/*************************************************************************
* *
* 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.Chemical;
import java.util.function.Function;
public class ChemicalsTransformer implements Function<L2Prediction, L2Prediction> {
private MongoDB mongoDB;
public ChemicalsTransformer(MongoDB mongoDB) {
this.mongoDB = mongoDB;
}
/**
* Filters prediction by looking up its substrates and products in DB, and adding info about any entries found.
* TODO: If performance becomes an issue, cache an inchi->ID map to avoid redundant database queries.
*
* @param prediction The prediction to be tested.
* @return The modified prediction.
*/
public L2Prediction apply(L2Prediction prediction) {
// Add product chemical ids.
for (L2PredictionChemical predictedChemical : prediction.getProducts()) {
String inchi = predictedChemical.getInchi();
Chemical product = mongoDB.getChemicalFromInChI(inchi);
if (product != null) {
predictedChemical.setId(product.getUuid());
predictedChemical.setName(product.getFirstName());
}
}
// Add substrate chemical ids.
for (L2PredictionChemical predictedChemical : prediction.getSubstrates()) {
String inchi = predictedChemical.getInchi();
Chemical substrate = mongoDB.getChemicalFromInChI(inchi);
if (substrate != null) {
predictedChemical.setId(substrate.getUuid());
predictedChemical.setName(substrate.getFirstName());
}
}
return prediction;
}
}