X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fdata%2Fmsa%2FMsaWS.java;h=43d158169fe8c78e28ebb5419026a7936b4eded4;hb=3644426ec0e9e9ceb798bd426085d8d9dd8dbb56;hp=b1735fbcfb1031843ba0a5482b090ab7e4c60547;hpb=fab6bab770b548a0c99ed6f5dfb46f5aa99f67c7;p=jabaws.git diff --git a/webservices/compbio/data/msa/MsaWS.java b/webservices/compbio/data/msa/MsaWS.java index b1735fb..43d1581 100644 --- a/webservices/compbio/data/msa/MsaWS.java +++ b/webservices/compbio/data/msa/MsaWS.java @@ -44,14 +44,14 @@ import compbio.metadata.WrongParameterException; * @param * executable type / web service type */ -@WebService(targetNamespace = "http://msa.data.compbio/01/12/2010/") -public interface MsaWS extends JManagement, Metadata { +@WebService(targetNamespace = "http://msa.data.compbio/01/01/2010/") +public interface MsaWS extends JABAService, JManagement, Metadata { /** * Align a list of sequences with default settings. * - * Any dataset containing a greater number of sequences or the average - * length of the sequences are greater then defined in the default Limit + * Any dataset containing a greater number of sequences or when the average + * length of the sequences are greater then defined in the default Limit, * will not be accepted for an alignment operation and * JobSubmissionException will be thrown. * @@ -59,25 +59,25 @@ public interface MsaWS extends JManagement, Metadata { * List of FastaSequence objects. The programme does not perform * any sequence validity checks. Nor does it checks whether the * sequences names are unique. It is responsibility of the caller - * to validate this information + * to make sure of this * @return jobId - unique identifier for the job - * @throws JobSubmissionException. This - * exception is thrown when the job could not be submitted due - * to the following reasons: 1) The number of sequences in the + * @throws JobSubmissionException + * is thrown when the job could not be submitted due to the + * following reasons: 1) The number of sequences in the * submission or their average length is greater then defined by * the default Limit. 2) Any problems on the server side e.g. it * is misconfigured or malfunction, is reported via this * exception. In the first case the information on the limit * could be obtained from an exception. * @throws InvalidParameterException - * thrown if input list of fasta sequence is null or empty + * thrown if input list of FASTA sequences is null or empty * @throws UnsupportedRuntimeException * thrown if server OS does not support native executables for a - * given web service, e.g. JWS2 is deployed on Windows and Mafft - * service is called + * given web service, e.g. JABAWS is deployed on Windows and + * Mafft service is called * @throws LimitExceededException - * is throw if the input sequences number or average length - * exceeds what is defined by the limit + * is throw if the input sequences number or their average + * length exceeds what is defined by the limit */ String align( @WebParam(name = "fastaSequences") List sequences) @@ -100,9 +100,9 @@ public interface MsaWS extends JManagement, Metadata { * @param options * A list of Options * @return jobId - unique identifier for the job - * @throws JobSubmissionException. This - * exception is thrown when the job could not be submitted due - * to the following reasons: 1) The number of sequences in the + * @throws JobSubmissionException + * is thrown when the job could not be submitted due to the + * following reasons: 1) The number of sequences in the * submission or their average length is greater then defined by * the default Limit. 2) Any problems on the server side e.g. it * is misconfigured or malfunction, is reported via this @@ -114,14 +114,14 @@ public interface MsaWS extends JManagement, Metadata { * boundaries. In both cases exception object contain the * information on the violating Option. * @throws InvalidParameterException - * thrown if input list of fasta sequence is null or empty + * thrown if input list of FASTA sequence is null or empty * @throws UnsupportedRuntimeException * thrown if server OS does not support native executables for a - * given web service, e.g. JWS2 is deployed on Windows and Mafft - * service is called + * given web service, e.g. JABAWS is deployed on Windows and + * Mafft service is called * @throws LimitExceededException - * is throw if the input sequences number or average length - * exceeds what is defined by the limit + * is throw if the input sequences number or their average + * length exceeds what is defined by the limit */ String customAlign( @WebParam(name = "fastaSequences") List sequences, @@ -130,7 +130,7 @@ public interface MsaWS extends JManagement, Metadata { JobSubmissionException, WrongParameterException; /** - * Align a list of sequences with preset. @see Preset + * Align a list of sequences with preset. * * Limit for a presetName is used whether the calculation will be permitted * or denied. If no Limit was defined for a presetName, than default limit @@ -144,9 +144,9 @@ public interface MsaWS extends JManagement, Metadata { * @param preset * A list of Options * @return String - jobId - unique identifier for the job - * @throws JobSubmissionException. This - * exception is thrown when the job could not be submitted due - * to the following reasons: 1) The number of sequences in the + * @throws JobSubmissionException + * is thrown when the job could not be submitted due to the + * following reasons: 1) The number of sequences in the * submission or their average length is greater then defined by * the default Limit. 2) Any problems on the server side e.g. it * is misconfigured or malfunction, is reported via this @@ -158,14 +158,15 @@ public interface MsaWS extends JManagement, Metadata { * boundaries. In both cases exception object contain the * information on the violating Option. * @throws InvalidParameterException - * thrown if input list of fasta sequence is null or empty + * thrown if input list of FASTA sequence is null or empty * @throws UnsupportedRuntimeException * thrown if server OS does not support native executables for a - * given web service, e.g. JWS2 is deployed on Windows and Mafft - * service is called + * given web service, e.g. JABAWS is deployed on Windows and + * Mafft service is called * @throws LimitExceededException * is throw if the input sequences number or average length * exceeds what is defined by the limit + * @see Preset */ String presetAlign( @WebParam(name = "fastaSequences") List sequences, @@ -174,7 +175,8 @@ public interface MsaWS extends JManagement, Metadata { JobSubmissionException, WrongParameterException; /** - * Return the result of the job. + * Return the result of the job. This method waits for the job + * jobId to complete before return. * * @param jobId * a unique job identifier @@ -182,13 +184,13 @@ public interface MsaWS extends JManagement, Metadata { * @throws ResultNotAvailableException * this exception is throw if the job execution was not * successful or the result of the execution could not be found. - * (e.g. removed). Exception could also be thrown is dues to the + * (e.g. removed). Exception could also be thrown due to the * lower level problems on the server i.e. IOException, * FileNotFoundException problems as well as * UnknownFileFormatException. * @throws InvalidParameterException - * thrown if jobId is empty or cannot be recognised e.g. in - * invalid format + * thrown if jobId is empty or is not recognised e.g. in invalid + * format */ Alignment getResult(@WebParam(name = "jobId") String jobId) throws ResultNotAvailableException;