package jalview.io.xdb.genbank;

/**
 * <p>
 * Free-format information including an abbreviated form of the organism name,
 * sometimes followed by a molecule type. (See section 3.4.10 of the GenBank
 * release notes for more info.)
 * </p>
 * <p>
 * Entrez Search Field: Organism [ORGN]
 * </p>
 * <p>
 * Search Tip: For some organisms that have well-established common names, such
 * as baker's yeast, mouse, and human, a search for the common name will yield
 * the same results as a search for the scientific name, e.g., a search for
 * "baker's yeast" in the organism field retrieves the same number of documents
 * as "Saccharomyces cerevisiae". This is true because the Organism field is
 * connected to the NCBI Taxonomy Database, which contains cross-references
 * between common names, scientific names, and synonyms for organisms
 * represented in the Sequence databases.
 * </p>
 * <h1>Organism</h1>
 * <p>
 * The formal scientific name for the source organism (genus and species, where
 * appropriate) and its lineage, based on the phylogenetic classification scheme
 * used in the NCBI Taxonomy Database. If the complete lineage of an organism is
 * very long, an abbreviated lineage will be shown in the GenBank record and the
 * complete lineage will be available in the Taxonomy Database. (See also the
 * /db_xref=taxon:nnnn Feature qualifer, below.)
 * </p>
 * <p>
 * Entrez Search Field: Organism [ORGN]
 * </p>
 * <p>
 * Search Tip: You can search the Organism field by any node in the taxonomic
 * hierarchy, e.g., you can search for the term "Saccharomyces cerevisiae",
 * "Saccharomycetales", "Ascomycota", etc. to retrieve all the sequences from
 * organisms in a particular taxon.
 * </p>
 * 
 */
public class GenBankSource
{
  private String source = "";

  private String organism = "";

  private String taxonomic = "";

  public GenBankSource()
  {
  }

  @Override
  public String toString()
  {
    return String.format("%s\n\t%s\n\t%s", getSource(), getOrganism(),
            getTaxonomic());
  }

  /**
   * @return the source
   */
  public String getSource()
  {
    return source;
  }

  /**
   * @param source
   *          the source to set
   */
  public void setSource(String source)
  {
    this.source = source;
  }

  /**
   * @return the organism
   */
  public String getOrganism()
  {
    return organism;
  }

  /**
   * @param organism
   *          the organism to set
   */
  public void setOrganism(String organism)
  {
    this.organism = organism;
  }

  /**
   * @return the taxonomic
   */
  public String getTaxonomic()
  {
    return taxonomic;
  }

  /**
   * @param taxonomic
   *          the taxonomic to set
   */
  public void setTaxonomic(String taxonomic)
  {
    this.taxonomic = taxonomic;
  }

}