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.mmtf;
022
023import java.io.IOException;
024import java.io.InputStream;
025import java.io.OutputStream;
026import java.nio.file.Path;
027
028import org.biojava.nbio.structure.Structure;
029import org.rcsb.mmtf.decoder.GenericDecoder;
030import org.rcsb.mmtf.decoder.StructureDataToAdapter;
031import org.rcsb.mmtf.decoder.ReaderUtils;
032import org.rcsb.mmtf.encoder.AdapterToStructureData;
033import org.rcsb.mmtf.encoder.WriterUtils;
034
035/**
036 * A class of functions for reading and writing Biojava structures using MMTF
037 * @author Anthony Bradley
038 *
039 */
040public class MmtfActions {
041
042        /**
043         * Get a Structure object from a mmtf file.
044         * @param filePath the mmtf file
045         * @return a Structure object relating to the input byte array.
046         * @throws IOException
047         */
048        public static Structure readFromFile(Path filePath) throws IOException {
049                // Get the reader - this is the bit that people need to implement.
050                MmtfStructureReader mmtfStructureReader = new MmtfStructureReader();
051                // Do the inflation
052                new StructureDataToAdapter(new GenericDecoder(ReaderUtils.getDataFromFile(filePath)), mmtfStructureReader);
053                // Get the structue
054                return mmtfStructureReader.getStructure();
055        }
056
057        /**
058         * Write a Structure object to a file.
059         * @param structure the Structure to write
060         * @param path the file to write
061         * @throws IOException
062         */
063        public static void writeToFile(Structure structure, Path path) throws IOException {
064                // Set up this writer
065                AdapterToStructureData writerToEncoder = new AdapterToStructureData();
066                // Get the writer - this is what people implement
067                new MmtfStructureWriter(structure, writerToEncoder);
068                // Now write this data to file
069                WriterUtils.writeDataToFile(writerToEncoder, path);
070        }
071
072        /**
073         * Write a Structure object to an {@link OutputStream}
074         * @param structure the Structure to write
075         * @param outputStream the {@link OutputStream} to write to
076         * @throws IOException an error transferring the byte[]
077         */
078        public static void writeToOutputStream(Structure structure, OutputStream outputStream) throws IOException{
079                // Set up this writer
080                AdapterToStructureData writerToEncoder = new AdapterToStructureData();
081                // Get the writer - this is what people implement
082                new MmtfStructureWriter(structure, writerToEncoder);
083                // Now write this data to file
084                byte[] outputBytes = WriterUtils.getDataAsByteArr(writerToEncoder);
085                outputStream.write(outputBytes,0,outputBytes.length);
086        }
087
088
089        /**
090         * Get a Biojava structure from the mmtf REST service.
091         * @param pdbId the PDB code of the required structure
092         * @return a Structure object relating to the input byte array
093         * @throws IOException
094         */
095        public static Structure readFromWeb(String pdbId) throws IOException {
096                // Get the reader - this is the bit that people need to implement.
097                MmtfStructureReader mmtfStructureReader = new MmtfStructureReader();
098                // Do the inflation
099                new StructureDataToAdapter(new GenericDecoder(ReaderUtils.getDataFromUrl(pdbId)), mmtfStructureReader);
100                // Get the structue
101                return mmtfStructureReader.getStructure();
102        }
103
104        /**
105         * Read a Biojava structure from an {@link InputStream}
106         * @param inStream the {@link InputStream} to read from
107         * @return the parsed {@link Structure}
108         * @throws IOException
109         */
110        public static Structure readFromInputStream(InputStream inStream) throws IOException {
111                // Get the reader - this is the bit that people need to implement.
112                MmtfStructureReader mmtfStructureReader = new MmtfStructureReader();
113                // Do the inflation
114                new StructureDataToAdapter(new GenericDecoder(ReaderUtils.getDataFromInputStream(inStream)), mmtfStructureReader);
115                // Get the structue
116                return mmtfStructureReader.getStructure();
117        }
118}