-_MsaService -

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- -compbio.ws.server -
-Class _MsaService<T>

-java.lang.Object
-  compbio.ws.server.GenericMetadataService
-      compbio.ws.server._MsaService<T>
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Type Parameters:: T -

public abstract class _MsaService<T>
extends GenericMetadataService
extends GenericMetadataService

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-TODO to complete after the approach is tested with SequenceAnnotation! - - Common methods for all SequenceAnnotation web services -

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Since:: 2.0
Version:: 1.0 June 2011
Author:: pvtroshin

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-Method Summary
- String align(List<FastaSequence> sequences) - -
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- String customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
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- Alignment getResult(String jobId) - -
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- String presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
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- ChunkHolder pullExecStatistics(String jobId, - long position) - -
-          Assume statistics is not supported
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Methods inherited from class compbio.ws.server.GenericMetadataService
cancelJob, getJobStatus, getLimit, getLimits, getPresets, getRunnerOptions
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Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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-Method Summary
- `String`	`align(List<FastaSequence> sequences)` - - -
- `String`	`customAlign(List<FastaSequence> sequences, - List<Option<T>> options)` - - -
- `Alignment`	`getResult(String jobId)` - - -
- `String`	`presetAlign(List<FastaSequence> sequences, - Preset<T> preset)` - - -
- `ChunkHolder`	`pullExecStatistics(String jobId, - long position)` - - - Assume statistics is not supported

Methods inherited from class compbio.ws.server.GenericMetadataService
`cancelJob, getJobStatus, getLimit, getLimits, getPresets, getRunnerOptions`

Methods inherited from class java.lang.Object
`equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

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-Method Detail
- -

-align

-public String align(List<FastaSequence> sequences)
-             throws JobSubmissionException

Throws: -: JobSubmissionException

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-presetAlign

-public String presetAlign(List<FastaSequence> sequences,
-                          Preset<T> preset)
-                   throws JobSubmissionException,
-                          WrongParameterException

Throws: -: JobSubmissionException -; WrongParameterException

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-customAlign

-public String customAlign(List<FastaSequence> sequences,
-                          List<Option<T>> options)
-                   throws JobSubmissionException,
-                          WrongParameterException

Throws: -: JobSubmissionException -; WrongParameterException

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-getResult

-public Alignment getResult(String jobId)
-                    throws ResultNotAvailableException

Throws: -: ResultNotAvailableException

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-pullExecStatistics

-public ChunkHolder pullExecStatistics(String jobId,
-                                      long position)

Description copied from class: GenericMetadataService

Assume statistics is not supported -

Overrides:: pullExecStatistics in class GenericMetadataService

Returns:: ChunkHolder

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