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.NXT;
  import java.util.Set;
  import java.util.HashSet;
  import act.installer.metacyc.OrganismComposition;
  import act.installer.metacyc.JsonHelper;
  import org.json.JSONObject;
  
  public class Complex extends BPElement {
    Set<Resource> componentStoichiometry;
    Set<Resource> components;
  
    public Complex(BPElement basics, Set<Resource> stoi, Set<Resource> comp) {
      super(basics);
      this.componentStoichiometry = stoi;
      this.components = comp;
    }
  
    @Override
    public Set<Resource> field(NXT typ) {
      Set<Resource> s = new HashSet<Resource>();
      if (typ == NXT.components) {
        s.addAll(this.components);
      }
      return s;
    }
  
    public JSONObject expandedJSON(OrganismComposition src) {
      JsonHelper o = new JsonHelper(src);
      o.add("name", super.standardName); // from BPElement
      if (components != null)
        for (BPElement c : src.resolve(components))
          o.add("component", c.expandedJSON(src));
      if (componentStoichiometry != null) {
        int pre = "R:http://biocyc.org/biopax/biopax-level3".length();
        String str = "";
        for (BPElement s : src.resolve(componentStoichiometry)) {
          JSONObject st = s.expandedJSON(src);
          str += (str.length()==0 ? "" : " + ") + st.get("c") + " x " + ((String)st.get("on")).substring(pre);
        }
        o.add("multiplicity", str);
      }
      return o.getJSON();
    }
  }
  
  
  