Package ubic.gemma.core.loader.expression.geo.model

Class GeoVariable

java.lang.Object

ubic.gemma.core.loader.expression.geo.model.GeoVariable

public class GeoVariable
extends Object

A GeoVariable represents variables which were investigated.

According to the GEO web site, the valid values for the "name" are: dose, time, tissue, strain, gender, cell line, development stage, age, agent, cell type, infection, isolate, metabolism, shock, stress, temperature, specimen, disease state, protocol, growth protocol, genotype/genetic variation, species, individual, or other.

These map to ExperimentalFactors in Gemma.

Author:

pavlidis

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	GeoVariable.VariableType	Permitted descriptions of terms.

Constructor Summary

Constructors

Constructor	Description
GeoVariable()

Method Summary

Modifier and Type	Method	Description
void	addToVariableSampleList(GeoSample sample)
static GeoVariable.VariableType	convertStringToType(String string)	Convert a string found in the GEO sample descriptions e.g., "age" to the corresponding category, represented here by VariableType.
boolean	equals(Object obj)
String	getDescription()
Collection<GeoSample>	getSamples()
GeoVariable.VariableType	getType()
int	hashCode()
void	setDescription(String description)
void	setSamples(Collection<GeoSample> variableSampleList)
void	setType(GeoVariable.VariableType name)
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

GeoVariable

public GeoVariable()

Method Detail

convertStringToType

public static GeoVariable.VariableType convertStringToType(String string)

Convert a string found in the GEO sample descriptions e.g., "age" to the corresponding category, represented here by VariableType. TODO: this list has gotten unwieldy and should be replaced with a config file that is read in, and it should be more directly related the list in EFO.factor.categories.txt

Parameters:

string - string

Returns:

variable type

addToVariableSampleList

public void addToVariableSampleList(GeoSample sample)

getDescription

public String getDescription()

Returns:

Returns the description.

setDescription

public void setDescription(String description)

Parameters:

description - The description to set.

getSamples

public Collection<GeoSample> getSamples()

Returns:

Returns the variableSampleList.

setSamples

public void setSamples(Collection<GeoSample> variableSampleList)

Parameters:

variableSampleList - The variableSampleList to set.

getType

public GeoVariable.VariableType getType()

Returns:

Returns the name.

setType

public void setType(GeoVariable.VariableType name)

Parameters:

name - The name to set.

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