-SequenceAnnotation -

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- -compbio.data.msa -
-Interface SequenceAnnotation<T>


Type Parameters:: T - executable type / web service type

All Superinterfaces:: JABAService, JManagement, Metadata<T>

All Known Implementing Classes:: AAConWS, DisemblWS, GlobPlotWS, IUPredWS, JronnWS

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

- - -

-Interface for tools that results to one or more annotation to sequence(s) - - Single, multiple sequences their groups or alignments can be annotated -

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Version:: 1.0 November 2010
Author:: Peter Troshin

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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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-Method Summary
- String analize(List<FastaSequence> sequences) - -
-          Analyse the sequences.
- String customAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
-          Analyse the sequences according to custom settings defined in options - list.
- ScoreManager getAnnotation(String jobId) - -
-          Return the result of the job.
- String presetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
-          Analyse the sequences according to the preset settings.
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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`

-Method Summary
- `String`	`analize(List<FastaSequence> sequences)` - - - Analyse the sequences.
- `String`	`customAnalize(List<FastaSequence> sequences, - List<Option<T>> options)` - - - Analyse the sequences according to custom settings defined in options - list.
- `ScoreManager`	`getAnnotation(String jobId)` - - - Return the result of the job.
- `String`	`presetAnalize(List<FastaSequence> sequences, - Preset<T> preset)` - - - Analyse the sequences according to the preset settings.

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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-Method Detail
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-analize

-String analize(List<FastaSequence> sequences)
-               throws UnsupportedRuntimeException,
-                      LimitExceededException,
-                      JobSubmissionException

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. -

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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: -: 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. -; 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

- -

-customAnalize

-String customAnalize(List<FastaSequence> sequences,
-                     List<Option<T>> options)
-                     throws UnsupportedRuntimeException,
-                            LimitExceededException,
-                            JobSubmissionException,
-                            WrongParameterException

Analyse the sequences according to custom settings defined in options - list. The actual analysis algorithm is defined by the type T. Default - Limit is used to decide whether the calculation will be permitted or - denied -

- -

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. -; 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:: Option

- -

-presetAnalize

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

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. -

- -

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. -; 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

- -

-getAnnotation

-ScoreManager getAnnotation(String jobId)
-                           throws ResultNotAvailableException

Return the result of the job. -

- -

Parameters:: jobId - a unique job identifier -
Returns:: the Map with the sequence names, sequence group names or the word - 'Alignment' in case of alignments and values the represented by a - Set of Score objects. The alignment can be represented in as - little as one key->value pair in this map, the list of sequences - will be represented by multiple key->value mappings. If multiple - annotations were calculated, then they are represented as a Set - of Scores. -
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 - lower level problems on the server i.e. IOException, - FileNotFoundException problems as well as - UnknownFileFormatException. -; InvalidParameterException - thrown if jobId is empty or cannot be recognised e.g. in - invalid format

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