content: /*************************************************************************
  *                                                                        *
  *  This file is part of the 20n/act project.                             *
  *  20n/act enables DNA prediction for synthetic biology/bioengineering.  *
  *  Copyright (C) 2017 20n Labs, Inc.                                     *
  *                                                                        *
  *  Please direct all queries to act@20n.com.                             *
  *                                                                        *
  *  This program is free software: you can redistribute it and/or modify  *
  *  it under the terms of the GNU General Public License as published by  *
  *  the Free Software Foundation, either version 3 of the License, or     *
  *  (at your option) any later version.                                   *
  *                                                                        *
  *  This program is distributed in the hope that it will be useful,       *
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of        *
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
  *  GNU General Public License for more details.                          *
  *                                                                        *
  *  You should have received a copy of the GNU General Public License     *
  *  along with this program.  If not, see <http://www.gnu.org/licenses/>. *
  *                                                                        *
  *************************************************************************/
  
  package act.installer.metacyc.annotations;
  
  import act.installer.metacyc.Resource;
  import act.installer.metacyc.BPElement;
  import act.installer.metacyc.OrganismComposition;
  import act.installer.metacyc.JsonHelper;
  import org.json.JSONObject;
  
  public class BioSource extends BPElement {
    // contains only a xref and a name (both from BPElement)
  
    // e.g.,  {
    //          ID: BioSource32423,
    //          xref: #UnificationXref32424,
    //          name: "Escherichia coli MS 124-1"
    //        }
    // the xref points to a unification ref:
    //        { id: "679205", db: "NCBI Taxonomy" }
    // which is great because we can then lookup the full lineage:
    // cellular organisms; Bacteria; Proteobacteria;
    //  Gammaproteobacteria; Enterobacteriales;
    //  Enterobacteriaceae; Escherichia; Escherichia coli
    // from http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=679205
  
    public BioSource(BPElement basics) {
      super(basics);
    }
  
    public JSONObject expandedJSON(OrganismComposition src) {
      JsonHelper o = new JsonHelper(src);
      if (name != null)
        o.add("name", this.name);
      return o.getJSON();
    }
  }
  
  