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

diff --git a/WEB-INF/sun-jaxws.xml b/WEB-INF/sun-jaxws.xml
index 994abef..03228f8 100644 (file)
--- a/WEB-INF/sun-jaxws.xml
+++ b/WEB-INF/sun-jaxws.xml
@@ -24,4 +24,8 @@
         name='AAConWS'\r
         implementation='compbio.ws.server.AAConWS'\r
         url-pattern='/AAConWS'/>\r
+    <endpoint\r
+        name='JronnWS'\r
+        implementation='compbio.ws.server.JronnWS'\r
+        url-pattern='/JronnWS'/>\r
 </endpoints>\r

diff --git a/WEB-INF/web.xml b/WEB-INF/web.xml
index ae99a94..f73b59c 100644 (file)
--- 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>\r
         <load-on-startup/>\r
     </servlet>\r
-    \r
+   \r
+     <servlet>\r
+        <servlet-name>JronnWS</servlet-name>\r
+        <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+        <load-on-startup/>\r
+    </servlet>\r
+     \r
     <servlet-mapping>\r
        <servlet-name>ClustalWS</servlet-name>\r
        <url-pattern>/ClustalWS</url-pattern>\r
@@ -84,6 +90,11 @@
        <url-pattern>/AAConWS</url-pattern>\r
    </servlet-mapping>\r
    \r
+    <servlet-mapping>\r
+       <servlet-name>JronnWS</servlet-name>\r
+       <url-pattern>/JronnWS</url-pattern>\r
+   </servlet-mapping>\r
+   \r
    <security-constraint>\r
     <web-resource-collection>\r
        <web-resource-name>Administrator pages</web-resource-name>\r

diff --git a/webservices/compbio/ws/server/JronnWS.java b/webservices/compbio/ws/server/JronnWS.java
index bcb6af5..9f5be63 100644 (file)
--- 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);\r
                return mas;\r
        }\r
-       /*\r
-        * @SuppressWarnings("unchecked") public JalviewAnnotation\r
-        * getJalviewAnnotation(String jobId) throws ResultNotAvailableException {\r
-        * MultiAnnotatedSequence<Method> result = getResult(jobId); // TODO //\r
-        * log(jobId, "getResults"); return result.toJalviewAnnotation(); }\r
-        */\r
 \r
        @Override\r
        public Limit<Jronn> getLimit(String presetName) {\r
@@ -136,9 +130,6 @@ public class JronnWS implements Annotation<Jronn> {
                ConfiguredExecutable<Jronn> confAAcon = init(sequences);\r
 \r
                // set default conservation method to fastest - SHENKIN\r
-               // TODO: This violates encapsulation, should be moved to the runners\r
-               // level.\r
-               // confAAcon.addParameters(Arrays.asList("-m=SHENKIN"));\r
                return analize(sequences, confAAcon, null, "analize", getLimit(""));\r
        }\r
 \r