Package ubic.gemma.web.services.rest.util.args

Class DatasetArg<T>

java.lang.Object

ubic.gemma.web.services.rest.util.args.AbstractArg<T>

ubic.gemma.web.services.rest.util.args.AbstractEntityArg<T,ExpressionExperiment,ExpressionExperimentService>

ubic.gemma.web.services.rest.util.args.DatasetArg<T>

All Implemented Interfaces:

Arg<T>

Direct Known Subclasses:

DatasetIdArg, DatasetStringArg

public abstract class DatasetArg<T>
extends AbstractEntityArg<T,ExpressionExperiment,ExpressionExperimentService>

Mutable argument type base class for dataset (ExpressionExperiment) API.

Author:

tesarst

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	DatasetArg(T value)

Method Summary

Modifier and Type	Method	Description
Set<AnnotationValueObject>	getAnnotations(ExpressionExperimentService service)
List<ArrayDesignValueObject>	getPlatforms(ExpressionExperimentService service, ArrayDesignService adService)	Retrieves the Platforms of the Dataset that this argument represents.
Set<QuantitationTypeValueObject>	getQuantitationTypes(ExpressionExperimentService service)	Retrieve a dataset with quantitation type initialized.
List<BioAssayValueObject>	getSamples(ExpressionExperimentService service, BioAssayService baService, OutlierDetectionService outlierDetectionService)
static DatasetArg<?>	valueOf(String s)	Used by RS to parse value of request parameters.

Methods inherited from class ubic.gemma.web.services.rest.util.args.AbstractEntityArg

checkEntity, getEntity, getObjectFilters, getPropertyName

Methods inherited from class ubic.gemma.web.services.rest.util.args.AbstractArg

getValue, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

DatasetArg

protected DatasetArg(T value)

Method Detail

valueOf

public static DatasetArg<?> valueOf(String s)
                             throws MalformedArgException

Used by RS to parse value of request parameters.

Parameters:

s - the request dataset argument

Returns:

instance of appropriate implementation of DatasetArg based on the actual Type the argument represents.

Throws:

MalformedArgException

getQuantitationTypes

public Set<QuantitationTypeValueObject> getQuantitationTypes(ExpressionExperimentService service)

Retrieve a dataset with quantitation type initialized.

getPlatforms

public List<ArrayDesignValueObject> getPlatforms(ExpressionExperimentService service,
                                                 ArrayDesignService adService)

Retrieves the Platforms of the Dataset that this argument represents.

Parameters:

service - service that will be used to retrieve the persistent EE object.

adService - service to use to retrieve the ADs.

Returns:

a collection of Platforms that the dataset represented by this argument is in.

getSamples

public List<BioAssayValueObject> getSamples(ExpressionExperimentService service,
                                            BioAssayService baService,
                                            OutlierDetectionService outlierDetectionService)

Parameters:

service - service that will be used to retrieve the persistent EE object.

baService - service that will be used to convert the samples (BioAssays) to VOs.

outlierDetectionService - service that will be used to detect which samples are outliers and fill their corresponding predictedOutlier attribute.

Returns:

a collection of BioAssays that represent the experiments samples.

getAnnotations

public Set<AnnotationValueObject> getAnnotations(ExpressionExperimentService service)

Parameters:

service - service that will be used to retrieve the persistent EE object.

Returns:

a collection of Annotations value objects that represent the experiments annotations.