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.cofactorremoval;
  
  import com.fasterxml.jackson.annotation.JsonProperty;
  import com.fasterxml.jackson.databind.ObjectMapper;
  
  import java.io.IOException;
  import java.io.InputStream;
  import java.util.HashMap;
  import java.util.List;
  import java.util.Map;
  
  public class CofactorsCorpus {
    private static final String COFACTORS_FILE_PATH = "cofactors.json";
    private final Class INSTANCE_CLASS_LOADER = getClass();
    private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
    private Map<String, String> inchiToName = new HashMap<>();
    private Map<String, Integer> inchiToRank = new HashMap<>();
  
    @JsonProperty("cofactors")
    private List<Cofactor> cofactors;
  
    public List<Cofactor> getCofactors() {
      return cofactors;
    }
  
    public void setCofactors(List<Cofactor> cofactors) {
      this.cofactors = cofactors;
    }
  
    public CofactorsCorpus() {}
  
    public void loadCorpus() throws IOException {
      InputStream cofactorsStream = INSTANCE_CLASS_LOADER.getResourceAsStream(COFACTORS_FILE_PATH);
      CofactorsCorpus corpus = OBJECT_MAPPER.readValue(cofactorsStream, CofactorsCorpus.class);
  
      this.cofactors = corpus.getCofactors();
      for (Cofactor cofactor : cofactors) {
        inchiToName.put(cofactor.getInchi(), cofactor.getName());
        inchiToRank.put(cofactor.getInchi(), cofactor.getRank());
      }
    }
  
    public Map<String, String> getInchiToName() {
      return inchiToName;
    }
  
    public Map<String, Integer> getInchiToRank() {
      return inchiToRank;
    }
  }
  