compbio.ws.server
Class _MsaService<T>

java.lang.Object
  compbio.ws.server.GenericMetadataService
      compbio.ws.server._MsaService<T>

Type Parameters:

T -

public abstract class _MsaService<T>
extends GenericMetadataService

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

Since:

2.0

Version:

1.0 June 2011

Author:

pvtroshin

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

Method Detail

align

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

Throws:

JobSubmissionException

presetAlign

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

Throws:

JobSubmissionException

WrongParameterException

customAlign

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

Throws:

JobSubmissionException

WrongParameterException

getResult

public Alignment getResult(String jobId)
                    throws ResultNotAvailableException

Throws:

ResultNotAvailableException

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