Package ubic.gemma.model.expression.bioAssayData

Class DoubleVectorValueObject

java.lang.Object

ubic.gemma.model.common.IdentifiableValueObject<DataVector>

ubic.gemma.model.expression.bioAssayData.DataVectorValueObject

ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject

All Implemented Interfaces:

Serializable, Identifiable

Direct Known Subclasses:

SlicedDoubleVectorValueObject

public class DoubleVectorValueObject
extends DataVectorValueObject

Value object for a BulkExpressionDataVector containing doubles.

Author:

paul

See Also:

Serialized Form

Field Summary

Fields inherited from class ubic.gemma.model.common.IdentifiableValueObject

id

Constructor Summary

Constructors

Modifier	Constructor	Description
	DoubleVectorValueObject()
	DoubleVectorValueObject(BulkExpressionDataVector dedv, ExpressionExperimentValueObject eevo, QuantitationTypeValueObject qtvo, BioAssayDimensionValueObject badVo, ArrayDesignValueObject advo, Collection<Long> genes)
	DoubleVectorValueObject(BulkExpressionDataVector dedv, ExpressionExperimentValueObject eevo, QuantitationTypeValueObject qtvo, BioAssayDimensionValueObject vectorsBadVo, ArrayDesignValueObject advo, Collection<Long> genes, BioAssayDimensionValueObject dimToMatch)	Create a vector where we expect to have to create one or more gaps to match other vectors, defined by dimToMatch.
protected	DoubleVectorValueObject(DoubleVectorValueObject dvvo)	Copy constructor.

Method Summary

Modifier and Type	Method	Description
DoubleVectorValueObject	copy()	Create a copy of this vector.
boolean	equals(Object obj)
int	hashCode()
SlicedDoubleVectorValueObject	slice(ExpressionExperimentSubsetValueObject subset, BioAssayDimensionValueObject bad)	Crate a vector that is a slice of this one.
double[]	standardize()

Methods inherited from class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject

getBioAssays, toString

Methods inherited from class ubic.gemma.model.common.IdentifiableValueObject

getId, setId

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

DoubleVectorValueObject

public DoubleVectorValueObject()

DoubleVectorValueObject

public DoubleVectorValueObject(BulkExpressionDataVector dedv,
                               ExpressionExperimentValueObject eevo,
                               QuantitationTypeValueObject qtvo,
                               BioAssayDimensionValueObject badVo,
                               ArrayDesignValueObject advo,
                               @Nullable
                               Collection<Long> genes)

See Also:

DoubleVectorValueObject(BulkExpressionDataVector, ExpressionExperimentValueObject, QuantitationTypeValueObject, BioAssayDimensionValueObject, ArrayDesignValueObject, Collection)

DoubleVectorValueObject

public DoubleVectorValueObject(BulkExpressionDataVector dedv,
                               ExpressionExperimentValueObject eevo,
                               QuantitationTypeValueObject qtvo,
                               BioAssayDimensionValueObject vectorsBadVo,
                               ArrayDesignValueObject advo,
                               @Nullable
                               Collection<Long> genes,
                               BioAssayDimensionValueObject dimToMatch)

Create a vector where we expect to have to create one or more gaps to match other vectors, defined by dimToMatch.

Parameters:

dimToMatch - ensure that the vector missing values to match the locations of any bioassays in dimToMatch that aren't in the dedv's bioAssayDimension.

dedv - dedv

eevo - a VO for the experiment

qtvo - a VO for the quantitation type

vectorsBadVo - BA dimension vo

genes - a collection of gene IDs that correspond to the design element of this vector, or null to ignore

dimToMatch - a dimension that the data should be aligned with, this will result in "gaps" where the provided vector is lacking assays

DoubleVectorValueObject

protected DoubleVectorValueObject(DoubleVectorValueObject dvvo)

Copy constructor.

Method Detail

equals

public boolean equals(Object obj)

Overrides:

equals in class DataVectorValueObject

hashCode

public int hashCode()

Overrides:

hashCode in class DataVectorValueObject

copy

public DoubleVectorValueObject copy()

Create a copy of this vector.

Use this if you intend to modify it as the original might be stored in a shared cache.

slice

public SlicedDoubleVectorValueObject slice(ExpressionExperimentSubsetValueObject subset,
                                           BioAssayDimensionValueObject bad)

Crate a vector that is a slice of this one.

Create a vector that is a slice of another one. The bioassays chosen are as given in the supplied bioassay dimension.

Parameters:

subset - a subset by which we are slicing

bad - all we nee is the id, the name and the list of bioassays from this.S

standardize

public double[] standardize()

Returns:

data adjusted to mean 0, variance 1.