AAConWS further work

[jabaws.git] / webservices / compbio / data / msa / Annotation.java

diff --git a/webservices/compbio/data/msa/Annotation.java b/webservices/compbio/data/msa/Annotation.java
index 1de9f30..27a1d55 100644 (file)
--- a/webservices/compbio/data/msa/Annotation.java
+++ b/webservices/compbio/data/msa/Annotation.java
@@ -9,7 +9,6 @@ import javax.jws.WebParam;
 import javax.jws.WebService;\r
 \r
 import compbio.data.sequence.FastaSequence;\r
-import compbio.data.sequence.SMERFSConstraints;\r
 import compbio.data.sequence.Score;\r
 import compbio.metadata.JobSubmissionException;\r
 import compbio.metadata.LimitExceededException;\r
@@ -164,48 +163,6 @@ public interface Annotation<T> extends JABAService, JManagement, Metadata<T> {
                        JobSubmissionException, WrongParameterException;\r
 \r
        /**\r
-        * \r
-        * Analyse the sequences. The actual analysis algorithm is defined by the\r
-        * type T.\r
-        * \r
-        * Any dataset containing a greater number of sequences or the average\r
-        * length of the sequences are greater then defined in the default Limit\r
-        * will not be accepted for an alignment operation and\r
-        * JobSubmissionException will be thrown.\r
-        * \r
-        * @param sequences\r
-        *            List of FastaSequence objects. The programme does not perform\r
-        *            any sequence validity checks. Nor does it checks whether the\r
-        *            sequences names are unique. It is responsibility of the caller\r
-        *            to validate this information\r
-        * @return jobId - unique identifier for the job\r
-        * @throws JobSubmissionException\r
-        *             is thrown when the job could not be submitted due to the\r
-        *             following reasons: 1) The number of sequences in the\r
-        *             submission or their average length is greater then defined by\r
-        *             the default Limit. 2) Any problems on the server side e.g. it\r
-        *             is misconfigured or malfunction, is reported via this\r
-        *             exception. In the first case the information on the limit\r
-        *             could be obtained from an exception.\r
-        * @throws InvalidParameterException\r
-        *             thrown if input list of fasta sequence is null or empty\r
-        * @throws UnsupportedRuntimeException\r
-        *             thrown if server OS does not support native executables for a\r
-        *             given web service, e.g. JABAWS is deployed on Windows and\r
-        *             Mafft service is called\r
-        * @throws LimitExceededException\r
-        *             is throw if the input sequences number or average length\r
-        *             exceeds what is defined by the limit\r
-        */\r
-       @WebMethod\r
-       String customSMERFS(\r
-                       @WebParam(name = "fastaSequences") List<FastaSequence> sequences,\r
-                       int windowWidth, SMERFSConstraints scoringMethod,\r
-                       float gapTreshold, boolean normalize)\r
-                       throws UnsupportedRuntimeException, LimitExceededException,\r
-                       JobSubmissionException;\r
-\r
-       /**\r
         * Return the result of the job.\r
         * \r
         * @param jobId\r