Class EnsemblGenomesSpecies

java.lang.Object
com.compomics.util.experiment.biology.taxonomy.mappings.EnsemblGenomesSpecies

public class EnsemblGenomesSpecies
extends Object
This class provides information about the species mapping in Ensembl Genomes (Bacteria, Fungi, Metazoa, Plants, Protists).
Author:
Marc Vaudel
  • Field Details

  • Constructor Details

  • Method Details

    • loadMapping

      public void loadMapping​(File speciesFile) throws IOException
      Loads the species mapping from a file. Previous mapping will be overwritten.
      Parameters:
      speciesFile - the species file
      Throws:
      IOException - exception thrown whenever an error occurred while reading the file.
    • getName

      public String getName​(Integer taxon)
      Returns the name corresponding to the given NCBI taxon.
      Parameters:
      taxon - the NCBI taxon
      Returns:
      the name
    • getDivision

      Returns the division corresponding to the given NCBI taxon.
      Parameters:
      taxon - the NCBI taxon
      Returns:
      the division
    • getAssembly

      public String getAssembly​(Integer taxon)
      Returns the Ensembl assembly corresponding to the given NCBI taxon.
      Parameters:
      taxon - the NCBI taxon
      Returns:
      the Ensembl assembly
    • getTaxons

      public HashSet<Integer> getTaxons()
      Returns the taxons in this map.
      Returns:
      the taxons in this map