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.sars;
  
  import com.fasterxml.jackson.annotation.JsonProperty;
  import com.fasterxml.jackson.databind.ObjectMapper;
  import com.fasterxml.jackson.databind.SerializationFeature;
  
  import java.io.BufferedReader;
  import java.io.BufferedWriter;
  import java.io.File;
  import java.io.FileReader;
  import java.io.FileWriter;
  import java.io.IOException;
  import java.util.ArrayList;
  import java.util.Arrays;
  import java.util.Collection;
  import java.util.Iterator;
  import java.util.List;
  
  /**
   * Represents a corpus of reaction groups. This should serve as the intermediate format between pipelines that group
   * reactions together, i.e. by sequence clustering, RO groups, LibMCS clustering, or any other method,
   * and pipelines that characterize those grouped reactions with SARs and generalized ROs.
   */
  public class ReactionGroupCorpus implements Iterable<ReactionGroup> {
  
    private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
  
    static {
      OBJECT_MAPPER.enable(SerializationFeature.INDENT_OUTPUT);
    }
  
    @JsonProperty
    private List<ReactionGroup> reactionGroups;
  
    public ReactionGroupCorpus() {
      reactionGroups = new ArrayList<>();
    }
  
    public ReactionGroupCorpus(Collection<ReactionGroup> groups) {
      reactionGroups = new ArrayList<>(groups);
    }
  
    @Override
    public Iterator<ReactionGroup> iterator() {
      return reactionGroups.iterator();
    }
  
    public void printToJsonFile(File outputFile) throws IOException {
      try (BufferedWriter writer = new BufferedWriter(new FileWriter(outputFile))) {
        OBJECT_MAPPER.writeValue(writer, this);
      }
    }
  
    public void addGroup(ReactionGroup group) {
      reactionGroups.add(group);
    }
  
    /**
     * Read a ReactionGroupCorpus corpus from file.
     *
     * @param corpusFile The file to read.
     * @return The ReactionGroupCorpus.
     * @throws IOException
     */
    public static ReactionGroupCorpus loadFromJsonFile(File corpusFile) throws IOException {
      return OBJECT_MAPPER.readValue(corpusFile, ReactionGroupCorpus.class);
    }
  
    /**
     * Read a ReactionGroupCorpus from a text file.
     * File should contain DB name on the first line.
     * Thereafter each line should have one group of reactions, written as a tab separated list of reaction IDs
     */
    public static ReactionGroupCorpus loadFromTextFile(File corpusFile) throws IOException {
      ReactionGroupCorpus corpus = new ReactionGroupCorpus();
  
      try (BufferedReader reader = new BufferedReader(new FileReader(corpusFile))) {
        String dbName = reader.readLine();
  
        String line;
        while ((line = reader.readLine()) != null) {
          List<String> fields = Arrays.asList(line.split(","));
          ReactionGroup group = new ReactionGroup(fields.get(0), dbName);
          for (String idString : fields.subList(1, fields.size())) {
            group.addReactionId(Long.parseLong(idString));
          }
          corpus.addGroup(group);
        }
      }
  
      return corpus;
    }
  }
  