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.processes;
  
  import act.installer.metacyc.BPElement;
  import act.installer.metacyc.JsonHelper;
  import act.installer.metacyc.NXT;
  import act.installer.metacyc.OrganismComposition;
  import act.installer.metacyc.Resource;
  import act.installer.metacyc.annotations.Stoichiometry;
  import org.biopax.paxtools.model.level3.ConversionDirectionType;
  import org.json.JSONObject;
  
  import java.util.HashMap;
  import java.util.HashSet;
  import java.util.Map;
  import java.util.Set;
  
  public class Conversion extends BPElement {
    public enum TYPE { BIOCHEMICAL_RXN, TRANSPORT, TRANSPORT_W_BIOCHEMICAL_RXN, COMPLEX_ASSEMBLY };
    TYPE type;
    public TYPE getTyp() { return this.type; }
    Set<Resource> left, right;
    Set<Resource> participantStoichiometry;
  
    ConversionDirectionType dir; // REVERSIBLE, LEFT-TO-RIGHT or RIGHT-TO-LEFT: If a reaction will run in a single direction under all biological contexts then it is considered irreversible and has a direction. Otherwise it is reversible. MOSTLY not set.
    Boolean spontaneous; // MOSTLY not set
    Set<String> ecNumber;
    Set<Resource> deltaG;
  
    public Set<String> getEc() { return this.ecNumber; }
    public Boolean getSpontaneous() { return this.spontaneous; }
    public ConversionDirectionType getDir() { return this.dir; }
  
    public Conversion(BPElement basics, Set<Resource> l, Set<Resource> r, Set<Resource> stoic, ConversionDirectionType dir, Boolean spont, Set<String> ec, Set<Resource> dG, TYPE t) {
      super(basics);
      this.left = l;
      this.right = r;
      this.participantStoichiometry = stoic;
      this.dir = dir;
      this.spontaneous = spont;
      this.ecNumber = ec;
      this.deltaG = dG;
      this.type = t;
    }
  
    @Override
    public Set<Resource> field(NXT typ) {
      Set<Resource> s = new HashSet<Resource>();
      if (typ == NXT.left) {
        s.addAll(this.left);
      } else if (typ == NXT.right) {
        s.addAll(this.right);
      }
      return s;
    }
  
    public String getStoichiometry(OrganismComposition src) {
      if (participantStoichiometry == null)
        return null;
  
      int pre = "R:http://biocyc.org/biopax/biopax-level3".length();
      String str = "";
      for (BPElement s : src.resolve(participantStoichiometry)) {
        Stoichiometry stoic = (Stoichiometry) s;
        Float coeff = stoic.getCoefficient();
        BPElement participant = src.resolve(stoic.getPhysicalEntity());
        str += (str.length()==0 ? "" : ", ") + coeff + " x " + participant.getStandardName();
        // the participant is either a SmallMolecule, Protein, Complex, Rna
        // JSONObject st = s.expandedJSON(src);
        // str += (str.length()==0 ? "" : " + ") + st.get("c") + " x " + ((String)st.get("on")).substring(pre);
      }
      return str;
    }
  
    /**
     * Produces a map of participant ids to corresponding Stoichiometry objects, using the specified OrganismComposition
     * to perform Metacyc entity resolution.
     * @param src The OrganismComposition to use when resolving this Conversion's participant stoichiometry entries.
     * @return A map of participant ids to Stoichiometry objects.
     */
    public Map<Resource, Stoichiometry> getRawStoichiometry(OrganismComposition src) {
      if (participantStoichiometry == null) {
        return null;
      }
  
      // TODO: would it be better to store the raw stoichiometry objects rather than resolving at call time?
      Map<Resource, Stoichiometry> stoichiometries = new HashMap<>(participantStoichiometry.size());
      for (BPElement s : src.resolve(participantStoichiometry)) {
        Stoichiometry stoic = (Stoichiometry) s;
        BPElement participant = src.resolve(stoic.getPhysicalEntity());
        stoichiometries.put(participant.getID(), stoic);
      }
      return stoichiometries;
    }
  
    public JSONObject expandedJSON(OrganismComposition src) {
      JsonHelper o = new JsonHelper(src);
      if (type != null) o.add("type", type.toString());
      if (dir != null) o.add("dir", dir.toString());
      if (left != null)
        for (BPElement l : src.resolve(left))
          o.add("left", l.expandedJSON(src));
      if (right != null)
        for (BPElement r : src.resolve(right))
          o.add("right", r.expandedJSON(src));
      if (participantStoichiometry != null) o.add("stoichiometry", getStoichiometry(src));
      if (spontaneous != null) o.add("spontaneous", spontaneous);
      if (ecNumber != null) o.add("ec", ecNumber.toString());
      if (deltaG != null)
        for (BPElement d : src.resolve(deltaG))
          o.add("deltaG", d.expandedJSON(src));
      return o.getJSON();
    }
  }
  