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 Stoichiometry extends BPElement {
    Float stoichiometricCoefficient;
    Resource physicalEntity; // Protein|Complex|Rna|SmallMolecule
  
    public Resource getPhysicalEntity() { return this.physicalEntity; }
    public Float getCoefficient() { return this.stoichiometricCoefficient; }
  
    public Stoichiometry(BPElement basics, Resource phyEnt, Float coeff) {
      super(basics);
      this.stoichiometricCoefficient = coeff;
      this.physicalEntity = phyEnt;
    }
  
    public JSONObject expandedJSON(OrganismComposition src) {
      JsonHelper o = new JsonHelper(src);
      if (stoichiometricCoefficient != null) o.add("c", stoichiometricCoefficient);
      if (physicalEntity != null) o.add("on", physicalEntity.toString()); // do not resolve the physical entity as this is always supposed to be a reference to the entity closely in the datastructures.
      return o.getJSON();
    }
  }
  
  