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The protein structure modules of BioJava.
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/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */
package org.biojava.nbio.structure.io.mmtf;

import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.nio.file.Path;

import org.biojava.nbio.structure.Structure;
import org.rcsb.mmtf.decoder.GenericDecoder;
import org.rcsb.mmtf.decoder.StructureDataToAdapter;
import org.rcsb.mmtf.decoder.ReaderUtils;
import org.rcsb.mmtf.encoder.AdapterToStructureData;
import org.rcsb.mmtf.encoder.WriterUtils;

/**
 * A class of functions for reading and writing Biojava structures using MMTF
 * @author Anthony Bradley
 *
 */
public class MmtfActions {

	/**
	 * Get a Structure object from a mmtf file.
	 * @param filePath the mmtf file
	 * @return a Structure object relating to the input byte array.
	 * @throws IOException
	 */
	public static Structure readFromFile(Path filePath) throws IOException {
		// Get the reader - this is the bit that people need to implement.
		MmtfStructureReader mmtfStructureReader = new MmtfStructureReader();
		// Do the inflation
		new StructureDataToAdapter(new GenericDecoder(ReaderUtils.getDataFromFile(filePath)), mmtfStructureReader);
		// Get the structue
		return mmtfStructureReader.getStructure();
	}

	/**
	 * Write a Structure object to a file.
	 * @param structure the Structure to write
	 * @param path the file to write
	 * @throws IOException
	 */
	public static void writeToFile(Structure structure, Path path) throws IOException {
		// Set up this writer
		AdapterToStructureData writerToEncoder = new AdapterToStructureData();
		// Get the writer - this is what people implement
		new MmtfStructureWriter(structure, writerToEncoder);
		// Now write this data to file
		WriterUtils.writeDataToFile(writerToEncoder, path);
	}

	/**
	 * Write a Structure object to an {@link OutputStream}
	 * @param structure the Structure to write
	 * @param outputStream the {@link OutputStream} to write to
	 * @throws IOException an error transferring the byte[]
	 */
	public static void writeToOutputStream(Structure structure, OutputStream outputStream) throws IOException{
		// Set up this writer
		AdapterToStructureData writerToEncoder = new AdapterToStructureData();
		// Get the writer - this is what people implement
		new MmtfStructureWriter(structure, writerToEncoder);
		// Now write this data to file
		byte[] outputBytes = WriterUtils.getDataAsByteArr(writerToEncoder);
		outputStream.write(outputBytes,0,outputBytes.length);
	}

	/**
	 * Read a Biojava structure from an {@link InputStream}
	 * @param inStream the {@link InputStream} to read from
	 * @return the parsed {@link Structure}
	 * @throws IOException
	 */
	public static Structure readFromInputStream(InputStream inStream) throws IOException {
		// Get the reader - this is the bit that people need to implement.
		MmtfStructureReader mmtfStructureReader = new MmtfStructureReader();
		// Do the inflation
		new StructureDataToAdapter(new GenericDecoder(ReaderUtils.getDataFromInputStream(inStream)), mmtfStructureReader);
		// Get the structue
		return mmtfStructureReader.getStructure();
	}
}