/*************************************************************************
* *
* 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 act.server.MongoDB;
import act.shared.Reaction;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import java.util.ArrayList;
import java.util.List;
import java.util.Set;
import java.util.function.Function;
public class ReactionsTransformer implements Function<L2Prediction, L2Prediction> {
private static final Logger LOGGER = LogManager.getFormatterLogger(ReactionsTransformer.class);
private final MongoDB mongoDB;
public ReactionsTransformer(MongoDB mongoDB) {
this.mongoDB = mongoDB;
}
/**
* Looks up prediction in reactions DB, and dds any reactions found in the DB that match all substrates
* and products of the prediction.
*
* @param prediction The prediction to be tested.
* @return The modified prediction.
*/
public L2Prediction apply(L2Prediction prediction) {
// Return unmodified prediction if there are no substrate ids or no product ids, or if some
// of the substrate or product inchis were not found in the DB.
if (prediction.getSubstrateIds().isEmpty() ||
prediction.getProductIds().isEmpty() ||
prediction.getSubstrateIds().size() < prediction.getSubstrates().size() ||
prediction.getProductIds().size() < prediction.getProducts().size()) {
return prediction;
}
// Get reactions that match all substrates and products.
List<Long> substrateIds = prediction.getSubstrateIds();
List<Long> productIds = prediction.getProductIds();
List<Reaction> reactionsFromDB = mongoDB.getRxnsWithAll(substrateIds, productIds);
// Bin reactions based on whether they match the prediction RO
List<Long> reactionsRoMatch = new ArrayList<Long>();
List<Long> reactionsNoRoMatch = new ArrayList<Long>();
for (Reaction reaction : reactionsFromDB) {
if (reactionMatchesRo(reaction, prediction.getProjectorName())) {
reactionsRoMatch.add(new Long(reaction.getUUID()));
} else {
reactionsNoRoMatch.add(new Long(reaction.getUUID()));
}
}
// Add reaction lists to prediction and return
prediction.setReactionsRoMatch(reactionsRoMatch);
prediction.setReactionsNoRoMatch(reactionsNoRoMatch);
return prediction;
}
/**
* Checks if a Reaction has a given Ro among its mechanistic validator results
*
* @param roIdString The RO id to look for
* @param reaction The Reaction to look in
* @return True if the given RO ID is found
*/
private boolean reactionMatchesRo(Reaction reaction, String roIdString) {
if (reaction.getMechanisticValidatorResult() != null) {
Set<String> validatorResults = reaction.getMechanisticValidatorResult().keySet();
return validatorResults.contains(roIdString);
} else {
return false; // Consider mismatch if there are no validator results at all.
}
}
}