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

  • Constructor Details

    • GeoVariable

      public GeoVariable()

  • Method Details

    • 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