/*
 *                    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 01-21-2010
 */
package org.biojava.nbio.core.sequence.io;

import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
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.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

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

/**
 * Use FastaReaderHelper as an example of how to use this class where FastaReaderHelper should be the
 * primary class used to read Fasta files
 * @author Scooter Willis ;lt;willishf at gmail dot com&gt;
 */
public class FastaReader<S extends Sequence<?>, C extends Compound> {

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

	SequenceCreatorInterface<C> sequenceCreator;
	SequenceHeaderParserInterface<S,C> headerParser;
	BufferedReaderBytesRead br;
	InputStreamReader isr;
	FileInputStream fi = null;
	long fileIndex = 0;
	long sequenceIndex = 0;
	String line = "";
	String header= "";

	/**
	 * 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 inputStream
	 * @param headerParser
	 * @param sequenceCreator
	 */
	public FastaReader(InputStream is, SequenceHeaderParserInterface<S,C> headerParser,
					   SequenceCreatorInterface<C> sequenceCreator) {
		this.headerParser = headerParser;
		isr = new InputStreamReader(is);
		this.br = new BufferedReaderBytesRead(isr);
		this.sequenceCreator = sequenceCreator;
	}

	/**
	 * 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 FastaReader(File file, SequenceHeaderParserInterface<S,C> headerParser,
					   SequenceCreatorInterface<C> sequenceCreator) throws FileNotFoundException {
		this.headerParser = headerParser;
		fi = new FileInputStream(file);
		isr = new InputStreamReader(fi);
		this.br = new BufferedReaderBytesRead(isr);
		this.sequenceCreator = sequenceCreator;
	}

	/**
	 * The parsing is done in this method.<br>
	 * This method tries to process all the available fasta 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 fasta records
	 * present, starting current fileIndex onwards.
	 * @throws IOException if an error occurs reading the input file
	 */
	public LinkedHashMap<String,S> process() throws IOException {
		LinkedHashMap<String,S> sequences = process(-1);
		close();

		return sequences;
	}

	/**
	 * 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 fasta records
	 * present, starting current fileIndex onwards.
	 * @throws IOException if an error occurs reading the input file
	 */
	public LinkedHashMap<String,S> process(int max) throws IOException {


		String line = "";
		if(this.line != null && this.line.length() > 0){
			line=this.line;
		}
		String header = "";
		if(this.header != null && this.header.length() > 0){
			header=this.header;
		}

		StringBuilder sb = new StringBuilder();
		int processedSequences=0;
		boolean keepGoing = true;


		LinkedHashMap<String,S> sequences = new LinkedHashMap<String,S>();

		do {
			line = line.trim(); // nice to have but probably not needed
			if (line.length() != 0) {
				if (line.startsWith(">")) {//start of new fasta record

					if (sb.length() > 0) {
						//i.e. if there is already a sequence before
						//logger.info("Sequence index=" + sequenceIndex);

						try {
							@SuppressWarnings("unchecked")
							S sequence = (S)sequenceCreator.getSequence(sb.toString(), sequenceIndex);
							headerParser.parseHeader(header, sequence);
							sequences.put(sequence.getAccession().getID(),sequence);
							processedSequences++;

						} catch (CompoundNotFoundException e) {
							logger.warn("Sequence with header '{}' has unrecognised compounds ({}), it will be ignored",
									header, e.getMessage());
						}

						sb.setLength(0); //this is faster than allocating new buffers, better memory utilization (same buffer)
					}
					header = line.substring(1);
				} else if (line.startsWith(";")) {
				} else {
					//mark the start of the sequence with the fileIndex before the line was read
					if(sb.length() == 0){
						sequenceIndex = fileIndex;
					}
					sb.append(line);
				}
			}
			fileIndex = br.getBytesRead();

			line = br.readLine();

			if (line == null) {


				// Fix for #282
				if ( sequences.size() == 0 && max != -1) {
					return null;
				}

				//i.e. EOF
				String seq = sb.toString();
				if ( seq.length() == 0) {
					logger.warn("Can't parse sequence {}. Got sequence of length 0!", sequenceIndex);
					logger.warn("header: {}", header);
				}
				//logger.info("Sequence index=" + sequenceIndex + " " + fileIndex );
				try {
					@SuppressWarnings("unchecked")
					S sequence = (S)sequenceCreator.getSequence(seq, sequenceIndex);
					headerParser.parseHeader(header, sequence);
					sequences.put(sequence.getAccession().getID(),sequence);
					processedSequences++;
				} catch (CompoundNotFoundException e) {
					logger.warn("Sequence with header '{}' has unrecognised compounds ({}), it will be ignored",
							header, e.getMessage());
				}
				keepGoing = false;
			}
			if (max > -1 && processedSequences>=max) {
				keepGoing=false;
			}
			if ( this.line == null)
				keepGoing = false;
		} while (keepGoing);

		this.line  = line;
		this.header= header;

		return sequences;
	}

	public void close() throws IOException {
		br.close();
		isr.close();
		//If stream was created from File object then we need to close it
		if (fi != null) {
			fi.close();
		}
		this.line=this.header = null;
	}

	public static void main(String[] args) {
		try {
			String inputFile = "/PF00104_small.fasta";
			InputStream is = FastaReader.class.getResourceAsStream(inputFile);


			if ( is == null)
				System.err.println("Could not get input file " + inputFile);
			FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(is, new GenericFastaHeaderParser<ProteinSequence,AminoAcidCompound>(), new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
			LinkedHashMap<String,ProteinSequence> proteinSequences = fastaReader.process();
			is.close();


			//logger.info("Protein Sequences: {}", proteinSequences);

			File file = new File(inputFile);
			FastaReader<ProteinSequence,AminoAcidCompound> fastaProxyReader =
					new FastaReader<ProteinSequence,AminoAcidCompound>(
							file,
							new GenericFastaHeaderParser<ProteinSequence,AminoAcidCompound>(),
							new FileProxyProteinSequenceCreator(
									file,
									AminoAcidCompoundSet.getAminoAcidCompoundSet(),
									new FastaSequenceParser()
							)
					);
			LinkedHashMap<String,ProteinSequence> proteinProxySequences = fastaProxyReader.process();

			for(String key : proteinProxySequences.keySet()){
				ProteinSequence proteinSequence = proteinProxySequences.get(key);
				logger.info("Protein Proxy Sequence Key: {}", key);
//                if(key.equals("Q98SJ1_CHICK/15-61")){
//                    int dummy = 1;
//                }
				logger.info("Protein Sequence: {}", proteinSequence.toString());

			}

		} catch (Exception e) {
			logger.warn("Exception: ", e);
		}
	}
}
