compbio.ws.server
Class AAConWS

java.lang.Object
  compbio.ws.server.GenericMetadataService
      compbio.ws.server.SequenceAnnotationService<AACon>
          compbio.ws.server.AAConWS

All Implemented Interfaces:

JABAService, JManagement, Metadata<AACon>, SequenceAnnotation<AACon>

public class AAConWS
extends SequenceAnnotationService<AACon>
implements SequenceAnnotation<AACon>

Field Summary

Fields inherited from interface compbio.data.msa.JABAService

SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE

Constructor Summary

AAConWS()

Method Summary

java.lang.String	analize(java.util.List<FastaSequence> sequences) Analyse the sequences.
ChunkHolder	pullExecStatistics(java.lang.String jobId, long position) Assume statistics is not supported

Methods inherited from class compbio.ws.server.SequenceAnnotationService

customAnalize, getAnnotation, presetAnalize

Methods inherited from class compbio.ws.server.GenericMetadataService

cancelJob, getJobStatus, getLimit, getLimits, getPresets, getRunnerOptions

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface compbio.data.msa.SequenceAnnotation

customAnalize, getAnnotation, presetAnalize

Methods inherited from interface compbio.data.msa.JManagement

cancelJob, getJobStatus

Methods inherited from interface compbio.data.msa.Metadata

getLimit, getLimits, getPresets, getRunnerOptions

Constructor Detail

AAConWS

public AAConWS()

Method Detail

analize

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

Description copied from interface: SequenceAnnotation

Analyse the sequences. The actual analysis algorithm is defined by the type T. Any dataset containing a greater number of sequences or 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.

Specified by:

analize in interface SequenceAnnotation<AACon>

Overrides:

analize in class SequenceAnnotationService<AACon>

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

Returns:

jobId - unique identifier for the job

Throws:

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

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.

pullExecStatistics

public ChunkHolder pullExecStatistics(java.lang.String jobId,
                                      long position)

Description copied from class: GenericMetadataService

Assume statistics is not supported

Specified by:

pullExecStatistics in interface JManagement

Overrides:

pullExecStatistics in class GenericMetadataService

Parameters:

jobId - - unique job identifier

position - - next position within the file to read

Returns:

ChunkHolder

See Also:

ChunkHolder