/*************************************************************************
* *
* 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;
}
}