Package ubic.gemma.model.association.coexpression

Class GeneCoexpressionNodeDegreeValueObject

java.lang.Object

ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject

All Implemented Interfaces:

Serializable

public class GeneCoexpressionNodeDegreeValueObject
extends Object
implements Serializable

Represents a GeneCoexpressionNodeDegree

Author:

Paul

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
GeneCoexpressionNodeDegreeValueObject()
GeneCoexpressionNodeDegreeValueObject(GeneCoexpressionNodeDegree entity)

Method Summary

Modifier and Type	Method	Description
double[]	asDoubleArrayNegRanks()
double[]	asDoubleArrayPosRanks()
int[]	asIntArrayNeg()
int[]	asIntArrayPos()
void	clear()	Used during recomputation only.
boolean	equals(Object obj)
Long	getGeneId()
Integer	getLinksWithExactSupport(Integer support, boolean positive)
Integer	getLinksWithMinimumSupport(int i)
Integer	getLinksWithMinimumSupport(Integer support, boolean positive)
int	getMaxSupportNeg()
int	getMaxSupportPos()
Double	getRankAtMinimumSupport(Integer support, boolean positive)
int	hashCode()
void	increment(Integer support, boolean positive)
GeneCoexpressionNodeDegree	toEntity()
String	toString()
int	total()	Equivalent to getLinksWithMinimumSupport( 0 )

Methods inherited from class java.lang.Object

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

Constructor Detail

GeneCoexpressionNodeDegreeValueObject

public GeneCoexpressionNodeDegreeValueObject()

GeneCoexpressionNodeDegreeValueObject

public GeneCoexpressionNodeDegreeValueObject(GeneCoexpressionNodeDegree entity)

Method Detail

asDoubleArrayNegRanks

public double[] asDoubleArrayNegRanks()

asDoubleArrayPosRanks

public double[] asDoubleArrayPosRanks()

asIntArrayNeg

public int[] asIntArrayNeg()

Returns:

counts at each level of support, starting from 0 (which will be 0), up to the maximum support.

asIntArrayPos

public int[] asIntArrayPos()

Returns:

counts at each level of support, starting from 0 (which will be 0), up to the maximum support.

getGeneId

public Long getGeneId()

getLinksWithExactSupport

public Integer getLinksWithExactSupport(Integer support,
                                        boolean positive)

Parameters:

support - value

positive - positive

Returns:

how many links have this much support (specifically).

getLinksWithMinimumSupport

public Integer getLinksWithMinimumSupport(int i)

Parameters:

i - support

Returns:

total number of links (this is just the total of positive and negative; if some of those are with the same genes it's a double count, sorry)

getLinksWithMinimumSupport

public Integer getLinksWithMinimumSupport(Integer support,
                                          boolean positive)

Parameters:

support - threshold

positive - positive

Returns:

how many links have at least this much support (cumulative)

getMaxSupportNeg

public int getMaxSupportNeg()

getMaxSupportPos

public int getMaxSupportPos()

Returns:

the largest value for support for this gene

getRankAtMinimumSupport

public Double getRankAtMinimumSupport(Integer support,
                                      boolean positive)

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

toString

public String toString()

Overrides:

toString in class Object

increment

public void increment(Integer support,
                      boolean positive)

total

public int total()

Equivalent to getLinksWithMinimumSupport( 0 )

Returns:

how many links this gene has in total, across all levels of support (positive and negative correlations combined)

clear

public void clear()

Used during recomputation only.

toEntity

public GeneCoexpressionNodeDegree toEntity()