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 org.biojava.nbio.structure.Structure;
024import org.biojava.nbio.structure.StructureException;
025
026import java.io.IOException;
027
028/** A class that can provide a protein structure object from somewhere.
029 *
030 * @author Andreas Prlic
031 * @since 3.2
032 */
033public interface StructureProvider {
034
035        /** get the structure for a PDB ID
036         *
037         * @param pdbId
038         * @return
039         */
040        public Structure getStructureById(String pdbId) throws StructureException,IOException;
041
042        /** get the biological unit for a file
043         *
044         * @param pdbId
045         * @return
046         * @deprecated Better to use {@link StructureIO#getBiologicalAssembly(String)}
047         * or a {@link BioUnitDataProvider}
048         */
049        //public Structure getBiologicalUnit(String pdbId) throws StructureException, IOException;
050
051
052        /** Set the parameters that should be used for file parsing
053         *
054         * @param params FileParsingParameters
055         */
056        public void setFileParsingParameters(FileParsingParameters params);
057
058
059        /** Get the parameters that should be used for file parsing
060         *
061         * @return the FileParsingParameters that are configuring the behavior of the parser
062         */
063        public FileParsingParameters getFileParsingParameters();
064
065
066}