Adding Jronn WS to conf files

[jabaws.git] / webservices / compbio / ws / server / JronnWS.java

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