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.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;
    }
  }
  