Package ubic.gemma.model.expression.bioAssayData

Class DoubleVectorValueObject

java.lang.Object

ubic.gemma.model.IdentifiableValueObject<DataVector>

ubic.gemma.model.expression.bioAssayData.DataVectorValueObject

ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject

All Implemented Interfaces:

Serializable, Identifiable

public class DoubleVectorValueObject
extends DataVectorValueObject

Simple wrapper for a double[] that is derived from a DesignElementDataVector.

Author:

paul

See Also:

Serialized Form

Field Summary

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

byteArrayConverter

Fields inherited from class ubic.gemma.model.IdentifiableValueObject

id

Constructor Summary

Constructors

Constructor	Description
DoubleVectorValueObject()	Required when using the class as a spring bean.
DoubleVectorValueObject(DesignElementDataVector dedv, Collection<Long> genes, BioAssayDimensionValueObject badVo)
DoubleVectorValueObject(DesignElementDataVector dedv, BioAssayDimensionValueObject badVo)
DoubleVectorValueObject(DesignElementDataVector dedv, BioAssayDimensionValueObject vectorsBadVo, Collection<Long> genes, BioAssayDimension dimToMatch)	Create a vector where we expect to have to create one or more gaps to match other vectors, defined by dimToMatch.
DoubleVectorValueObject(ExpressionExperimentSubSet bioassaySet, DoubleVectorValueObject vec, BioAssayDimensionValueObject bad)	Create a vector that is a slice of another one.

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object obj)
double[]	getData()
Double	getPvalue()
Double	getRank()
Long	getSourceVectorId()
int	hashCode()
boolean	isMasked()
boolean	isReorganized()
boolean	isSliced()
void	setMasked(boolean masked)
void	setPvalue(Double pvalue)
void	setRank(Double rank)
void	setReorganized(boolean reorganized)
double[]	standardize()
DesignElementDataVector	toDesignElementDataVector(ExpressionExperiment ee, CompositeSequence cs, QuantitationType updatedQuantitationType)

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

getBioAssayDimension, getBioAssays, getDesignElement, getExpressionExperiment, getGenes, getQuantitationType, setBioAssayDimension, setDesignElement, setExpressionExperiment, setGenes, setQuantitationType, toString

Methods inherited from class ubic.gemma.model.IdentifiableValueObject

getId, setId

Methods inherited from class java.lang.Object

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

Constructor Detail

DoubleVectorValueObject

public DoubleVectorValueObject()

Required when using the class as a spring bean.

DoubleVectorValueObject

public DoubleVectorValueObject(ExpressionExperimentSubSet bioassaySet,
                               DoubleVectorValueObject vec,
                               BioAssayDimensionValueObject bad)

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

Parameters:

bioassaySet - , possibly a subset, which we are going to slice.

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

vec - VO

DoubleVectorValueObject

public DoubleVectorValueObject(DesignElementDataVector dedv,
                               BioAssayDimensionValueObject badVo)

DoubleVectorValueObject

public DoubleVectorValueObject(DesignElementDataVector dedv,
                               BioAssayDimensionValueObject vectorsBadVo,
                               Collection<Long> genes,
                               BioAssayDimension 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.

genes - genes

dedv - dedv

vectorsBadVo - BA dimension vo

DoubleVectorValueObject

public DoubleVectorValueObject(DesignElementDataVector dedv,
                               Collection<Long> genes,
                               BioAssayDimensionValueObject badVo)

Method Detail

equals

public boolean equals(Object obj)

Overrides:

equals in class DataVectorValueObject

hashCode

public int hashCode()

Overrides:

hashCode in class DataVectorValueObject

getData

public double[] getData()

getPvalue

public Double getPvalue()

setPvalue

public void setPvalue(Double pvalue)

getRank

public Double getRank()

setRank

public void setRank(Double rank)

getSourceVectorId

public Long getSourceVectorId()

Returns:

If this returns non-null, it means the vector is a slice of another vector identified by the return value.

isMasked

public boolean isMasked()

setMasked

public void setMasked(boolean masked)

isReorganized

public boolean isReorganized()

Returns:

true if the data has been rearranged relative to the bioassay dimension (as a matter of practice the bioassay dimension should be set to null if it is not valid; this boolean is an additional check)

setReorganized

public void setReorganized(boolean reorganized)

isSliced

public boolean isSliced()

standardize

public double[] standardize()

Returns:

data adjusted to mean 0, variance 1.

toDesignElementDataVector

public DesignElementDataVector toDesignElementDataVector(ExpressionExperiment ee,
                                                         CompositeSequence cs,
                                                         QuantitationType updatedQuantitationType)

Parameters:

ee - required

cs - required

updatedQuantitationType - required because this might be changed.

Returns:

design element data vector; log2 isensured.