compbio.data.msa

Interface MsaWS<T>

Type Parameters:

T - executable type / web service type

All Superinterfaces:

JABAService, JManagement, Metadata<T>

All Known Implementing Classes:

ClustalOWS, ClustalWS, GLprobsWS, MafftWS, MSAprobsWS, MuscleWS, ProbconsWS, TcoffeeWS

public interface MsaWS<T>
extends JABAService, JManagement, Metadata<T>

Multiple Sequence Alignment (MSA) Web Services Interface

Author:

pvtroshin Date November 2010

Field Summary

Fields inherited from interface compbio.data.msa.JABAService

JABAWS_VERSION, SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE, V3_SERVICE_NAMESPACE

Method Summary

Modifier and Type	Method and Description
java.lang.String	align(java.util.List<FastaSequence> sequences) Align a list of sequences with default settings.
java.lang.String	customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<T>> options) Align a list of sequences with options.
Alignment	getResult(java.lang.String jobId) Return the result of the job.
java.lang.String	presetAlign(java.util.List<FastaSequence> sequences, Preset<T> preset) Align a list of sequences with preset.

Methods inherited from interface compbio.data.msa.JManagement

cancelJob, getJobStatus, pullExecStatistics

Methods inherited from interface compbio.data.msa.Metadata

getLimit, getLimits, getPresets, getRunnerOptions

Method Detail

align

java.lang.String align(java.util.List<FastaSequence> sequences)
                throws UnsupportedRuntimeException,
                       LimitExceededException,
                       JobSubmissionException

Align a list of sequences with default settings. 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.

Parameters:

sequences - List of FastaSequence objects. The program does not perform any sequence validity checks. Nor does it checks whether the sequences names are unique. It is responsibility of the caller to make sure of this

Returns:

jobId - unique identifier for the job

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.

java.security.InvalidParameterException - thrown if input list of FASTA sequences is null or empty

UnsupportedRuntimeException - thrown if server OS does not support native executables for a given web service, e.g. JABAWS is deployed on Windows and Mafft service is called

LimitExceededException - is throw if the input sequences number or their average length exceeds what is defined by the limit

customAlign

java.lang.String customAlign(java.util.List<FastaSequence> sequences,
                             java.util.List<Option<T>> options)
                      throws UnsupportedRuntimeException,
                             LimitExceededException,
                             JobSubmissionException,
                             WrongParameterException

Align a list of sequences with options.

Parameters:

sequences - 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

options - A list of Options

Returns:

jobId - unique identifier for the job

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.

WrongParameterException - is throws when 1) One of the Options provided is not supported, 2) The value of the option is defined outside the boundaries. In both cases exception object contain the information on the violating Option.

java.security.InvalidParameterException - thrown if input list of FASTA sequence is null or empty

UnsupportedRuntimeException - thrown if server OS does not support native executables for a given web service, e.g. JABAWS is deployed on Windows and Mafft service is called

LimitExceededException - is throw if the input sequences number or their average length exceeds what is defined by the limit

See Also:

Default Limit is used to decide whether the calculation will be permitted or denied

presetAlign

java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
                             Preset<T> preset)
                      throws UnsupportedRuntimeException,
                             LimitExceededException,
                             JobSubmissionException,
                             WrongParameterException

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 is used.

Parameters:

sequences - 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

preset - A list of Options

Returns:

String - jobId - unique identifier for the job

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.

WrongParameterException - is throws when 1) One of the Options provided is not supported, 2) The value of the option is defined outside the boundaries. In both cases exception object contain the information on the violating Option.

java.security.InvalidParameterException - thrown if input list of FASTA sequence is null or empty

UnsupportedRuntimeException - thrown if server OS does not support native executables for a given web service, e.g. JABAWS is deployed on Windows and Mafft service is called

LimitExceededException - is throw if the input sequences number or average length exceeds what is defined by the limit

See Also:

Preset

getResult

Alignment getResult(java.lang.String jobId)
             throws ResultNotAvailableException

Return the result of the job. This method waits for the job jobId to complete before return.

Parameters:

jobId - a unique job identifier

Returns:

Alignment

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 due to the lower level problems on the server i.e. IOException, FileNotFoundException problems as well as UnknownFileFormatException.

java.security.InvalidParameterException - thrown if jobId is empty or is not recognised e.g. in invalid format