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T
- executable type / web service typepublic interface MsaWS<T>
Multiple Sequence Alignment (MSA) Web Services Interface
Method Summary | |
---|---|
String |
align(List<FastaSequence> sequences)
Align a list of sequences with default settings. |
boolean |
cancelJob(String jobId)
Stop running the job jobId but leave its output untouched |
String |
customAlign(List<FastaSequence> sequences,
List<Option<T>> options)
Align a list of sequences with options. |
JobStatus |
getJobStatus(String jobId)
Return the status of the job. |
Limit<T> |
getLimit(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(String jobId)
Return the result of the job. |
RunnerConfig<T> |
getRunnerOptions()
Get options supported by a web service |
String |
presetAlign(List<FastaSequence> sequences,
Preset<T> preset)
Align a list of sequences with preset. |
ChunkHolder |
pullExecStatistics(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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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 limitString 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
formatboolean cancelJob(String jobId)
jobId
but leave its output untouched
InvalidParameterException
- is thrown if jobId is empty or cannot be recognised e.g. in
invalid formatJobStatus getJobStatus(String jobId)
jobId
- - unique job identifier
InvalidParameterException
- is thrown if jobId is empty or cannot be recognised e.g. in
invalid formatJobStatus
ChunkHolder pullExecStatistics(String jobId, long position)
position
. If in time of a request less then
1kb data is available from the position to the end of the file, then it
returns all the data available from the position to the end of the file.
jobId
- - unique job identifierposition
- - next position within the file to read
InvalidParameterException
- thrown if jobId is empty or cannot be recognised e.g. in
invalid format and also if the position value is negativeChunkHolder
RunnerConfig<T> getRunnerOptions()
PresetManager<T> getPresets()
Limit<T> getLimit(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()
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