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.struc.Molecule;
  import com.act.biointerpretation.sars.CharacterizedGroup;
  import com.act.biointerpretation.sars.Sar;
  import com.act.biointerpretation.sars.SerializableReactor;
  import org.apache.logging.log4j.LogManager;
  import org.apache.logging.log4j.Logger;
  
  import java.util.ArrayList;
  import java.util.Arrays;
  import java.util.List;
  
  public class SingleSubstrateSarExpander extends L2Expander {
  
    private static final Logger LOGGER = LogManager.getFormatterLogger(SingleSubstrateSarExpander.class);
  
    final Iterable<CharacterizedGroup> sarGroups;
    final Iterable<Molecule> substrates;
  
    public SingleSubstrateSarExpander(Iterable<CharacterizedGroup> sarGroups,
                                      Iterable<Molecule> substrates,
                                      PredictionGenerator generator) {
      super(generator);
      this.sarGroups = sarGroups;
      this.substrates = substrates;
    }
  
    @Override
    public Iterable<PredictionSeed> getPredictionSeeds() {
  
      List<PredictionSeed> result = new ArrayList<>();
  
      for (CharacterizedGroup sarGroup : sarGroups) {
        List<Sar> sars = sarGroup.getSars();
        SerializableReactor reactor = sarGroup.getReactor();
  
        for (Molecule mol : substrates) {
          List<Molecule> singleSubstrateContainer = Arrays.asList(mol);
  
          result.add(new PredictionSeed(sarGroup.getGroupName(), singleSubstrateContainer, reactor, sars));
        }
  
      }
      return result;
    }
  }
  