compbio.ws.server

Class ClustalWS

java.lang.Object

compbio.ws.server.ClustalWS

All Implemented Interfaces:

JABAService, JManagement, Metadata<ClustalW>, MsaWS<ClustalW>

public class ClustalWS
extends java.lang.Object
implements MsaWS<ClustalW>

Field Summary

Fields

Modifier and Type	Field and Description
private static RunnerConfig<ClustalW>	clustalOptions
private static PresetManager<ClustalW>	clustalPresets
private static LimitsManager<ClustalW>	limitMan
private static org.apache.log4j.Logger	log

Fields inherited from interface compbio.data.msa.JABAService

JABAWS_VERSION, SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE, V3_SERVICE_NAMESPACE

Constructor Summary

Constructors

Constructor and Description
ClustalWS()

Method Summary

Modifier and Type	Method and Description
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 the job jobId but leave its output untouched
java.lang.String	customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<ClustalW>> options) Align a list of sequences with options.
JobStatus	getJobStatus(java.lang.String jobId) Return the status of the job.
Limit<ClustalW>	getLimit(java.lang.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(java.lang.String jobId) Return the result of the job.
RunnerConfig<ClustalW>	getRunnerOptions() Get options supported by a web service
(package private) ConfiguredExecutable<ClustalW>	init(java.util.List<FastaSequence> dataSet)
java.lang.String	presetAlign(java.util.List<FastaSequence> sequences, Preset<ClustalW> 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

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

Field Detail

log

private static org.apache.log4j.Logger log

clustalOptions

private static final RunnerConfig<ClustalW> clustalOptions

clustalPresets

private static final PresetManager<ClustalW> clustalPresets

limitMan

private static final LimitsManager<ClustalW> limitMan

Constructor Detail

ClustalWS

public ClustalWS()

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 when 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<ClustalW>

Parameters:

sequences - List of FastaSequence objects. The program 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

Returns:

jobId - unique identifier for the job

Throws:

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

init

ConfiguredExecutable<ClustalW> init(java.util.List<FastaSequence> dataSet)
                             throws JobSubmissionException

Throws:

JobSubmissionException

presetAlign

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

Description copied from interface: MsaWS

Align a list of sequences with 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<ClustalW>

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:

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.

See Also:

Preset

customAlign

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

Description copied from interface: MsaWS

Align a list of sequences with options.

Specified by:

customAlign in interface MsaWS<ClustalW>

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:

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.

See Also:

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

getRunnerOptions

public RunnerConfig<ClustalW> getRunnerOptions()

Description copied from interface: Metadata

Get options supported by a web service

Specified by:

getRunnerOptions in interface Metadata<ClustalW>

Returns:

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

getResult

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

Description copied from interface: MsaWS

Return the result of the job. This method waits for the job jobId to complete before return.

Specified by:

getResult in interface MsaWS<ClustalW>

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 due to the lower level problems on the server i.e. IOException, FileNotFoundException problems as well as UnknownFileFormatException.

getLimit

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

Description copied from interface: Metadata

Get a Limit for a preset.

Specified by:

getLimit in interface Metadata<ClustalW>

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<ClustalW> getLimits()

Description copied from interface: Metadata

List Limits supported by a web service.

Specified by:

getLimits in interface Metadata<ClustalW>

Returns:

LimitManager

cancelJob

public boolean cancelJob(java.lang.String jobId)

Description copied from interface: JManagement

Stop running the job jobId but leave its output untouched

Specified by:

cancelJob in interface JManagement

Returns:

true if job was cancelled successfully, false otherwise

getJobStatus

public JobStatus getJobStatus(java.lang.String jobId)

Description copied from interface: JManagement

Return the status of the job.

Specified by:

getJobStatus in interface JManagement

Parameters:

jobId - - unique job identifier

Returns:

JobStatus - status of the job

See Also:

JobStatus

getPresets

public PresetManager<ClustalW> getPresets()

Description copied from interface: Metadata

Get presets supported by a web service

Specified by:

getPresets in interface Metadata<ClustalW>

Returns:

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

pullExecStatistics

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

Description copied from interface: JManagement

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 JManagement

Parameters:

jobId - - unique job identifier

position - - next position within the file to read

Returns:

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

See Also:

ChunkHolder