/*
 *                    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.
 *
 * @author Scooter Willis ;lt;willishf at gmail dot com>
 * @author Karl Nicholas <github:karlnicholas>
 * @author Paolo Pavan
 *
 * 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 01-21-2010
 */
package org.biojava.nbio.core.sequence.io;

import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
import org.biojava.nbio.core.sequence.DNASequence;
import org.biojava.nbio.core.sequence.DataSource;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.TaxonomyID;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
import org.biojava.nbio.core.sequence.compound.DNACompoundSet;
import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
import org.biojava.nbio.core.sequence.features.AbstractFeature;
import org.biojava.nbio.core.sequence.features.DBReferenceInfo;
import org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface;
import org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface;
import org.biojava.nbio.core.sequence.template.AbstractSequence;
import org.biojava.nbio.core.sequence.template.Compound;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.*;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.LinkedHashMap;

/**
 * Use GenbankReaderHelper as an example of how to use this class where GenbankReaderHelper should be the
 * primary class used to read Genbank files
 *
 */
public class GenbankReader<S extends AbstractSequence<C>, C extends Compound> {

        private SequenceCreatorInterface<C> sequenceCreator;
        private GenbankSequenceParser<S,C> genbankParser;
        private BufferedReader bufferedReader;
        private boolean closed;
        private final Logger logger = LoggerFactory.getLogger(this.getClass());

        public boolean isClosed() {
                return closed;
        }

        /**
         * If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about
         * local file offsets for quick reads. InputStreams does not give you the name of the stream to access quickly via file seek. A seek in
         * an inputstream is forced to read all the data so you don't gain anything.
         * @param is
         * @param headerParser
         * @param sequenceCreator
         */
        public GenbankReader(final InputStream is, final SequenceHeaderParserInterface<S,C> headerParser,
                                                 final SequenceCreatorInterface<C> sequenceCreator) {
                this.sequenceCreator = sequenceCreator;
                bufferedReader = new BufferedReader(new InputStreamReader(is));
                genbankParser = new GenbankSequenceParser<>();
                closed = false;
        }

        /**
         * If you are going to use the FileProxyProteinSequenceCreator then you
         * need to use this constructor because we need details about
         * the location of the file.
         * @param file
         * @param headerParser
         * @param sequenceCreator
         * @throws FileNotFoundException if the file does not exist, is a directory
         *      rather than a regular file, or for some other reason cannot be opened
         *      for reading.
         * @throws SecurityException if a security manager exists and its checkRead
         *      method denies read access to the file.
         */
        public GenbankReader(
                        final File file,
                        final SequenceHeaderParserInterface<S,C> headerParser,
                        final SequenceCreatorInterface<C> sequenceCreator
                        ) throws FileNotFoundException {

                this.bufferedReader = new BufferedReader(new FileReader(file));
                this.sequenceCreator = sequenceCreator;
                genbankParser = new GenbankSequenceParser<>();
        }

        /**
         * The parsing is done in this method.<br>
         * This method tries to process all the available Genbank records
         * in the File or InputStream, closes the underlying resource,
         * and return the results in {@link LinkedHashMap}.<br>
         * You don't need to call {@link #close()} after calling this method.
         * @see #process(int)
         * @return {@link HashMap} containing all the parsed Genbank records
         * present, starting current fileIndex onwards.
         * @throws IOException
         * @throws CompoundNotFoundException
         */
        public LinkedHashMap<String,S> process() throws IOException, CompoundNotFoundException {
                return process(-1);
        }

        /**
         * This method tries to parse maximum <code>max</code> records from
         * the open File or InputStream, and leaves the underlying resource open.<br>
         *
         * Subsequent calls to the same method continue parsing the rest of the file.<br>
         * This is particularly useful when dealing with very big data files,
         * (e.g. NCBI nr database), which can't fit into memory and will take long
         * time before the first result is available.<br>
         * <b>N.B.</b>
         * <ul>
         * <li>This method can't be called after calling its NO-ARGUMENT twin.</li>
         * <li>remember to close the underlying resource when you are done.</li>
         * </ul>
         * @see #process()
         * @author Amr AL-Hossary
         * @since 3.0.6
         * @param max maximum number of records to return, <code>-1</code> for infinity.
         * @return {@link HashMap} containing maximum <code>max</code> parsed Genbank records
         * present, starting current fileIndex onwards.
         * @throws IOException
         * @throws CompoundNotFoundException
         */
        public LinkedHashMap<String,S> process(final int max) throws IOException, CompoundNotFoundException {
                LinkedHashMap<String,S> sequences = new LinkedHashMap<>();
                @SuppressWarnings("unchecked")
                int i=0;
                while(true) {
                        if(max>0 && i>=max) break;
                        i++;
                        String seqString = genbankParser.getSequence(bufferedReader, 0);
                        //reached end of file?
                        if(seqString==null) break;
                        @SuppressWarnings("unchecked")
                        S sequence = (S) sequenceCreator.getSequence(seqString, 0);
                        genbankParser.getSequenceHeaderParser().parseHeader(genbankParser.getHeader(), sequence);

                        // add features to new sequence
                        for (String k: genbankParser.getFeatures().keySet()){
                                for (AbstractFeature f: genbankParser.getFeatures(k)){
                                        //f.getLocations().setSequence(sequence);  // can't set proper sequence source to features. It is actually needed? Don't think so...
                                        sequence.addFeature(f);
                                }
                        }

                        // add taxonomy ID to new sequence
                        ArrayList<DBReferenceInfo> dbQualifier = genbankParser.getDatabaseReferences().get("db_xref");
                        if (dbQualifier != null){
                                DBReferenceInfo q = dbQualifier.get(0);
                                sequence.setTaxonomy(new TaxonomyID(q.getDatabase()+":"+q.getId(), DataSource.GENBANK));
                        }

                        sequences.put(sequence.getAccession().getID(), sequence);
                }

                if (max < 0) {
                        close();
                }

                return sequences;
        }

        public void close() {
                try {
                        bufferedReader.close();
                        this.closed = true;
                } catch (IOException e) {
                        logger.error("Couldn't close the reader. {}", e.getMessage());
                        this.closed = false;
                }
        }

        public static void main(String[] args) throws Exception {
                String proteinFile = "src/test/resources/BondFeature.gb";
                FileInputStream is = new FileInputStream(proteinFile);

                GenbankReader<ProteinSequence, AminoAcidCompound> proteinReader = new GenbankReader<>(is, new GenericGenbankHeaderParser<>(), new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
                LinkedHashMap<String,ProteinSequence> proteinSequences = proteinReader.process();
                System.out.println(proteinSequences);

                String inputFile = "src/test/resources/NM_000266.gb";
                is = new FileInputStream(inputFile);
                GenbankReader<DNASequence, NucleotideCompound> dnaReader = new GenbankReader<>(is, new GenericGenbankHeaderParser<>(), new DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
                LinkedHashMap<String,DNASequence> dnaSequences = dnaReader.process();
                System.out.println(dnaSequences);

                String crazyFile = "src/test/resources/CraftedFeature.gb";
                is = new FileInputStream(crazyFile);
                GenbankReader<DNASequence, NucleotideCompound> crazyReader = new GenbankReader<>(is, new GenericGenbankHeaderParser<>(), new DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
                LinkedHashMap<String,DNASequence> crazyAnnotatedSequences = crazyReader.process();

                is.close();
                System.out.println(crazyAnnotatedSequences);
        }

}