compbio.ws.server
Class MafftWS

java.lang.Object
  compbio.ws.server.MafftWS

All Implemented Interfaces:

MsaWS<Mafft>

public class MafftWS
extends java.lang.Object
implements MsaWS<Mafft>

Constructor Summary

MafftWS()

Method Summary

java.lang.String	align(java.util.List<FastaSequence> sequences) Align a list of sequences with default settings.
boolean	cancelJob(java.lang.String jobId) Stop running job but leave its output untouched
java.lang.String	customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<Mafft>> options) Align a list of sequences with options.
JobStatus	getJobStatus(java.lang.String jobId) Return the status of the job.
Limit<Mafft>	getLimit(java.lang.String presetName) Get a Limit for a preset.
LimitsManager<Mafft>	getLimits() List Limits supported by a web service.
PresetManager<Mafft>	getPresets() Get presets supported by a web service
Alignment	getResult(java.lang.String jobId) Return the result of the job.
RunnerConfig<Mafft>	getRunnerOptions() Get options supported by a web service
java.lang.String	presetAlign(java.util.List<FastaSequence> sequences, Preset<Mafft> preset) Align a list of sequences with preset.
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.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MafftWS

public MafftWS()

Method Detail

align

public java.lang.String align(java.util.List<FastaSequence> sequences)
                       throws JobSubmissionException

Description copied from interface: MsaWS

Align a list of sequences with default settings. Any dataset containing a greater number of sequences or the average length of the sequences are greater then defined in the default Limit will not be accepted for an alignment operation and JobSubmissionException will be thrown.

Specified by:

align in interface MsaWS<Mafft>

Parameters:

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

Returns:

jobId - unique identifier for the job

Throws:

UnsupportedRuntimeException - thrown if server OS does not support native executables for a given web service, e.g. JWS2 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

JobSubmissionException

customAlign

public java.lang.String customAlign(java.util.List<FastaSequence> sequences,
                                    java.util.List<Option<Mafft>> options)
                             throws JobSubmissionException,
                                    WrongParameterException

Description copied from interface: MsaWS

Align a list of sequences with options.

Specified by:

customAlign in interface MsaWS<Mafft>

Parameters:

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

options - A list of Options

Returns:

jobId - unique identifier for the job

Throws:

UnsupportedRuntimeException - thrown if server OS does not support native executables for a given web service, e.g. JWS2 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.

JobSubmissionException

See Also:

Default Limit is used to decide whether the calculation will be permitted or denied

presetAlign

public java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
                                    Preset<Mafft> preset)
                             throws JobSubmissionException,
                                    WrongParameterException

Description copied from interface: MsaWS

Align a list of sequences with preset. @see Preset Limit for a presetName is used whether the calculation will be permitted or denied. If no Limit was defined for a presetName, than default limit is used.

Specified by:

presetAlign in interface MsaWS<Mafft>

Parameters:

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

preset - A list of Options

Returns:

String - jobId - unique identifier for the job

Throws:

UnsupportedRuntimeException - thrown if server OS does not support native executables for a given web service, e.g. JWS2 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.

JobSubmissionException

getResult

public Alignment getResult(java.lang.String jobId)
                    throws ResultNotAvailableException

Description copied from interface: MsaWS

Return the result of the job.

Specified by:

getResult in interface MsaWS<Mafft>

Parameters:

jobId - a unique job identifier

Returns:

Alignment

Throws:

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.

getLimit

public Limit<Mafft> getLimit(java.lang.String presetName)

Description copied from interface: MsaWS

Get a Limit for a preset.

Specified by:

getLimit in interface MsaWS<Mafft>

Parameters:

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

Returns:

Limit

getLimits

public LimitsManager<Mafft> getLimits()

Description copied from interface: MsaWS

List Limits supported by a web service.

Specified by:

getLimits in interface MsaWS<Mafft>

Returns:

LimitManager

pullExecStatistics

public ChunkHolder pullExecStatistics(java.lang.String jobId,
                                      long position)

Description copied from interface: MsaWS

Reads 1kb chunk from the statistics file which is specific to a given web service from the position. 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.

Specified by:

pullExecStatistics in interface MsaWS<Mafft>

Parameters:

jobId - - unique job identifier

position - - next position within the file to read

Returns:

ChunkHolder - @see ChunkHolder which contains a chuink of data and a next position within the file from which no data has been read

cancelJob

public boolean cancelJob(java.lang.String jobId)

Description copied from interface: MsaWS

Stop running job but leave its output untouched

Specified by:

cancelJob in interface MsaWS<Mafft>

Returns:

true if job was cancelled successfully, false otherwise

getJobStatus

public JobStatus getJobStatus(java.lang.String jobId)

Description copied from interface: MsaWS

Return the status of the job. @see JobStatus

Specified by:

getJobStatus in interface MsaWS<Mafft>

Parameters:

jobId - - unique job identifier

Returns:

JobStatus - status of the job

getPresets

public PresetManager<Mafft> getPresets()

Description copied from interface: MsaWS

Get presets supported by a web service

Specified by:

getPresets in interface MsaWS<Mafft>

Returns:

PresetManager the object contains information about presets supported by a web service

getRunnerOptions

public RunnerConfig<Mafft> getRunnerOptions()

Description copied from interface: MsaWS

Get options supported by a web service

Specified by:

getRunnerOptions in interface MsaWS<Mafft>

Returns:

RunnerConfig the list of options and parameters supported by a web service.