java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.advanced.GeneParameters
All Implemented Interfaces:
Serializable

public class GeneParameters
extends ExperimentObject
Contains methods for downloading gene and GO mappings.
Author:
Harald Barsnes, Marc Vaudel
See Also:
Serialized Form
  • Constructor Details

    • GeneParameters

      public GeneParameters()
      Create a new GenePreferences object.
    • GeneParameters

      public GeneParameters​(GeneParameters genePreferences)
      Creates new gene preferences based on a GenePreferences object.
      Parameters:
      genePreferences - the gene preferences
  • Method Details

    • getUseGeneMapping

      public Boolean getUseGeneMapping()
      Returns a boolean indicating whether gene mappings should be used.
      Returns:
      a boolean indicating whether gene mappings should be used
    • setUseGeneMapping

      public void setUseGeneMapping​(Boolean useGeneMapping)
      Sets whether gene mappings should be used.
      Parameters:
      useGeneMapping - a boolean indicating whether gene mappings should be used
    • getAutoUpdate

      public Boolean getAutoUpdate()
      Indicates whether the gene mappings should be automatically updated.
      Returns:
      a boolean indicating whether the gene mappings should be automatically updated
    • setAutoUpdate

      public void setAutoUpdate​(Boolean autoUpdate)
      Sets whether the gene mappings should be automatically updated.
      Parameters:
      autoUpdate - a boolean indicating whether the gene mappings should be automatically updated
    • equals

      public boolean equals​(GeneParameters genePreferences)
      Compares these preferences to other preferences.
      Parameters:
      genePreferences - other preferences to compare to.
      Returns:
      a boolean indicating whether the other preferences are the same as these ones.
    • getBackgroundSpecies

      public Integer getBackgroundSpecies()
      Returns the taxon of the species selected as background species.
      Returns:
      the taxon of the species selected as background species
    • setBackgroundSpecies

      public void setBackgroundSpecies​(Integer selectedBackgroundSpecies)
      Sets the taxon of the species selected as background species.
      Parameters:
      selectedBackgroundSpecies - the taxon of the species selected as background species
    • setBackgroundSpeciesFromFastaSummary

      public void setBackgroundSpeciesFromFastaSummary​(FastaSummary fastaSummary)
      Set the background species to the most common species in the FASTA file.
      Parameters:
      fastaSummary - the FASTA summary
    • getShortDescription

      public String getShortDescription()
      Returns a short description of the parameters.
      Returns:
      a short description of the parameters