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T
- executable type / web service typepublic interface Annotation<T>
Interface for tools that results to one or more annotation to sequence(s)
Method Summary | |
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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. |
HashSet<Score> |
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 |
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cancelJob, getJobStatus, pullExecStatistics |
Methods inherited from interface compbio.data.msa.Metadata |
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getLimit, getLimits, getPresets, getRunnerOptions |
Method Detail |
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String analize(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 validate this information
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 limitString customAnalize(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 average length
exceeds what is defined by the limitOption
String presetAnalize(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 limitHashSet<Score> getAnnotation(String jobId) throws ResultNotAvailableException
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 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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