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T - executable type / web service typepublic interface MsaWS<T>
-Multiple Sequence Alignment (MSA) Web Services Interface -
- -
-
| -Field Summary | -
|---|
| Fields inherited from interface compbio.data.msa.JABAService | -
|---|
SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE |
-
| -Method Summary | -|
|---|---|
- String |
-align(List<FastaSequence> sequences)
-
-- Align a list of sequences with default settings. |
-
- String |
-customAlign(List<FastaSequence> sequences,
- List<Option<T>> options)
-
-- Align a list of sequences with options. |
-
- Alignment |
-getResult(String jobId)
-
-- Return the result of the job. |
-
- String |
-presetAlign(List<FastaSequence> sequences,
- Preset<T> preset)
-
-- Align a list of sequences with preset. |
-
| Methods inherited from interface compbio.data.msa.JManagement | -
|---|
cancelJob, getJobStatus, pullExecStatistics |
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| Methods inherited from interface compbio.data.msa.Metadata | -
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getLimit, getLimits, getPresets, getRunnerOptions |
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| -Method Detail | -
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-String align(List<FastaSequence> sequences) - throws UnsupportedRuntimeException, - LimitExceededException, - JobSubmissionException-
-
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 make sure of this
-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 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-String customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - throws UnsupportedRuntimeException, - LimitExceededException, - JobSubmissionException, - WrongParameterException-
-
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 informationoptions - A list of Options
-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 their average
- length exceeds what is defined by the limitDefault Limit is used to decide whether the calculation will be
- permitted or denied-String presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - throws UnsupportedRuntimeException, - LimitExceededException, - JobSubmissionException, - WrongParameterException-
-
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 informationpreset - A list of Options
-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 limitPreset-Alignment getResult(String jobId) - throws ResultNotAvailableException-
jobId to complete before return.
--
jobId - a unique job identifier
-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.
-InvalidParameterException - thrown if jobId is empty or is not recognised e.g. in invalid
- format
-
-
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