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.entities;
  
  import act.installer.metacyc.Resource;
  import act.installer.metacyc.BPElement;
  import act.installer.metacyc.entities.SmallMoleculeRef;
  import act.installer.metacyc.OrganismComposition;
  import act.installer.metacyc.NXT;
  import act.installer.metacyc.JsonHelper;
  import java.util.Set;
  import java.util.HashSet;
  import org.json.JSONObject;
  
  public class SmallMolecule extends BPElement {
    Resource smRef; // entityReference field pointing to a SmallMoleculeRef
    Resource cellularLocation;
  
    public Resource getSMRef() { return this.smRef; }
    public Resource getCellularLocation() { return this.cellularLocation; }
  
    public SmallMolecule(BPElement basics, Resource smRef, Resource loc) {
      super(basics);
      this.smRef = smRef;
      this.cellularLocation = loc;
    }
  
    @Override
    public Set<Resource> field(NXT typ) {
      Set<Resource> s = new HashSet<Resource>();
      if (typ == NXT.ref) {
        s.add(this.smRef);
      }
      return s;
    }
  
    public JSONObject expandedJSON(OrganismComposition src) {
      JsonHelper o = new JsonHelper(src);
      o.add("ref", src.resolve(smRef).expandedJSON(src));
      if (cellularLocation != null)
        o.add("loc", src.resolve(cellularLocation).expandedJSON(src));
      return o.getJSON();
    }
  
  }
  
  