/*************************************************************************
* *
* 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();
}
}