From 48a41a20fc325be91f8e6da1f42a75a983437b70 Mon Sep 17 00:00:00 2001
From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Wed, 2 Feb 2011 16:53:10 +0000
Subject: [PATCH] Adding Jronn WS to conf files

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3661 e3abac25-378b-4346-85de-24260fe3988d
---
 WEB-INF/sun-jaxws.xml                      |    4 ++++
 WEB-INF/web.xml                            |   13 ++++++++++++-
 webservices/compbio/ws/server/JronnWS.java |    9 ---------
 3 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/WEB-INF/sun-jaxws.xml b/WEB-INF/sun-jaxws.xml
index 994abef..03228f8 100644
--- a/WEB-INF/sun-jaxws.xml
+++ b/WEB-INF/sun-jaxws.xml
@@ -24,4 +24,8 @@
         name='AAConWS'
         implementation='compbio.ws.server.AAConWS'
         url-pattern='/AAConWS'/>
+    <endpoint
+        name='JronnWS'
+        implementation='compbio.ws.server.JronnWS'
+        url-pattern='/JronnWS'/>
 </endpoints>
diff --git a/WEB-INF/web.xml b/WEB-INF/web.xml
index ae99a94..f73b59c 100644
--- a/WEB-INF/web.xml
+++ b/WEB-INF/web.xml
@@ -53,7 +53,13 @@
         <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
         <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/>
+    </servlet>
+     
     <servlet-mapping>
     	<servlet-name>ClustalWS</servlet-name>
     	<url-pattern>/ClustalWS</url-pattern>
@@ -84,6 +90,11 @@
     	<url-pattern>/AAConWS</url-pattern>
    </servlet-mapping>
    
+    <servlet-mapping>
+    	<servlet-name>JronnWS</servlet-name>
+    	<url-pattern>/JronnWS</url-pattern>
+   </servlet-mapping>
+   
    <security-constraint>
     <web-resource-collection>
     	<web-resource-name>Administrator pages</web-resource-name>
diff --git a/webservices/compbio/ws/server/JronnWS.java b/webservices/compbio/ws/server/JronnWS.java
index bcb6af5..9f5be63 100644
--- a/webservices/compbio/ws/server/JronnWS.java
+++ b/webservices/compbio/ws/server/JronnWS.java
@@ -68,12 +68,6 @@ public class JronnWS implements Annotation<Jronn> {
 		log.trace(jobId + " getConservation : " + mas);
 		return mas;
 	}
-	/*
-	 * @SuppressWarnings("unchecked") public JalviewAnnotation
-	 * getJalviewAnnotation(String jobId) throws ResultNotAvailableException {
-	 * MultiAnnotatedSequence<Method> result = getResult(jobId); // TODO //
-	 * log(jobId, "getResults"); return result.toJalviewAnnotation(); }
-	 */
 
 	@Override
 	public Limit<Jronn> getLimit(String presetName) {
@@ -136,9 +130,6 @@ public class JronnWS implements Annotation<Jronn> {
 		ConfiguredExecutable<Jronn> confAAcon = init(sequences);
 
 		// set default conservation method to fastest - SHENKIN
-		// TODO: This violates encapsulation, should be moved to the runners
-		// level.
-		// confAAcon.addParameters(Arrays.asList("-m=SHENKIN"));
 		return analize(sequences, confAAcon, null, "analize", getLimit(""));
 	}
 
-- 
1.7.10.2