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.BufferedWriter;
  import java.io.File;
  import java.io.FileWriter;
  import java.io.IOException;
  import java.util.ArrayList;
  import java.util.Iterator;
  import java.util.List;
  
  public class SarCorpus implements Iterable<CharacterizedGroup> {
  
    private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
  
    static {
      OBJECT_MAPPER.enable(SerializationFeature.INDENT_OUTPUT);
    }
  
    @JsonProperty
    List<CharacterizedGroup> characterizedGroups;
  
    public SarCorpus() {
      characterizedGroups = new ArrayList<>();
    }
  
    public void addCharacterizedGroup(CharacterizedGroup group) {
      characterizedGroups.add(group);
    }
  
    public Integer size() {
      return characterizedGroups.size();
    }
  
    public void printToJsonFile(File outputFile) throws IOException {
      try (BufferedWriter predictionWriter = new BufferedWriter(new FileWriter(outputFile))) {
        OBJECT_MAPPER.writeValue(predictionWriter, this);
      }
    }
  
    /**
     * Read a sar corpus from file.
     *
     * @param corpusFile The file to read.
     * @return The SarCorpus.
     * @throws IOException
     */
    public static SarCorpus readCorpusFromJsonFile(File corpusFile) throws IOException {
      return OBJECT_MAPPER.readValue(corpusFile, SarCorpus.class);
    }
  
    /**
     * Returns an iterator over the CharacterizedGroups generated by this corpus.
     *
     * @return The iterator.
     */
    @Override
    public Iterator<CharacterizedGroup> iterator() {
      return characterizedGroups.iterator();
    }
  }
  