/*
 *                    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/
 *
 * Created on 16.03.2004
 * @author Andreas Prlic
 *
 *
 */
package org.biojava.nbio.structure.io;


import org.biojava.nbio.structure.Chain;
import org.biojava.nbio.structure.Compound;
import org.biojava.nbio.structure.Group;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.align.util.UserConfiguration;
import java.io.IOException;
import java.io.InputStream;
import java.util.List;

/**
 * <p>
 *  The wrapper class for parsing a PDB file.
 *  </p>
 *
 *
 *  <p>
 *  Several flags can be set for this class
 *  <ul>
 *
 * <li> {@link #setAutoFetch(boolean)} - if the PDB file can not be found locally, should it be fetched
 *  from the PDB ftp servers? (default:false)</li>
 *  <li> Other parameters can be set using the {@link #setFileParsingParameters(FileParsingParameters)}</li>
 *  </ul>
 *  </p>
 *
 *
 *
 *<h2>Example</h2>
 * <p>
 * Q: How can I get a Structure object from a PDB file?
 * </p>
 * <p>
 * A:
 * <pre>
 * public {@link Structure} loadStructure(String pathToPDBFile){
 *      {@link PDBFileReader} pdbreader = new {@link PDBFileReader}();
 *
 *      {@link Structure} structure = null;
 *      try{
 *              structure = pdbreader.getStructure(pathToPDBFile);
 *              System.out.println(structure);
 *      } catch (IOException e) {
 *              e.printStackTrace();
 *      }
 *      return structure;
 * }
 * </pre>
 *
 * Access PDB files from a directory, take care of compressed PDB files
 * <pre>
 * public {@link Structure} loadStructureById() {
 *      String path = "/path/to/PDB/directory/";
 *
 *      {@link PDBFileReader} pdbreader = new {@link PDBFileReader}();
 *      pdbreader.setPath(path);
 *      {@link Structure} structure = null;
 *      try {
 *              structure = pdbreader.getStructureById("5pti");
 *      } catch (IOException e){
 *              e.printStackTrace();
 *      }
 *      return structure;
 *
 * }
 * </pre>
 *
 *
 * @author Andreas Prlic
 *
 */
public class PDBFileReader extends LocalPDBDirectory {

        //private static final Logger logger = LoggerFactory.getLogger(PDBFileReader.class);

        // a list of big pdb files for testing
        //  "1htq",
        //  "1c2w",
        //  "1ffk",
        //  "1giy",
        //  "1j5a",
        //  "1jj2",
        //  "1jzx",
        //  "1jzy",
        //  "1jzz",
        //  "1k01",
        //  "1k73",
        //  "1k8a",
        //  "1k9m",
        //  "1kc8",
        //  "1kd1",
        //  "1kqs",
        //  "1m1k",
        //  "1m90",
        //  "1mkz",
        //  "1ml5",
        //  "1n8r",

        public static final String[] PDB_SPLIT_DIR    = new String[]{"data","structures","divided" ,"pdb"};
        public static final String[] PDB_OBSOLETE_DIR = new String[]{"data","structures","obsolete","pdb"};

        public static void main(String[] args){


                PDBFileReader pdbreader = new PDBFileReader();


                // set the path to cache files
                String property = "java.io.tmpdir";
                String tempdir = System.getProperty(property);
                // tempdir = "/path/to/local/PDB/installation/";
                pdbreader.setPath(tempdir);


                FileParsingParameters params = new FileParsingParameters();
                pdbreader.setFileParsingParameters(params);


                try{

                        Structure struc = pdbreader.getStructureById("193D");
                        System.out.println(struc);

                        List<Compound>  compounds = struc.getCompounds();
                        for (Compound comp : compounds  ){
                                List<Chain> chains = comp.getChains();
                                System.out.print(">Chains :" );
                                for (Chain c : chains){
                                        System.out.print(c.getChainID() + " " );
                                }
                                System.out.println();
                                if ( chains.size() > 0) {
                                        System.out.println(chains.get(0).getAtomSequence());
                                        System.out.println(chains.get(0).getSeqResSequence());
                                        System.out.print("  Atom Ligands: ");

                                        for ( Group g: chains.get(0).getAtomLigands()){
                                                System.out.print( g.getPDBName() + " ");
                                        }

                                        System.out.println(" ");
                                }
                        }


                        /*
                        GroupIterator gi = new GroupIterator(struc);
                        while (gi.hasNext()){
                                Group g = (Group) gi.next();
                                Chain  c = g.getParent();
                                if ( g instanceof AminoAcid ){

                                        AminoAcid aa = (AminoAcid)g;

                                        Map<String,String> sec = aa.getSecStruc();

                                        //System.out.println(c.getName() + " " + g + " " + sec);

                                        ChemComp cc = g.getChemComp();

                                        System.out.println(c.getName() + " " + g.getPDBCode() + " " + g.getPDBName() + " " + cc + " " +sec);
                                }

                        }
                         */
                } catch (IOException e) {
                        e.printStackTrace();
                }
        }





        /**
         * Constructs a new PDBFileReader, initializing the extensions member variable.
         * The path is initialized in the same way as {@link UserConfiguration},
         * i.e. to system property/environment variable {@link UserConfiguration#PDB_DIR}.
         * Both autoFetch and splitDir are initialized to false
         */
        public PDBFileReader() {
                this(null);
        }

        /**
         * Constructs a new PDBFileReader, initializing the extensions member variable.
         * The path is initialized to the given path, both autoFetch and splitDir are initialized to false.
         *
         * <p>If path is null, initialize using the system property/environment variable
         * {@link UserConfiguration#PDB_DIR}.
         * @param path Path to the PDB file directory
         */
        public PDBFileReader(String path) {
                super(path);

                addExtension(".ent");
                addExtension(".pdb");
                addExtension(".ent.gz");
                addExtension(".pdb.gz");
                addExtension(".ent.Z");
                addExtension(".pdb.Z");
        }


        @Deprecated
        public void downloadPDB(String pdbId) throws IOException {
                downloadStructure(pdbId);
        }

        /**
         * <b>N.B.</b> This feature won't work unless the structure wasn't found & autoFetch is set to <code>true</code>.
         * @param fetchFileEvenIfObsolete the fetchFileEvenIfObsolete to set
         * @deprecated Use {@link FileParsingParameters#setObsoleteBehavior(ObsoleteBehavior)}
         */
        @Deprecated
        public void setFetchFileEvenIfObsolete(boolean fetchFileEvenIfObsolete) {
                if(fetchFileEvenIfObsolete) {
                        setObsoleteBehavior(ObsoleteBehavior.FETCH_OBSOLETE);
                } else {
                        if(getObsoleteBehavior() == ObsoleteBehavior.FETCH_OBSOLETE) {
                                setObsoleteBehavior(ObsoleteBehavior.DEFAULT);
                        }
                }
        }

        /**forces the reader to fetch the file if its status is OBSOLETE.
         * This feature has a higher priority than {@link #setFetchCurrent(boolean)}. <br>
         * <b>N.B.</b> This feature won't work unless the structure wasn't found & autoFetch is set to <code>true</code>.
         * @return the fetchFileEvenIfObsolete
         * @author Amr AL-Hossary
         * @see #fetchCurrent
         * @since 3.0.2
         * @deprecated Use {@link FileParsingParameters#getObsoleteBehavior()}
         */
        @Deprecated
        public boolean isFetchFileEvenIfObsolete() {
                return getObsoleteBehavior() == ObsoleteBehavior.FETCH_OBSOLETE;
        }


        /**if enabled, the reader searches for the newest possible PDB ID, if not present in he local installation.
         * The {@link #setFetchFileEvenIfObsolete(boolean)} function has a higher priority than this function. <br>
         * <b>N.B.</b> This feature won't work unless the structure wasn't found & autoFetch is set to <code>true</code>.
         * @param fetchCurrent the fetchCurrent to set
         * @author Amr AL-Hossary
         * @see #setFetchFileEvenIfObsolete(boolean)
         * @since 3.0.2
         * @deprecated Use {@link FileParsingParameters#setObsoleteBehavior(ObsoleteBehavior)}
         */
        @Deprecated
        public void setFetchCurrent(boolean fetchNewestCurrent) {
                if(fetchNewestCurrent) {
                        setObsoleteBehavior(ObsoleteBehavior.FETCH_CURRENT);
                } else {
                        if(getObsoleteBehavior() == ObsoleteBehavior.FETCH_CURRENT) {
                                setObsoleteBehavior(ObsoleteBehavior.DEFAULT);
                        }
                }
        }

        /**
         * <b>N.B.</b> This feature won't work unless the structure wasn't found & autoFetch is set to <code>true</code>.
         * @return the fetchCurrent
         * @deprecated Use {@link FileParsingParameters#getObsoleteBehavior()}
         */
        @Deprecated
        public boolean isFetchCurrent() {
                return getObsoleteBehavior() == ObsoleteBehavior.FETCH_CURRENT;
        }

        @Override
        protected String getFilename(String pdbId) {
                return "pdb"+pdbId.toLowerCase()+".ent.gz";
        }

        @Override
        public Structure getStructure(InputStream inStream) throws IOException {
                PDBFileParser pdbpars = new PDBFileParser();
                pdbpars.setFileParsingParameters(getFileParsingParameters());

                Structure struc = pdbpars.parsePDBFile(inStream) ;
                return struc ;
        }

        @Override
        protected String[] getSplitDirPath() {
                return PDB_SPLIT_DIR;
        }

        @Override
        protected String[] getObsoleteDirPath() {
                return PDB_OBSOLETE_DIR;
        }



}