-IUPredWS -

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- -compbio.ws.server -
-Class IUPredWS

-java.lang.Object
-  compbio.ws.server.GenericMetadataService
-      compbio.ws.server.SequenceAnnotationService<IUPred>
-          compbio.ws.server.IUPredWS
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All Implemented Interfaces:: JABAService, JManagement, Metadata<IUPred>, SequenceAnnotation<IUPred>

public class IUPredWS
extends SequenceAnnotationService<IUPred>
implements SequenceAnnotation<IUPred>
extends SequenceAnnotationService<IUPred>
implements SequenceAnnotation<IUPred>

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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
IUPredWS() - -
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-Method Summary
- String presetAnalize(List<FastaSequence> sequences, - Preset<IUPred> preset) - -
- Analyse the sequences according to the preset settings.
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Methods inherited from class compbio.ws.server.SequenceAnnotationService
analize, customAnalize, getAnnotation
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Methods inherited from class compbio.ws.server.GenericMetadataService
cancelJob, getJobStatus, getLimit, getLimits, getPresets, getRunnerOptions, pullExecStatistics
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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
analize, customAnalize, getAnnotation
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Methods inherited from interface compbio.data.msa.JManagement
cancelJob, getJobStatus, pullExecStatistics
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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
`IUPredWS()` - - -

-Method Summary
- `String`	`presetAnalize(List<FastaSequence> sequences, - Preset<IUPred> preset)` - - - Analyse the sequences according to the preset settings.

Methods inherited from class compbio.ws.server.SequenceAnnotationService
`analize, customAnalize, getAnnotation`

Methods inherited from class compbio.ws.server.GenericMetadataService
`cancelJob, getJobStatus, getLimit, getLimits, getPresets, getRunnerOptions, pullExecStatistics`

Methods inherited from class java.lang.Object
`equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Methods inherited from interface compbio.data.msa.SequenceAnnotation
`analize, customAnalize, getAnnotation`

Methods inherited from interface compbio.data.msa.JManagement
`cancelJob, getJobStatus, pullExecStatistics`

Methods inherited from interface compbio.data.msa.Metadata
`getLimit, getLimits, getPresets, getRunnerOptions`

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-Constructor Detail
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-IUPredWS

-public IUPredWS()

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-Method Detail

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-presetAnalize

-public String presetAnalize(List<FastaSequence> sequences,
-                            Preset<IUPred> preset)
-                     throws UnsupportedRuntimeException,
-                            LimitExceededException,
-                            JobSubmissionException,
-                            WrongParameterException

Description copied from interface: SequenceAnnotation

Analyse the sequences according to the preset settings. The actual - analysis algorithm is defined by the type T. - - 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. -

Specified by:: presetAnalize in interface SequenceAnnotation<IUPred>
Overrides:: presetAnalize in class SequenceAnnotationService<IUPred>

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: -: 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. -; 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.

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