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

public class EnsemblSpecies
extends Object
Mapping of the Ensembl species.
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.
    • getScientificName

      public String getScientificName​(Integer id)
      Returns the scientific name corresponding to the given NCBI taxon.
      Parameters:
      id - the NCBI taxon
      Returns:
      the scientific name
    • getCommonName

      public String getCommonName​(Integer id)
      Returns the common name corresponding to the given NCBI taxon.
      Parameters:
      id - the NCBI taxon
      Returns:
      the common name
    • getAssembly

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

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