Package com.compomics.util.parameters.identification.advanced

Class GeneParameters

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:

  • 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 String getBackgroundSpecies()
      Returns the Latin name of the species selected as background species.
      Returns:
      the Latin name of the species selected as background species

    • setBackgroundSpecies

      public void setBackgroundSpecies(String selectedBackgroundSpecies)
      Sets the taxon of the species selected as background species.
      Parameters:
      selectedBackgroundSpecies - the Latin name 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