />
-					<classpath refid="project.classpath" />
+				sourcedestdir="${basedir}/webservices" 
+				destdir="${classes}" 
+				resourcedestdir="${wsdl.dir}" 
+				keep="true" genwsdl="true" 
+				extension="false" 
+				xendorsed="true" 
+				verbose="true">
+				<classpath refid="classes.path" />
+				<classpath refid="project.classpath" />
 		</wsgen>
-
 		<wsgen sei="compbio.ws.server.ClustalWS" 
-					sourcedestdir="${basedir}/webservices" 
-					destdir="${classes}" 
-					resourcedestdir="${wsdl.dir}" 
-					keep="true" genwsdl="true" 
-					extension="false" 
-					xendorsed="true"
-					verbose="true">
-					<classpath refid="classes.path" />
-					<classpath refid="project.classpath" />
+				sourcedestdir="${basedir}/webservices" 
+				destdir="${classes}" 
+				resourcedestdir="${wsdl.dir}" 
+				keep="true" genwsdl="true" 
+				extension="false" 
+				xendorsed="true"
+				verbose="true">
+				<classpath refid="classes.path" />
+				<classpath refid="project.classpath" />
 		</wsgen>
 		<wsgen sei="compbio.ws.server.MuscleWS" 
-						sourcedestdir="${basedir}/webservices" 
-						destdir="${classes}" 
-						resourcedestdir="${wsdl.dir}" 
-						keep="true" genwsdl="true" 
-						extension="false"
-						xendorsed="true"
-						verbose="true">
-						<classpath refid="classes.path" />
-						<classpath refid="project.classpath" />
-			</wsgen>
+				sourcedestdir="${basedir}/webservices" 
+				destdir="${classes}" 
+				resourcedestdir="${wsdl.dir}" 
+				keep="true" genwsdl="true" 
+				extension="false"
+				xendorsed="true"
+				verbose="true">
+				<classpath refid="classes.path" />
+				<classpath refid="project.classpath" />
+		</wsgen>
 		<wsgen sei="compbio.ws.server.MafftWS" 
-						sourcedestdir="${basedir}/webservices" 
-						destdir="${classes}" 
-						resourcedestdir="${wsdl.dir}" 
-						keep="true" genwsdl="true" 
-						extension="false"
-						xendorsed="true"
-						verbose="true">
-						<classpath refid="classes.path" />
-						<classpath refid="project.classpath" />
-			</wsgen>
+				sourcedestdir="${basedir}/webservices" 
+				destdir="${classes}" 
+				resourcedestdir="${wsdl.dir}" 
+				keep="true" genwsdl="true" 
+				extension="false"
+				xendorsed="true"
+				verbose="true">
+				<classpath refid="classes.path" />
+				<classpath refid="project.classpath" />
+		</wsgen>
 		<wsgen sei="compbio.ws.server.TcoffeeWS" 
-						sourcedestdir="${basedir}/webservices" 
-						destdir="${classes}" 
-						resourcedestdir="${wsdl.dir}" 
-						keep="true" genwsdl="true" 
-						extension="false" 
-						xendorsed="true"			
-						verbose="true">
-						<classpath refid="classes.path" />
-						<classpath refid="project.classpath" />
+				sourcedestdir="${basedir}/webservices" 
+				destdir="${classes}" 
+				resourcedestdir="${wsdl.dir}" 
+				keep="true" genwsdl="true" 
+				extension="false" 
+				xendorsed="true" 
+				verbose="true">
+				<classpath refid="classes.path" />
+				<classpath refid="project.classpath" />
 		</wsgen>
-		
 		<wsgen sei="compbio.ws.server.DisemblWS" 
-						sourcedestdir="${basedir}/webservices" 
-						destdir="${classes}" 
-						resourcedestdir="${wsdl.dir}" 
-						keep="true" genwsdl="true" 
-						extension="false" 
-						xendorsed="true"			
-						verbose="true">
-						<classpath refid="classes.path" />
-						<classpath refid="project.classpath" />
+				sourcedestdir="${basedir}/webservices" 
+				destdir="${classes}" 
+				resourcedestdir="${wsdl.dir}" 
+				keep="true" genwsdl="true" 
+				extension="false" 
+				xendorsed="true" 
+				verbose="true">
+				<classpath refid="classes.path" />
+				<classpath refid="project.classpath" />
 		</wsgen>
 		<wsgen sei="compbio.ws.server.GlobPlotWS" 
-						sourcedestdir="${basedir}/webservices" 
-						destdir="${classes}" 
-						resourcedestdir="${wsdl.dir}" 
-						keep="true" genwsdl="true" 
-						extension="false" 
-						xendorsed="true"			
-						verbose="true">
-						<classpath refid="classes.path" />
-						<classpath refid="project.classpath" />
+				sourcedestdir="${basedir}/webservices" 
+				destdir="${classes}" 
+				resourcedestdir="${wsdl.dir}" 
+				keep="true" genwsdl="true" 
+				extension="false" 
+				xendorsed="true" 
+				verbose="true">
+				<classpath refid="classes.path" />
+				<classpath refid="project.classpath" />
 		</wsgen>
 		<wsgen sei="compbio.ws.server.JronnWS" 
-						sourcedestdir="${basedir}/webservices" 
-						destdir="${classes}" 
-						resourcedestdir="${wsdl.dir}" 
-						keep="true" genwsdl="true" 
-						extension="false" 
-						xendorsed="true"			
-						verbose="true">
-						<classpath refid="classes.path" />
-						<classpath refid="project.classpath" />
+				sourcedestdir="${basedir}/webservices" 
+				destdir="${classes}" 
+				resourcedestdir="${wsdl.dir}" 
+				keep="true" genwsdl="true" 
+				extension="false" 
+				xendorsed="true" 
+				verbose="true">
+				<classpath refid="classes.path" />
+				<classpath refid="project.classpath" />
 		</wsgen>
 		<wsgen sei="compbio.ws.server.IUPredWS" 
-								sourcedestdir="${basedir}/webservices" 
-								destdir="${classes}" 
-								resourcedestdir="${wsdl.dir}" 
-								keep="true" genwsdl="true" 
-								extension="false" 
-								xendorsed="true"			
-								verbose="true">
-								<classpath refid="classes.path" />
-								<classpath refid="project.classpath" />
+				sourcedestdir="${basedir}/webservices" 
+				destdir="${classes}" 
+				resourcedestdir="${wsdl.dir}" 
+				keep="true" genwsdl="true" 
+				extension="false" 
+				xendorsed="true" 
+				verbose="true">
+				<classpath refid="classes.path" />
+				<classpath refid="project.classpath" />
 		</wsgen>
 		<wsgen sei="compbio.ws.server.RegistryWS" 
-						sourcedestdir="${basedir}/webservices" 
-						destdir="${classes}" 
-						resourcedestdir="${wsdl.dir}" 
-						keep="true" genwsdl="true" 
-						extension="false" 
-						xendorsed="true"			
-						verbose="true">
-						<classpath refid="classes.path" />
-						<classpath refid="project.classpath" />
+				sourcedestdir="${basedir}/webservices" 
+				destdir="${classes}" 
+				resourcedestdir="${wsdl.dir}" 
+				keep="true" genwsdl="true" 
+				extension="false" 
+				xendorsed="true" 
+				verbose="true">
+				<classpath refid="classes.path" />
+				<classpath refid="project.classpath" />
 		</wsgen>
 	</target>
 
-
 	<taskdef name="wsimport" classname="com.sun.tools.ws.ant.WsImport">
 		<classpath refid="project.classpath" />
 	</taskdef>
@@ -182,54 +179,48 @@
 			<wsimport wsdl="${clustal.wsdl}" 
 				sourcedestdir="${basedir}/webservices/" 
 				keep="true" extension="false" 
-				verbose="true" xnocompile="true" xendorsed="true"
-				package="compbio.ws.client.stub" target="2.1"
+				verbose="true" xnocompile="true" xendorsed="true"
+				package="compbio.ws.client.stub" target="2.1"
 				quiet="false">
 			</wsimport>
 			<wsimport wsdl="${muscle.wsdl}" 
 				sourcedestdir="${basedir}/webservices/" 
 				keep="true" extension="false" 
-				verbose="true" xnocompile="true" xendorsed="true"
-				package="compbio.ws.client.stub" target="2.1"
+				verbose="true" xnocompile="true" xendorsed="true"
+				package="compbio.ws.client.stub" target="2.1"
 				quiet="false">
 			</wsimport>
 			<wsimport wsdl="${mafft.wsdl}" 
 				sourcedestdir="${basedir}/webservices/" 
 				keep="true" extension="false" 
-				verbose="true" xnocompile="true" xendorsed="true"
-				package="compbio.ws.client.stub" target="2.1"
+				verbose="true" xnocompile="true" xendorsed="true"
+				package="compbio.ws.client.stub" target="2.1"
 				quiet="false">
 			</wsimport>
 			<wsimport wsdl="${tcoffee.wsdl}" 
 				sourcedestdir="${basedir}/webservices/" 
 				keep="true" extension="false" 
-				verbose="true" xnocompile="true" xendorsed="true"
-				package="compbio.ws.client.stub" target="2.1"
+				verbose="true" xnocompile="true" xendorsed="true"
+				package="compbio.ws.client.stub" target="2.1"
 				quiet="false">
 			</wsimport>
 			<wsimport wsdl="${iupred.wsdl}" 
-						sourcedestdir="${basedir}/webservices/" 
-						keep="true" extension="false" 
-						verbose="true" xnocompile="true" xendorsed="true"
-						package="compbio.ws.client.stub" target="2.1"
-						quiet="false">
+				sourcedestdir="${basedir}/webservices/" 
+				keep="true" extension="false" 
+				verbose="true" xnocompile="true" xendorsed="true"
+				package="compbio.ws.client.stub" target="2.1"
+				quiet="false">
 			</wsimport>
-		    <wsimport wsdl="${registry.wsdl}" 
-						sourcedestdir="${basedir}/webservices/" 
-						keep="true" extension="false" 
-						verbose="true" xnocompile="true" xendorsed="true"
-						package="compbio.ws.client.stub" target="2.1"
-						quiet="false">
+			<wsimport wsdl="${registry.wsdl}" 
+				sourcedestdir="${basedir}/webservices/" 
+				keep="true" extension="false" 
+				verbose="true" xnocompile="true" xendorsed="true"
+				package="compbio.ws.client.stub" target="2.1"
+				quiet="false">
 			</wsimport>
-			<!--		<xjcarg value="-cp" />
-						<xjcarg pathref="project.classpath" />
-						<xjcarg value="-Xcommons-lang" /> -->
-				
 		</target>
 
-	
 	<!-- 
-	
 	<target name="Build artifacts from schema" description="Test task to generate JaxB commons annotated data classes DOES NOT REALLY WORK">
 		<taskdef name="xjc" classname="com.sun.tools.xjc.XJCTask">
 			<classpath refid="project.classpath" />
@@ -259,10 +250,7 @@
 					-XhashCode
 					-Xcopyable
 					-Xmergeable
-	
-	
-	
-	
+
 	<target name="build-Clustal-client-from-live-server">
 
 		<wsimport wsdl="http://localhost:7979/ClustalWS?wsdl" 
-- 
1.7.10.2