-AAConWS -

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- -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>
extends SequenceAnnotationService<AACon>
implements SequenceAnnotation<AACon>

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-Field Summary
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Fields inherited from interface compbio.data.msa.JABAService
SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
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-Constructor Summary
AAConWS() - -
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-Method Summary
- String analize(List<FastaSequence> sequences) - -
-          Analyse the sequences.
- ChunkHolder pullExecStatistics(String jobId, - long position) - -
-          Assume statistics is not supported
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Methods inherited from class compbio.ws.server.SequenceAnnotationService
customAnalize, getAnnotation, presetAnalize
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Methods inherited from class compbio.ws.server.GenericMetadataService
cancelJob, getJobStatus, getLimit, getLimits, getPresets, getRunnerOptions
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Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface compbio.data.msa.SequenceAnnotation
customAnalize, getAnnotation, presetAnalize
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Methods inherited from interface compbio.data.msa.JManagement
cancelJob, getJobStatus
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Methods inherited from interface compbio.data.msa.Metadata
getLimit, getLimits, getPresets, getRunnerOptions
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Fields inherited from interface compbio.data.msa.JABAService
`SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE`

-Constructor Summary
`AAConWS()` - - -

-Method Summary
- `String`	`analize(List<FastaSequence> sequences)` - - - Analyse the sequences.
- `ChunkHolder`	`pullExecStatistics(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`

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-Constructor Detail
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-AAConWS

-public AAConWS()

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-Method Detail

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-analize

-public String analize(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.

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-pullExecStatistics

-public ChunkHolder pullExecStatistics(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

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