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 org.apache.logging.log4j.LogManager;
  import org.apache.logging.log4j.Logger;
  
  import java.util.List;
  
  public class SarCorpusBuilder {
  
    private static final Logger LOGGER = LogManager.getFormatterLogger(SarCorpusBuilder.class);
  
    private final Iterable<ReactionGroup> reactionGroups;
    private final ReactionGroupCharacterizer characterizer;
  
    public SarCorpusBuilder(Iterable<ReactionGroup> reactionGroups, ReactionGroupCharacterizer characterizer) {
      this.reactionGroups = reactionGroups;
      this.characterizer = characterizer;
    }
  
    public SarCorpus build() {
      SarCorpus corpus = new SarCorpus();
      int counter = 1;
      for (ReactionGroup group : reactionGroups) {
  
        List<CharacterizedGroup> characterizations = characterizer.characterizeGroup(group);
        for (CharacterizedGroup characterization : characterizations) {
          corpus.addCharacterizedGroup(characterization);
        }
  
        LOGGER.info("Processed %d groups, characterized %d so far.", counter, corpus.size());
        counter++;
      }
      return corpus;
    }
  }
  