Java tutorial
/** * Title: Force Field X. * * Description: Force Field X - Software for Molecular Biophysics. * * Copyright: Copyright (c) Michael J. Schnieders 2001-2015. * * 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; import java.io.File; import java.io.IOException; import java.nio.file.Path; import java.nio.file.Paths; import java.util.logging.Logger; import static org.apache.commons.io.FilenameUtils.isExtension; import static org.apache.commons.io.FilenameUtils.removeExtension; import ffx.potential.MolecularAssembly; /** * <p> * DiffractionFile class.</p> * * @author Timothy D. Fenn * */ public class DiffractionFile { private static final Logger logger = Logger.getLogger(DiffractionFile.class.getName()); protected final String filename; protected final double weight; protected final boolean neutron; protected final DiffractionFileFilter diffractionfilter; /** * read in a diffraction file, weight set to 1.0 and neutron value of false * * @param filename file name to read in */ public DiffractionFile(String filename) { this(filename, 1.0, false); } /** * read in a diffraction file, neutron value set to false * * @param filename file name to read in * @param weight the weight of the data */ public DiffractionFile(String filename, double weight) { this(filename, weight, false); } /** * read in a diffraction file * * @param filename file name to read in * @param weight the weight of the data * @param neutron if true, this is a neutron data set */ public DiffractionFile(String filename, double weight, boolean neutron) { File tmp = new File(filename); if (!tmp.exists()) { logger.severe(" Data file: " + filename + " not found!"); } if (isExtension(filename, "mtz")) { diffractionfilter = new MTZFilter(); } else if (isExtension(filename, new String[] { "cif", "ent", "sf" })) { diffractionfilter = new CIFFilter(); } else if (isExtension(filename, new String[] { "cns", "hkl" })) { diffractionfilter = new CNSFilter(); } else { diffractionfilter = null; } if (diffractionfilter == null) { logger.severe( "input data file format not recognized!\n Please use an appropriate file extension: [MTZ: mtz] [CIF: cif, ent, sf] [CNS: cns, hkl] to identify your data file type!"); } this.filename = filename; this.weight = weight; this.neutron = neutron; } /** * read in a diffraction file based on the molecular assembly filename, * using a weight of 1.0 and neutron value of false * * @param assembly {@link ffx.potential.MolecularAssembly} from which a * filename will be determined */ public DiffractionFile(MolecularAssembly assembly[]) { this(assembly[0], 1.0, false); } /** * <p> * Constructor for DiffractionFile.</p> * * @param assembly an array of {@link ffx.potential.MolecularAssembly} * objects. * @param weight a double. */ public DiffractionFile(MolecularAssembly assembly[], double weight) { this(assembly[0], weight, false); } /** * <p> * Constructor for DiffractionFile.</p> * * @param assembly an array of {@link ffx.potential.MolecularAssembly} * objects. * @param weight a double. * @param neutron a boolean. */ public DiffractionFile(MolecularAssembly assembly[], double weight, boolean neutron) { this(assembly[0], weight, neutron); } /** * read in a diffraction file based on the molecular assembly filename, * using a weight of 1.0 and neutron value of false * * @param assembly {@link ffx.potential.MolecularAssembly} from which a * filename will be determined */ public DiffractionFile(MolecularAssembly assembly) { this(assembly, 1.0, false); } /** * read in a diffraction file based on the molecular assembly filename, * using a neutron value of false * * @param assembly {@link ffx.potential.MolecularAssembly} from which a * filename will be determined * @param weight the weight of the data */ public DiffractionFile(MolecularAssembly assembly, double weight) { this(assembly, weight, false); } /** * read in a diffraction file based on the molecular assembly filename, * using a weight of 1.0 and neutron value of false * * @param assembly {@link ffx.potential.MolecularAssembly} from which a * filename will be determined * @param weight the weight of the data * @param neutron if true, this is a neutron data set */ public DiffractionFile(MolecularAssembly assembly, double weight, boolean neutron) { String name = removeExtension(assembly.getFile().getPath()); File tmp = new File(name + ".mtz"); if (tmp.exists()) { //logger.info("\n Data file: " + tmp.getName()); diffractionfilter = new MTZFilter(); } else { tmp = new File(name + ".cif"); if (tmp.exists()) { //logger.info("\n Data file: " + tmp.getName()); diffractionfilter = new CIFFilter(); } else { tmp = new File(name + ".ent"); if (tmp.exists()) { //logger.info("\n Data file: " + tmp.getName()); diffractionfilter = new CIFFilter(); } else { tmp = new File(name + ".sf"); if (tmp.exists()) { //logger.info("\n Data file: " + tmp.getName()); diffractionfilter = new CIFFilter(); } else { tmp = new File(name + ".cns"); if (tmp.exists()) { //logger.info("\n Data file: " + tmp.getName()); diffractionfilter = new CNSFilter(); } else { tmp = new File(name + ".hkl"); if (tmp.exists()) { //logger.info("\n Data file: " + tmp.getName()); diffractionfilter = new CNSFilter(); } else { logger.severe("no input data found!"); diffractionfilter = null; } } } } } } String filenameHolder; // Compiler complains if I set this.filename directly. try { Path filepath = Paths.get(tmp.getCanonicalPath()); Path pwdPath = Paths.get(new File("").getCanonicalPath()); filenameHolder = pwdPath.relativize(filepath).toString(); } catch (IOException ex) { logger.warning( " Relative path to provided data file could not be resolved: using data file name instead."); filenameHolder = tmp.getName(); } this.filename = filenameHolder; this.weight = weight; this.neutron = neutron; } /** * return the weight of this dataset * * @return weight wA */ public double getWeight() { return weight; } /** * is this a neutron dataset? * * @return true if neutron */ public boolean isNeutron() { return neutron; } }