Package ubic.gemma.core.analysis.expression.coexpression

Class CoexpressionMetaValueObject

java.lang.Object

ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject

All Implemented Interfaces:

Serializable

public class CoexpressionMetaValueObject
extends Object
implements Serializable

Author:

luke

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
CoexpressionMetaValueObject()

Method Summary

Modifier and Type	Method	Description
String	getErrorState()
int	getMaxEdges()
int	getNumDatasetsQueried()
Collection<GeneValueObject>	getQueryGenes()
int	getQueryStringency()
List<CoexpressionValueObjectExt>	getResults()	A sorted list of the results (sorting must be done elsewhere!)
CoexpressionSearchCommand	getSearchSettings()	The original search settings from the client.
Map<Long,CoexpressionSummaryValueObject>	getSummaries()
boolean	isQueryGenesOnly()
void	setErrorState(String errorState)
void	setMaxEdges(int maxEdges)	Override the value of gemma.cytoscapeweb.maxEdges (or DEFAULT_MAX_EDGES_PER_GRAPH )
void	setNumDatasetsQueried(int numDatasetsQueried)
void	setQueryGenes(Collection<GeneValueObject> queryGenes)
void	setQueryGenesOnly(boolean queryGenesOnly)
void	setQueryStringency(int queryStringency)
void	setResults(List<CoexpressionValueObjectExt> results)
void	setSearchSettings(CoexpressionSearchCommand searchSettings)
void	setSummaries(Map<Long,CoexpressionSummaryValueObject> summary)
String	toString()
void	trim()	Deprecated. because this is too ad hoc and messy

Methods inherited from class java.lang.Object

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

Constructor Detail

CoexpressionMetaValueObject

public CoexpressionMetaValueObject()

Method Detail

getErrorState

public String getErrorState()

setErrorState

public void setErrorState(String errorState)

getMaxEdges

public int getMaxEdges()

Returns:

How many edges total are we allowed to have in the graph? Above this, they can get trimmed.

setMaxEdges

public void setMaxEdges(int maxEdges)

Override the value of gemma.cytoscapeweb.maxEdges (or DEFAULT_MAX_EDGES_PER_GRAPH )

Parameters:

maxEdges - max edges

getNumDatasetsQueried

public int getNumDatasetsQueried()

setNumDatasetsQueried

public void setNumDatasetsQueried(int numDatasetsQueried)

Parameters:

numDatasetsQueried - the number of data sets which were actually used in the query (a subset of those requested by the user if they didn't have coexpression analysis done)

getQueryGenes

public Collection<GeneValueObject> getQueryGenes()

setQueryGenes

public void setQueryGenes(Collection<GeneValueObject> queryGenes)

getQueryStringency

public int getQueryStringency()

setQueryStringency

public void setQueryStringency(int queryStringency)

getResults

public List<CoexpressionValueObjectExt> getResults()

A sorted list of the results (sorting must be done elsewhere!)

Returns:

coexp VOs

setResults

public void setResults(List<CoexpressionValueObjectExt> results)

Parameters:

results - please be sorted.

getSearchSettings

public CoexpressionSearchCommand getSearchSettings()

The original search settings from the client. made to the stringency

Returns:

coexp search command

setSearchSettings

public void setSearchSettings(CoexpressionSearchCommand searchSettings)

Parameters:

searchSettings - , should be the original settings

getSummaries

public Map<Long,CoexpressionSummaryValueObject> getSummaries()

setSummaries

public void setSummaries(Map<Long,CoexpressionSummaryValueObject> summary)

isQueryGenesOnly

public boolean isQueryGenesOnly()

setQueryGenesOnly

public void setQueryGenesOnly(boolean queryGenesOnly)

toString

public String toString()

Overrides:

toString in class Object

trim

@Deprecated
public void trim()

Deprecated.

because this is too ad hoc and messy

This method just removes low stringency results until it goes below the limit, regardless of whether the genes involved were query genes or not. This means, in effect, the original query could have been done at this higher stringency. The other trim method only removes non-query gene edges, so it is suitable for large 'query genes only'. Warning, this method can remove results that user may have expected.