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.lcms;
  
  import com.act.utils.TSVParser;
  import org.apache.commons.lang3.tuple.Pair;
  import org.junit.Test;
  
  import java.io.InputStream;
  import java.util.List;
  import java.util.Map;
  
  import static org.junit.Assert.assertEquals;
  
  public class MassCalculator2Test {
    public static final String TEST_CASE_RESOURCE = "mass_calculator_test_cases.txt";
    public static final Double ACCEPTABLE_MASS_DELTA_THRESHOLD = 0.00054858; // one electron's mass in Daltons.
  
    @Test
    public void testMC2MatchesMC1WithinMeaningfulTolerance() throws Exception {
      List<Map<String, String>> rows;
      try (InputStream is = MassCalculator2Test.class.getResourceAsStream(TEST_CASE_RESOURCE)) {
        TSVParser parser = new TSVParser();
        parser.parse(is);
        rows = parser.getResults();
      }
  
      int testCase = 1;
      for (Map<String, String> row : rows) {
        String inchi = row.get("InChI");
        Double expectedMass = Double.valueOf(row.get("Mass"));
        Integer expectedCharge = Integer.valueOf(row.get("Charge"));
  
        Pair<Double, Integer> actualMassAndCharge = MassCalculator2.calculateMassAndCharge(inchi);
  
  
        Double threshold = ACCEPTABLE_MASS_DELTA_THRESHOLD;
        if (actualMassAndCharge.getRight() < 0) {
          // Widen the window for added electrons' masses included in Chemaxon's calculations for negative ions.
          threshold += ACCEPTABLE_MASS_DELTA_THRESHOLD * -1.0 * actualMassAndCharge.getRight().doubleValue();
        } else if (actualMassAndCharge.getRight() > 0) {
          // Positively charged molecules have the missing electrons' masses subtracted
          threshold += ACCEPTABLE_MASS_DELTA_THRESHOLD * actualMassAndCharge.getRight().doubleValue();
        }
  
        assertEquals(String.format("Case %d: mass for %s is within delta threshold: %.6f vs. %.6f",
            testCase, inchi, expectedMass, actualMassAndCharge.getLeft()),
            expectedMass, actualMassAndCharge.getLeft(), threshold);
        assertEquals(String.format("Case %d: charge %s matches expected", testCase, inchi),
            expectedCharge, actualMassAndCharge.getRight());
        testCase++;
      }
    }
  }
  