package jalview.datamodel;

import jalview.util.MapList;

/**
 * A data bean to model one or more contiguous regions on one chromosome
 */
public class GeneLoci
{
  /*
   * implemented as an adapter over DBRefEntry with
   * source -> species id
   * version -> reference
   * accession -> chromosome
   */
  private DBRefEntry loci;

  boolean forwardStrand;

  /**
   * Constructor
   * 
   * @param taxon
   * @param ref
   * @param chrId
   * @param map
   * @param forward
   */
  public GeneLoci(String taxon, String ref, String chrId, MapList map,
          boolean forward)
  {
    loci = new DBRefEntry(taxon, ref, chrId, new Mapping(map));
    forwardStrand = forward;
  }

  /**
   * Answers the identifier for the species
   * 
   * @return
   */
  public String getSpecies()
  {
    return loci.getSource();
  }

  /**
   * Answers the identifier for the genomic reference assembly
   */
  public String getReference()
  {
    return loci.getVersion();
  }

  /**
   * Answers the chromosome identifier
   * 
   * @return
   */
  public String getChromosome()
  {
    return loci.getAccessionId();
  }

  /**
   * Answers the mapping from sequence positions (in sequence start..end
   * coordinates) to the corresponding loci in the chromosome (in reference
   * assembly coordinates, base 1)
   * 
   * @return
   */
  public MapList getMapping()
  {
    return loci.getMap().getMap();
  }

  public boolean isForwardStrand()
  {
    return forwardStrand;
  }
}