-/* 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
\r
import compbio.data.sequence.Alignment;\r
import compbio.data.sequence.FastaSequence;\r
-import compbio.metadata.ChunkHolder;\r
-import compbio.metadata.JobStatus;\r
import compbio.metadata.JobSubmissionException;\r
-import compbio.metadata.Limit;\r
import compbio.metadata.LimitExceededException;\r
-import compbio.metadata.LimitsManager;\r
import compbio.metadata.Option;\r
import compbio.metadata.Preset;\r
-import compbio.metadata.PresetManager;\r
import compbio.metadata.ResultNotAvailableException;\r
-import compbio.metadata.RunnerConfig;\r
import compbio.metadata.UnsupportedRuntimeException;\r
import compbio.metadata.WrongParameterException;\r
\r
* \r
* @author pvtroshin\r
* \r
- * Date September 2009\r
+ * Date November 2010\r
* \r
* @param <T>\r
* executable type / web service type\r
*/\r
@WebService(targetNamespace = "http://msa.data.compbio/01/01/2010/")\r
-public interface MsaWS<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
- * 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. 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
- * 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. JWS2 is deployed on Windows and Mafft\r
- * 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
- String align(\r
- @WebParam(name = "fastaSequences") List<FastaSequence> sequences)\r
- throws UnsupportedRuntimeException, LimitExceededException,\r
- JobSubmissionException;\r
-\r
- /**\r
- * Align a list of sequences with options.\r
- * \r
- * @see Option\r
- * \r
- * Default Limit is used to decide whether the calculation will be\r
- * permitted or denied\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
- * @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
- * 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 WrongParameterException\r
- * is throws when 1) One of the Options provided is not\r
- * supported, 2) The value of the option is defined outside the\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
- * @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
- * @throws LimitExceededException\r
- * is throw if the input sequences number or average length\r
- * exceeds what is defined by the limit\r
- */\r
- String customAlign(\r
- @WebParam(name = "fastaSequences") List<FastaSequence> sequences,\r
- @WebParam(name = "options") List<Option<T>> options)\r
- throws UnsupportedRuntimeException, LimitExceededException,\r
- JobSubmissionException, WrongParameterException;\r
-\r
- /**\r
- * Align a list of sequences with preset. @see 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
- * is used.\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
- * @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
- * 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 WrongParameterException\r
- * is throws when 1) One of the Options provided is not\r
- * supported, 2) The value of the option is defined outside the\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
- * @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
- * @throws LimitExceededException\r
- * is throw if the input sequences number or average length\r
- * exceeds what is defined by the limit\r
- */\r
- String presetAlign(\r
- @WebParam(name = "fastaSequences") List<FastaSequence> sequences,\r
- @WebParam(name = "preset") Preset<T> preset)\r
- throws UnsupportedRuntimeException, LimitExceededException,\r
- JobSubmissionException, WrongParameterException;\r
-\r
- /**\r
- * Return the result of the job.\r
- * \r
- * @param jobId\r
- * a unique job identifier\r
- * @return Alignment\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
- * 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
- */\r
- Alignment getResult(@WebParam(name = "jobId") String jobId)\r
- throws ResultNotAvailableException;\r
-\r
- /**\r
- * Stop running job but leave its output untouched\r
- * \r
- * @return true if job was cancelled successfully, false otherwise\r
- * @throws InvalidParameterException\r
- * thrown if jobId is empty or cannot be recognised e.g. in\r
- * invalid format\r
- */\r
- boolean cancelJob(@WebParam(name = "jobId") String jobId);\r
-\r
- /**\r
- * Return the status of the job. @see JobStatus\r
- * \r
- * @param jobId\r
- * - unique job identifier\r
- * @return JobStatus - status of the job\r
- * @throws InvalidParameterException\r
- * thrown if jobId is empty or cannot be recognised e.g. in\r
- * invalid format\r
- */\r
- JobStatus getJobStatus(@WebParam(name = "jobId") String jobId);\r
-\r
- /**\r
- * Reads 1kb chunk from the statistics file which is specific to a given web\r
- * service from the position. If in time of a request less then 1kb data is\r
- * available from the position to the end of the file, then it returns all\r
- * the data available from the position to the end of the file.\r
- * \r
- * @param jobId\r
- * - unique job identifier\r
- * @param position\r
- * - next position within the file to read\r
- * @return ChunkHolder - @see ChunkHolder which contains a chuink of data\r
- * and a next position within the file from which no data has been\r
- * read\r
- * @throws InvalidParameterException\r
- * thrown if jobId is empty or cannot be recognised e.g. in\r
- * invalid format and also if the position value is negative\r
- */\r
- ChunkHolder pullExecStatistics(@WebParam(name = "jobId") String jobId,\r
- @WebParam(name = "position") long position);\r
-\r
- /*\r
- * TODO\r
- * \r
- * @param jobId\r
- * \r
- * @return\r
- * \r
- * byte getProgress(@WebParam(name = "jobId") String jobId);\r
- */\r
-\r
- /**\r
- * Get options supported by a web service\r
- * \r
- * @return RunnerConfig the list of options and parameters supported by a\r
- * web service.\r
- */\r
- RunnerConfig<T> getRunnerOptions();\r
-\r
- /**\r
- * Get presets supported by a web service\r
- * \r
- * @return PresetManager the object contains information about presets\r
- * supported by a web service\r
- */\r
- PresetManager<T> getPresets();\r
-\r
- /**\r
- * Get a Limit for a preset.\r
- * \r
- * @param presetName\r
- * the name of the preset. if no name is provided, then the\r
- * default preset is returned. If no limit for a particular\r
- * preset is defined then the default preset is returned\r
- * @return Limit\r
- */\r
- Limit<T> getLimit(@WebParam(name = "presetName") String presetName);\r
-\r
- /**\r
- * List Limits supported by a web service.\r
- * \r
- * @param presetName\r
- * the name of the preset. if no name is provided, then the\r
- * default preset is returned. If no limit for a particular\r
- * preset is defined then the default preset is returned\r
- * @return LimitManager\r
- */\r
- LimitsManager<T> getLimits();\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 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 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 make sure of this\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 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. JABAWS is deployed on Windows and\r
+ * Mafft service is called\r
+ * @throws LimitExceededException\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
+ throws UnsupportedRuntimeException, LimitExceededException,\r
+ JobSubmissionException;\r
+\r
+ /**\r
+ * Align a list of sequences with options.\r
+ * \r
+ * @see Option\r
+ * \r
+ * Default Limit is used to decide whether the calculation will be\r
+ * permitted or denied\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
+ * @param options\r
+ * A list of Options\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 WrongParameterException\r
+ * is throws when 1) One of the Options provided is not\r
+ * supported, 2) The value of the option is defined outside the\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
+ * @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 their average\r
+ * length exceeds what is defined by the limit\r
+ */\r
+ String customAlign(\r
+ @WebParam(name = "fastaSequences") List<FastaSequence> sequences,\r
+ @WebParam(name = "options") List<Option<T>> options)\r
+ throws UnsupportedRuntimeException, LimitExceededException,\r
+ JobSubmissionException, WrongParameterException;\r
+\r
+ /**\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
+ * is used.\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
+ * @param preset\r
+ * A list of Options\r
+ * @return String - 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 WrongParameterException\r
+ * is throws when 1) One of the Options provided is not\r
+ * supported, 2) The value of the option is defined outside the\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
+ * @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
+ * @see Preset\r
+ */\r
+ String presetAlign(\r
+ @WebParam(name = "fastaSequences") List<FastaSequence> sequences,\r
+ @WebParam(name = "preset") Preset<T> preset)\r
+ throws UnsupportedRuntimeException, LimitExceededException,\r
+ JobSubmissionException, WrongParameterException;\r
+\r
+ /**\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
+ * @return Alignment\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 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 is not recognised e.g. in invalid\r
+ * format\r
+ */\r
+ Alignment getResult(@WebParam(name = "jobId") String jobId)\r
+ throws ResultNotAvailableException;\r
\r
}\r
git://source.jalview.org / jabaws.git / blobdiff