/*************************************************************************
*                                                                        *
*  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.l2expansion;

import chemaxon.reaction.ReactionException;
import chemaxon.struc.Molecule;
import com.act.biointerpretation.mechanisminspection.Ero;
import com.act.biointerpretation.mechanisminspection.ErosCorpus;
import com.act.biointerpretation.sars.SerializableReactor;
import org.apache.commons.logging.Log;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

/**
 * Carries out the main logic of L2 expansion by applying a set of ROs to a set of substrates.
 */
public class SingleSubstrateRoExpander extends L2Expander {

  private static final Logger LOGGER = LogManager.getFormatterLogger(SingleSubstrateRoExpander.class);
  private static final Integer ONE_SUBSTRATES = 1;

  private ErosCorpus roCorpus;
  private List<Molecule> substrates;

  /**
   * @param roCorpus A corpus of all ros to be tested
   * @param substrates A list of all substrates on which to test the ROs.
   */
  public SingleSubstrateRoExpander(ErosCorpus roCorpus, List<Molecule> substrates, PredictionGenerator generator) {
    super(generator);
    this.roCorpus = roCorpus;
    this.substrates = substrates;
  }

  @Override
  public Iterable<PredictionSeed> getPredictionSeeds() {
    List<PredictionSeed> result = new ArrayList<>();

    // Use only single substrate reactions
    roCorpus.filterCorpusBySubstrateCount(ONE_SUBSTRATES);

    for (Ero ro : roCorpus.getRos()) {
      SerializableReactor reactor;
      try {
        reactor = new SerializableReactor(ro.getReactor(), ro.getId());
      } catch (ReactionException e) {
        LOGGER.info("Skipping ro %d, couldn't get Reactor.", ro.getId());
        continue;
      }

      //iterate over every (substrate, ro) pair
      for (Molecule substrate : substrates) {
        result.add(new PredictionSeed(ro.getId().toString(), Arrays.asList(substrate), reactor, NO_SAR));
      }
    }

    LOGGER.info("Created %d prediction seeds", result.size());
    return result;
  }
}