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 com.act.biointerpretation.networkanalysis;
  
  import com.act.lcms.v2.ChemicalFormula;
  import com.act.lcms.v2.Metabolite;
  import com.act.lcms.v2.MolecularStructure;
  import com.fasterxml.jackson.annotation.JsonCreator;
  import com.fasterxml.jackson.annotation.JsonIgnore;
  import com.fasterxml.jackson.annotation.JsonProperty;
  
  import java.util.Optional;
  
  /**
   * Represents a metabolite in the metabolite network.
   * For now this class only stores an inchi, but in the future it can represent multiple levels of abstraction: a
   * structure in any format, a chemical formula, or only a mass.
   * TODO: Implement full serialization on LcmsMetabolite, and replace every use of InchiMetabolite with LcmsMetabolite.
   */
  public class InchiMetabolite implements Metabolite {
  
    @JsonProperty("inchi")
    private String inchi;
  
    private MolecularStructure structure;
  
    @JsonCreator
    public InchiMetabolite(@JsonProperty("inchi") String inchi) {
      this.inchi = inchi;
      this.structure = new InchiStructure(inchi);
    }
  
    @JsonIgnore
    public String getInchi() {
      return inchi;
    }
  
    @JsonIgnore
    @Override
    public Optional<MolecularStructure> getStructure() {
      return Optional.of(structure);
    }
  
    @JsonIgnore
    @Override
    public Optional<ChemicalFormula> getFormula() {
      return Optional.empty();
    }
  
    @JsonIgnore
    @Override
    public Double getMonoIsotopicMass() {
      return structure.getMonoIsotopicMass();
    }
  }
  