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.mechanisminspection;
  
  import com.fasterxml.jackson.annotation.JsonProperty;
  import com.fasterxml.jackson.databind.ObjectMapper;
  
  import java.io.File;
  import java.io.IOException;
  import java.io.InputStream;
  import java.util.List;
  
  public class BlacklistedInchisCorpus {
    private static final String FILE_PATH = "blacklisted_inchis.json";
    private final Class INSTANCE_CLASS_LOADER = getClass();
    private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
  
    @JsonProperty("blacklist_inchis")
    private List<BlacklistedInchi> blacklistedInchis;
  
    public List<BlacklistedInchi> getInchis() {
      return blacklistedInchis;
    }
  
    public void setInchis(List<BlacklistedInchi> inchis) {
      this.blacklistedInchis = inchis;
    }
  
    public BlacklistedInchisCorpus() {}
  
    public void loadCorpus() throws IOException {
      InputStream inputStream = INSTANCE_CLASS_LOADER.getResourceAsStream(FILE_PATH);
      BlacklistedInchisCorpus corpus = OBJECT_MAPPER.readValue(inputStream, BlacklistedInchisCorpus.class);
      setInchis(corpus.getInchis());
    }
  
    /**
     * This function renames a given inchi to the correct one if the inchi matches the busted inchi list.
     * @param inchi The inchi to compare against
     * @return The renamed inchi if it is busted. Else, return the input back.
     */
    public String renameInchiIfFoundInBlacklist(String inchi) {
      if (blacklistedInchis != null) {
        for (BlacklistedInchi blacklistedInchi : blacklistedInchis) {
          if (inchi.equals(blacklistedInchi.getWrong_inchi())) {
            return blacklistedInchi.getCorrect_inchi();
          }
        }
      }
      return inchi;
    }
  }
  