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T
- executable type / web service typepublic interface MsaWS<T>
Multiple Sequence Alignment (MSA) Web Services Interface
Method Summary | |
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java.lang.String |
align(java.util.List<FastaSequence> sequences)
Align a list of sequences with default settings. |
boolean |
cancelJob(java.lang.String jobId)
Stop running job but leave its output untouched |
java.lang.String |
customAlign(java.util.List<FastaSequence> sequences,
java.util.List<Option<T>> options)
Align a list of sequences with options. |
JobStatus |
getJobStatus(java.lang.String jobId)
Return the status of the job. |
Limit<T> |
getLimit(java.lang.String presetName)
Get a Limit for a preset. |
LimitsManager<T> |
getLimits()
List Limits supported by a web service. |
PresetManager<T> |
getPresets()
Get presets supported by a web service |
Alignment |
getResult(java.lang.String jobId)
Return the result of the job. |
RunnerConfig<T> |
getRunnerOptions()
Get options supported by a web service |
java.lang.String |
presetAlign(java.util.List<FastaSequence> sequences,
Preset<T> preset)
Align a list of sequences with preset. |
ChunkHolder |
pullExecStatistics(java.lang.String jobId,
long position)
Reads 1kb chunk from the statistics file which is specific to a given web service from the position. |
Method Detail |
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java.lang.String align(java.util.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.
- This
exception 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.
java.security.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
JobSubmissionException
java.lang.String customAlign(java.util.List<FastaSequence> sequences, java.util.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.
- This
exception 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.
java.security.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
JobSubmissionException
Default Limit is used to decide whether the calculation will be
permitted or denied
java.lang.String presetAlign(java.util.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.
- This
exception 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.
java.security.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
JobSubmissionException
Alignment getResult(java.lang.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.
java.security.InvalidParameterException
- thrown if jobId is empty or cannot be recognised e.g. in
invalid formatboolean cancelJob(java.lang.String jobId)
java.security.InvalidParameterException
- thrown if jobId is empty or cannot be recognised e.g. in
invalid formatJobStatus getJobStatus(java.lang.String jobId)
jobId
- - unique job identifier
java.security.InvalidParameterException
- thrown if jobId is empty or cannot be recognised e.g. in
invalid formatChunkHolder pullExecStatistics(java.lang.String jobId, long position)
jobId
- - unique job identifierposition
- - next position within the file to read
java.security.InvalidParameterException
- thrown if jobId is empty or cannot be recognised e.g. in
invalid format and also if the position value is negativeRunnerConfig<T> getRunnerOptions()
PresetManager<T> getPresets()
Limit<T> getLimit(java.lang.String presetName)
presetName
- the name of the preset. if no name is provided, then the
default preset is returned. If no limit for a particular
preset is defined then the default preset is returned
LimitsManager<T> getLimits()
presetName
- the name of the preset. if no name is provided, then the
default preset is returned. If no limit for a particular
preset is defined then the default preset is returned
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