compbio.ws.server.ClustalWS
+
+
+
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+java.lang.Object ++
+
| +Field Summary | +
|---|
| Fields inherited from interface compbio.data.msa.JABAService | +
|---|
SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE |
+
| +Constructor Summary | +|
|---|---|
ClustalWS()
+
++ |
+|
| +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<ClustalW>> options)
+
++ Align a list of sequences with options. |
+
+ JobStatus |
+getJobStatus(String jobId)
+
++ Return the status of the job. |
+
+ Limit<ClustalW> |
+getLimit(String presetName)
+
++ Get a Limit for a preset. |
+
+ LimitsManager<ClustalW> |
+getLimits()
+
++ List Limits supported by a web service. |
+
+ PresetManager<ClustalW> |
+getPresets()
+
++ Get presets supported by a web service |
+
+ Alignment |
+getResult(String jobId)
+
++ Return the result of the job. |
+
+ RunnerConfig<ClustalW> |
+getRunnerOptions()
+
++ Get options supported by a web service |
+
+ String |
+presetAlign(List<FastaSequence> sequences,
+ Preset<ClustalW> 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 ClustalWS()+
| +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 presetAlign(List<FastaSequence> sequences, + Preset<ClustalW> preset) + throws JobSubmissionException, + WrongParameterException+
MsaWS+
presetAlign in interface MsaWS<ClustalW>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 String customAlign(List<FastaSequence> sequences, + List<Option<ClustalW>> options) + throws JobSubmissionException, + WrongParameterException+
MsaWS+
customAlign in interface MsaWS<ClustalW>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 RunnerConfig<ClustalW> getRunnerOptions()+
Metadata+
getRunnerOptions in interface Metadata<ClustalW>+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<ClustalW> 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<ClustalW> getLimits()+
Metadata+
+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<ClustalW> getPresets()+
Metadata+
getPresets in interface Metadata<ClustalW>+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
+
+
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