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