Package ubic.gemma.persistence.service.association.coexpression

Class CoexpressionValueObject

java.lang.Object

ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject

All Implemented Interfaces:

Serializable, Comparable<CoexpressionValueObject>

public class CoexpressionValueObject
extends Object
implements Comparable<CoexpressionValueObject>, Serializable

Lightweight/convenient object for manipulating coexpression for a pair of genes. Importantly, this does not necessarily reflect the coexpression data in the database: it may have been filtered in accordance to the query settings in terms of the data sets searched and the maximum number of results. Note that hashCode and equals do not use the ID of the coexpression; they only use the genes (ignoring which is query vs. found) and the sign, since those are in effect unique in the system.

Author:

Paul

See Also:

• Serialized Form

Constructor Summary

Constructors

Modifier	Constructor	Description
	CoexpressionValueObject()
protected	CoexpressionValueObject(Long queryGeneId, Long coexGeneId, Boolean positiveCorrelation, Integer support, Long supportDetailsId, Set<Long> supportingDatasets)
protected	CoexpressionValueObject(Long coexGeneId, String coexGeneSymbol, boolean positiveCorrelation, Long queryGeneId, String queryGeneSymbol, Integer support, Long supportDetailsId, Collection<Long> supportingDatasets, Collection<Long> testedInDatasets)
protected	CoexpressionValueObject(Long coexGeneId, String coexGeneSymbol, boolean positiveCorrelation, Long queryGeneId, String queryGeneSymbol, Integer support, Long supportDetailsId, Set<Long> supportingDatasets, Set<Long> testedInDatasets)
	CoexpressionValueObject(Gene2GeneCoexpression g2g)	Construct a value object.

Method Summary

Modifier and Type	Method	Description
int	compareTo(CoexpressionValueObject o)
boolean	equals(Object obj)
Long	getCoexGeneId()
String	getCoexGeneSymbol()
int	getMaxResults()
Integer	getNumDatasetsSupporting()
Integer	getNumDatasetsTestedIn()
Long	getQueryGeneId()
String	getQueryGeneSymbol()
int	getQueryStringency()
Long	getSupportDetailsId()
Set<Long>	getSupportingDatasets()
Set<Long>	getTestedInDatasets()
int	hashCode()
boolean	isEeConstraint()
boolean	isFromCache()
boolean	isInterQueryLink()
boolean	isPositiveCorrelation()
void	setCoexGeneSymbol(String coexGeneSymbol)
void	setFromCache(boolean fromCache)
void	setInterQueryLink(boolean interQueryLink)
void	setQueryGeneSymbol(String queryGeneSymbol)
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Details

CoexpressionValueObject

public CoexpressionValueObject()

CoexpressionValueObject

public CoexpressionValueObject(Gene2GeneCoexpression g2g)

Construct a value object. The "tested-in" component is not filled in, it must be done later.

Parameters:

g2g - g2g

CoexpressionValueObject

protected CoexpressionValueObject(Long queryGeneId,
 Long coexGeneId,
 Boolean positiveCorrelation,
 Integer support,
 Long supportDetailsId,
 Set<Long> supportingDatasets)

CoexpressionValueObject

protected CoexpressionValueObject(Long coexGeneId,
 String coexGeneSymbol,
 boolean positiveCorrelation,
 Long queryGeneId,
 String queryGeneSymbol,
 Integer support,
 Long supportDetailsId,
 Collection<Long> supportingDatasets,
 Collection<Long> testedInDatasets)

CoexpressionValueObject

protected CoexpressionValueObject(Long coexGeneId,
 String coexGeneSymbol,
 boolean positiveCorrelation,
 Long queryGeneId,
 String queryGeneSymbol,
 Integer support,
 Long supportDetailsId,
 Set<Long> supportingDatasets,
 Set<Long> testedInDatasets)

Method Details

compareTo

public int compareTo(CoexpressionValueObject o)

Specified by:

compareTo in interface Comparable<CoexpressionValueObject>

getCoexGeneId

public Long getCoexGeneId()

getCoexGeneSymbol

public String getCoexGeneSymbol()

setCoexGeneSymbol

public void setCoexGeneSymbol(String coexGeneSymbol)

getMaxResults

public int getMaxResults()

getNumDatasetsSupporting

public Integer getNumDatasetsSupporting()

Returns:

number of data sets this link was found in

getNumDatasetsTestedIn

public Integer getNumDatasetsTestedIn()

Returns:

number of data sets this link was tested in, of -1 if the information was not retrieved or if the value is zero (which is basically an error).

getQueryGeneId

public Long getQueryGeneId()

getQueryGeneSymbol

public String getQueryGeneSymbol()

setQueryGeneSymbol

public void setQueryGeneSymbol(String queryGeneSymbol)

getQueryStringency

public int getQueryStringency()

getSupportDetailsId

public Long getSupportDetailsId()

getSupportingDatasets

public Set<Long> getSupportingDatasets()

Returns:

the IDs of the supporting data sets; or an empty collection if the information was not retrieved

getTestedInDatasets

public Set<Long> getTestedInDatasets()

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

isEeConstraint

public boolean isEeConstraint()

isFromCache

public boolean isFromCache()

setFromCache

public void setFromCache(boolean fromCache)

isInterQueryLink

public boolean isInterQueryLink()

setInterQueryLink

public void setInterQueryLink(boolean interQueryLink)

isPositiveCorrelation

public boolean isPositiveCorrelation()