001/*
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 */
021package org.biojava.nbio.structure.io;
022
023import java.io.IOException;
024import java.io.InputStream;
025
026import org.biojava.nbio.structure.Structure;
027import org.biojava.nbio.structure.align.util.UserConfiguration;
028import org.biojava.nbio.structure.io.mmtf.MmtfActions;
029
030/**
031 * A class to read MMTF files and cache them locally.
032 * @author Anthony Bradley
033 *
034 */
035public class MMTFFileReader extends LocalPDBDirectory {
036
037
038        public static final String[] MMTF_SPLIT_DIR    = new String[]{"data","structures","divided" ,"mmtf"};
039        public static final String[] MMTF_OBSOLETE_DIR = new String[]{"data","structures","obsolete","mmtf"};
040
041        public static void main(String[] args) throws Exception {
042                MMTFFileReader reader = new MMTFFileReader();
043                FileParsingParameters params = new FileParsingParameters();
044                reader.setFileParsingParameters(params);
045                Structure struc = reader.getStructureById("1m4x");
046                System.out.println(struc);
047        }
048
049        /**
050         * Constructs a new {@link MMTFFileReader}, initializing the extensions member variable.
051         * The path is initialized in the same way as {@link UserConfiguration},
052         * i.e. to system property/environment variable {@link UserConfiguration#PDB_DIR}.
053         * Both autoFetch and splitDir are initialized to false
054         */
055        public MMTFFileReader() {
056                this(null);
057        }
058
059        /**
060         * Constructs a new {@link MMTFFileReader}, initializing the extensions member variable.
061         * The path is initialized to the given path, both autoFetch and splitDir are initialized to false.
062         */
063        public MMTFFileReader(String path) {
064                super(path);
065                addExtension(".mmtf");
066                addExtension(".mmtf.gz");
067                }
068
069        @Override
070        public Structure getStructure(InputStream inStream) throws IOException {
071                return MmtfActions.readFromInputStream(inStream);
072        }
073
074        @Override
075        protected String getFilename(String pdbId) {
076                return pdbId.toLowerCase()+".mmtf.gz";
077        }
078
079        @Override
080        protected String[] getSplitDirPath() {
081                return MMTF_SPLIT_DIR;
082        }
083
084        @Override
085        protected String[] getObsoleteDirPath() {
086                return MMTF_OBSOLETE_DIR;
087        }
088
089
090}