-/* Copyright (c) 2009 Peter Troshin\r
+/* Copyright (c) 2011 Peter Troshin\r
* \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
+ * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 \r
* \r
* This library is free software; you can redistribute it and/or modify it under the terms of the\r
* Apache License version 2 as published by the Apache Software Foundation\r
* @param <T>\r
* executable type / web service type\r
*/\r
-@WebService(targetNamespace = "http://msa.data.compbio/01/12/2010/")\r
-public interface MsaWS<T> extends JManagement, Metadata<T> {\r
+@WebService(targetNamespace = "http://msa.data.compbio/01/01/2010/")\r
+public interface MsaWS<T> extends JABAService, JManagement, Metadata<T> {\r
\r
/**\r
* Align a list of sequences with default settings.\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
+ * Any dataset containing a greater number of sequences or when 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
+ * List of FastaSequence objects. The program 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
+ * to make sure of this\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
* 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
+ * thrown if input list of FASTA sequences 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
+ * is throw if the input sequences number or their average\r
+ * length exceeds what is defined by the limit\r
*/\r
String align(\r
@WebParam(name = "fastaSequences") List<FastaSequence> sequences)\r
* @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
* boundaries. In both cases exception object contain the\r
* information on the violating Option.\r
* @throws InvalidParameterException\r
- * thrown if input list of fasta sequence is null or empty\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. 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
+ * is throw if the input sequences number or their average\r
+ * length exceeds what is defined by the limit\r
*/\r
String customAlign(\r
@WebParam(name = "fastaSequences") List<FastaSequence> sequences,\r
JobSubmissionException, WrongParameterException;\r
\r
/**\r
- * Align a list of sequences with preset. @see Preset\r
+ * Align a list of sequences with preset.\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
* @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
* boundaries. In both cases exception object contain the\r
* information on the violating Option.\r
* @throws InvalidParameterException\r
- * thrown if input list of fasta sequence is null or empty\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. 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 Preset\r
*/\r
String presetAlign(\r
@WebParam(name = "fastaSequences") List<FastaSequence> sequences,\r
JobSubmissionException, WrongParameterException;\r
\r
/**\r
- * Return the result of the job.\r
+ * Return the result of the job. This method waits for the job\r
+ * <code>jobId</code> to complete before return.\r
* \r
* @param jobId\r
* a unique job identifier\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
- * (e.g. removed). Exception could also be thrown is dues to the\r
+ * (e.g. removed). Exception could also be thrown due to the\r
* lower level problems on the server i.e. IOException,\r
* FileNotFoundException problems as well as\r
* UnknownFileFormatException.\r
* @throws InvalidParameterException\r
- * thrown if jobId is empty or cannot be recognised e.g. in\r
- * invalid format\r
+ * thrown if jobId is empty or is not recognised e.g. in invalid\r
+ * format\r
*/\r
Alignment getResult(@WebParam(name = "jobId") String jobId)\r
throws ResultNotAvailableException;\r
git://source.jalview.org / jabaws.git / blobdiff