// ******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2024.
   //
   // This file is part of Force Field X.
   //
   // Force Field X is free software; you can redistribute it and/or modify it
  // under the terms of the GNU General Public License version 3 as published by
  // the Free Software Foundation.
  //
  // Force Field X 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
  // Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple
  // Place, Suite 330, Boston, MA 02111-1307 USA
  //
  // Linking this library statically or dynamically with other modules is making a
  // combined work based on this library. Thus, the terms and conditions of the
  // GNU General Public License cover the whole combination.
  //
  // As a special exception, the copyright holders of this library give you
  // permission to link this library with independent modules to produce an
  // executable, regardless of the license terms of these independent modules, and
  // to copy and distribute the resulting executable under terms of your choice,
  // provided that you also meet, for each linked independent module, the terms
  // and conditions of the license of that module. An independent module is a
  // module which is not derived from or based on this library. If you modify this
  // library, you may extend this exception to your version of the library, but
  // you are not obligated to do so. If you do not wish to do so, delete this
  // exception statement from your version.
  //
  // ******************************************************************************
  package ffx.xray.parsers;
  
  import static org.junit.Assert.assertEquals;
  import static org.junit.Assert.assertNotNull;
  import static org.junit.Assert.assertTrue;
  
  import ffx.algorithms.misc.AlgorithmsTest;
  import ffx.crystal.Crystal;
  import ffx.crystal.HKL;
  import ffx.crystal.ReflectionList;
  import ffx.crystal.Resolution;
  import ffx.utilities.Keyword;
  import ffx.xray.DiffractionRefinementData;
  
  import java.io.File;
  
  import org.apache.commons.configuration2.CompositeConfiguration;
  import org.junit.Test;
  
  /**
   * Test the MTZ Filter.
   *
   * @author Timothy D. Fenn
   */
  public class MTZFilterTest extends AlgorithmsTest {
  
    private final File mtzFile = getResourceFile("2DRM.mtz");
    // Load any properties associated with it
    private final CompositeConfiguration properties = Keyword.loadProperties(mtzFile);
    // set up the crystal data
    private final Crystal crystal = new Crystal(29.97, 37.86, 44.51, 90.28, 90.11, 90.64, "P1");
    private final Resolution resolution = new Resolution(1.30);
    private final ReflectionList reflectionList = new ReflectionList(crystal, resolution);
    private final DiffractionRefinementData refinementData =
        new DiffractionRefinementData(properties, reflectionList);
  
    @Test
    public void testMTZHKL() {
      MTZFilter mtzFilter = new MTZFilter();
      assertTrue(
          "mtz file errors", mtzFilter.readFile(mtzFile, reflectionList, refinementData, null));
      HKL hkl = reflectionList.getHKL(-10, 1, 1);
      assertEquals("-10 1 1 FP value", 229.90, refinementData.getF(hkl.getIndex()), 0.02);
      assertEquals("-10 1 1 SIGFP value", 2.50, refinementData.getSigF(hkl.getIndex()), 0.02);
      assertEquals("-10 1 1 FREE value", 1, refinementData.getFreeR(hkl.getIndex()));
      hkl = reflectionList.getHKL(-10, 1, 10);
      assertEquals(
          "-10 1 10 FP value should be NaN", Double.NaN, refinementData.getF(hkl.getIndex()), 0.1);
      assertEquals(
          "-10 1 10 SIGFP value should be NaN", Double.NaN, refinementData.getSigF(hkl.getIndex()), 0.1);
    }
  
    @Test
    public void testMTZParams() {
      MTZFilter mtzFilter = new MTZFilter();
      assertTrue(
          "mtz file should be read in without errors",
          mtzFilter.readFile(mtzFile, reflectionList, refinementData, null));
      assertEquals("mtz file number of columns", 6, mtzFilter.getnColumns());
      assertEquals("mtz file number of reflections", 48115, mtzFilter.getnReflections());
      assertEquals("mtz file space group number", 1, mtzFilter.getSpaceGroupNum());
    }
 
   @Test
   public void testMTZReadFile() {
     MTZFilter mtzFilter = new MTZFilter();
     assertTrue(
         "mtz file should be read in without errors",
         mtzFilter.readFile(mtzFile, reflectionList, refinementData, null));
   }
 
   @Test
   public void testMTZReflectionList() {
     MTZFilter mtzFilter = new MTZFilter();
     ReflectionList tmp = mtzFilter.getReflectionList(mtzFile);
     assertNotNull("mtz file should return a reflection list", tmp);
     assertEquals("reflection list space group", 1, tmp.spaceGroup.number);
     assertEquals("reflection list cell dimension", 29.969, tmp.crystal.a, 0.01);
     assertEquals("reflection list resolution", 1.30, tmp.resolution.resolutionLimit(), 0.01);
   }
 }