T - executable type / web service typepublic interface MsaWS<T>
public interface MsaWS<T>
@@ -108,14 +111,32 @@ Multiple Sequence Alignment (MSA) Web Services Interface
| +Field Summary | +
|---|
| Fields inherited from interface compbio.data.msa.JABAService | +
|---|
SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE |
+
java.lang.Stringalign(java.util.List<FastaSequence> sequences)
+ Stringalign(List<FastaSequence> sequences)
booleancancelJob(java.lang.String jobId)
-
- java.lang.StringcustomAlign(java.util.List<FastaSequence> sequences,
- java.util.List<Option<T>> options)
+ StringcustomAlign(List<FastaSequence> sequences,
+ List<Option<T>> options)
JobStatusgetJobStatus(java.lang.String jobId)
-
- Limit<T>getLimit(java.lang.String presetName)
-
- LimitsManager<T>getLimits()
-
- PresetManager<T>getPresets()
-
- AlignmentgetResult(java.lang.String jobId)
+getResult(String jobId)
RunnerConfig<T>getRunnerOptions()
-
- java.lang.StringpresetAlign(java.util.List<FastaSequence> sequences,
+ StringpresetAlign(List<FastaSequence> sequences,
Preset<T> preset)
| Methods inherited from interface compbio.data.msa.JManagement | +||
|---|---|---|
- 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. |
+cancelJob, getJobStatus, pullExecStatistics |
+
| Methods inherited from interface compbio.data.msa.Metadata | +
|---|
getLimit, getLimits, getPresets, getRunnerOptions |
-java.lang.String align(java.util.List<FastaSequence> sequences) - throws UnsupportedRuntimeException, - LimitExceededException, - JobSubmissionException+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 validate this information
+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. - 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
+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.
-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
-JobSubmissionExceptionInvalidParameterException - 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-java.lang.String customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<T>> options) - throws UnsupportedRuntimeException, - LimitExceededException, - JobSubmissionException, - WrongParameterException+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
+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
+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
+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
-JobSubmissionExceptionDefault Limit is used to decide whether the calculation will be
+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 limit- See Also:
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+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
+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
+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
+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
-JobSubmissionExceptionInvalidParameterException - 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(java.lang.String jobId) +Alignment getResult(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 format-boolean cancelJob(java.lang.String jobId)-
jobId to complete before return.
java.security.InvalidParameterException - thrown if jobId is empty or cannot be recognised e.g. in
- invalid format-JobStatus 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 format-ChunkHolder pullExecStatistics(java.lang.String jobId, - long position)-
jobId - - unique job identifierposition - - next position within the file to read
-jobId - a unique job identifier
+java.security.InvalidParameterException - thrown if jobId is empty or cannot be recognised e.g. in
- invalid format and also if the position value is negative-RunnerConfig<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
-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