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 fb8436d..27a1d55 100644 (file)
--- a/webservices/compbio/data/msa/Annotation.java
+++ b/webservices/compbio/data/msa/Annotation.java
@@ -21,18 +21,21 @@ import compbio.metadata.WrongParameterException;
 /**\r
  * Interface for tools that results to one or more annotation to sequence(s)\r
  * \r
- * @author pvtroshin\r
- * \r
- *         Date November 2010\r
+ * @author Peter Troshin\r
  * \r
  * @param <T>\r
  *            executable type / web service type\r
+ * \r
+ * @version 1.0 November 2010\r
  */\r
 @WebService(targetNamespace = "http://msa.data.compbio/01/12/2010/")\r
-public interface Annotation<T> extends JManagement, Metadata<T> {\r
+public interface Annotation<T> extends JABAService, JManagement, Metadata<T> {\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
@@ -56,8 +59,8 @@ public interface Annotation<T> extends JManagement, Metadata<T> {
         *             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. JWS2 is deployed on Windows and Mafft\r
-        *             service is called\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
@@ -69,11 +72,10 @@ public interface Annotation<T> extends JManagement, Metadata<T> {
                        JobSubmissionException;\r
 \r
        /**\r
-        * \r
-        * @see Option\r
-        * \r
-        *      Default Limit is used to decide whether the calculation will be\r
-        *      permitted or denied\r
+        * Analyse the sequences according to custom settings defined in options\r
+        * list. The actual analysis algorithm is defined by the type T. Default\r
+        * Limit is used to decide whether the calculation will be permitted or\r
+        * denied\r
         * \r
         * @param sequences\r
         *            List of FastaSequence objects. The programme does not perform\r
@@ -83,9 +85,9 @@ public interface Annotation<T> extends JManagement, Metadata<T> {
         * @param options\r
         *            A list of Options\r
         * @return jobId - unique identifier for the job\r
-        * @throws JobSubmissionException. This\r
-        *             exception is thrown when the job could not be submitted due\r
-        *             to the following reasons: 1) The number of sequences in the\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
@@ -100,11 +102,12 @@ public interface Annotation<T> extends JManagement, Metadata<T> {
         *             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. JWS2 is deployed on Windows and Mafft\r
-        *             service is called\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
+        * @see Option\r
         */\r
        @WebMethod\r
        String customAnalize(\r
@@ -114,7 +117,8 @@ public interface Annotation<T> extends JManagement, Metadata<T> {
                        JobSubmissionException, WrongParameterException;\r
 \r
        /**\r
-        * \r
+        * Analyse the sequences according to the preset settings. The actual\r
+        * analysis algorithm is defined by the type T.\r
         * \r
         * Limit for a presetName is used whether the calculation will be permitted\r
         * or denied. If no Limit was defined for a presetName, than default limit\r
@@ -128,9 +132,9 @@ public interface Annotation<T> extends JManagement, Metadata<T> {
         * @param preset\r
         *            A list of Options\r
         * @return String - jobId - unique identifier for the job\r
-        * @throws JobSubmissionException. This\r
-        *             exception is thrown when the job could not be submitted due\r
-        *             to the following reasons: 1) The number of sequences in the\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
@@ -145,8 +149,8 @@ public interface Annotation<T> extends JManagement, Metadata<T> {
         *             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. JWS2 is deployed on Windows and Mafft\r
-        *             service is called\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
@@ -163,7 +167,7 @@ public interface Annotation<T> extends JManagement, Metadata<T> {
         * \r
         * @param jobId\r
         *            a unique job identifier\r
-        * @return\r
+        * @return the HashSet of Score objects\r
         * @throws ResultNotAvailableException\r
         *             this exception is throw if the job execution was not\r
         *             successful or the result of the execution could not be found.\r
@@ -176,7 +180,7 @@ public interface Annotation<T> extends JManagement, Metadata<T> {
         *             invalid format\r
         */\r
        @WebMethod\r
-       HashSet<Score> getConservation(@WebParam(name = "jobId") String jobId)\r
+       HashSet<Score> getAnnotation(@WebParam(name = "jobId") String jobId)\r
                        throws ResultNotAvailableException;\r
 \r
 }\r