compbio.ws.server.ProbconsWS
-
-
-
|
-- - | -|||||||||
| - PREV CLASS - NEXT CLASS | -- FRAMES - NO FRAMES - - - - - | -|||||||||
| - SUMMARY: NESTED | FIELD | CONSTR | METHOD | --DETAIL: FIELD | CONSTR | METHOD | -|||||||||
-java.lang.Object --
-
| -Field Summary | -
|---|
| Fields inherited from interface compbio.data.msa.JABAService | -
|---|
SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE |
-
| -Constructor Summary | -|
|---|---|
ProbconsWS()
-
-- |
-|
| -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<Probcons>> options)
-
-- Align a list of sequences with options. |
-
- JobStatus |
-getJobStatus(String jobId)
-
-- Return the status of the job. |
-
- Limit<Probcons> |
-getLimit(String presetName)
-
-- Get a Limit for a preset. |
-
- LimitsManager<Probcons> |
-getLimits()
-
-- List Limits supported by a web service. |
-
- PresetManager<Probcons> |
-getPresets()
-
-- Get presets supported by a web service |
-
- Alignment |
-getResult(String jobId)
-
-- Return the result of the job. |
-
- RunnerConfig<Probcons> |
-getRunnerOptions()
-
-- Get options supported by a web service |
-
- String |
-presetAlign(List<FastaSequence> sequences,
- Preset<Probcons> 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. |
-
| Methods inherited from class java.lang.Object | -
|---|
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
-
| -Constructor Detail | -
|---|
-public ProbconsWS()-
| -Method Detail | -
|---|
-public String align(List<FastaSequence> sequences) - throws JobSubmissionException-
MsaWS-
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.
-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-public String customAlign(List<FastaSequence> sequences, - List<Option<Probcons>> options) - throws JobSubmissionException, - WrongParameterException-
MsaWS-
customAlign in interface MsaWS<Probcons>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.
-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
-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.Default Limit is used to decide whether the calculation will be
- permitted or denied-public String presetAlign(List<FastaSequence> sequences, - Preset<Probcons> preset) - throws JobSubmissionException, - WrongParameterException-
MsaWS-
presetAlign in interface MsaWS<Probcons>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.
-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
-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.Preset-public Alignment getResult(String jobId) - throws ResultNotAvailableException-
MsaWSjobId 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.-public Limit<Probcons> getLimit(String presetName)-
Metadata-
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
--public LimitsManager<Probcons> getLimits()-
Metadata-
-public ChunkHolder pullExecStatistics(String jobId, - long position)-
JManagementposition. 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.
--
pullExecStatistics in interface JManagementjobId - - unique job identifierposition - - next position within the file to read
-ChunkHolder-public boolean cancelJob(String jobId)-
JManagementjobId but leave its output untouched
--
cancelJob in interface JManagement-public JobStatus getJobStatus(String jobId)-
JManagement-
getJobStatus in interface JManagementjobId - - unique job identifier
-JobStatus-public PresetManager<Probcons> getPresets()-
Metadata-
getPresets in interface Metadata<Probcons>-public RunnerConfig<Probcons> getRunnerOptions()-
Metadata-
getRunnerOptions in interface Metadata<Probcons>
-
-
|
-- - | -|||||||||
| - PREV CLASS - NEXT CLASS | -- FRAMES - NO FRAMES - - - - - | -|||||||||
| - SUMMARY: NESTED | FIELD | CONSTR | METHOD | --DETAIL: FIELD | CONSTR | METHOD | -|||||||||