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

public class BiomartMapping
extends Object
Mapping of the species to BioMart dataset.
Author:
Marc Vaudel
  • Field Details

  • Constructor Details

  • Method Details

    • loadMapping

      public void loadMapping​(File ensemblFile, File ensemblGenomeFile) throws IOException
      Loads the species mapping from a file. Previous mapping will be overwritten.
      Parameters:
      ensemblFile - the Ensembl BioMart file
      ensemblGenomeFile - the Ensembl genome BioMart file
      Throws:
      IOException - exception thrown whenever an error occurred while reading the file.
    • getDataset

      public String getDataset​(String assembly)
      Returns the Ensembl dataset for the given assembly. Null if not found.
      Parameters:
      assembly - the assembly
      Returns:
      the Ensembl dataset