/*
 *                    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.sequence.*;
import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
import org.biojava.nbio.core.sequence.io.template.FastaHeaderFormatInterface;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.OutputStream;
import java.util.ArrayList;
import java.util.Collection;

/**
 * A Gene sequence has a Positive or Negative Strand where we want to write out to a stream the 5 to 3 prime version.
 * It is also an option to write out the gene sequence where the exon regions are upper case
 * 6/22/2010 FastaWriter needs to be sequence aware to handle writing out a GeneSequence which is negative Strand with the proper sequence
 * @author Scooter Willis <willishf at gmail dot com>
 */
public class FastaGeneWriter {

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

	boolean showExonUppercase = false;
	OutputStream os;
	Collection<GeneSequence> sequences;
	FastaHeaderFormatInterface<GeneSequence, NucleotideCompound> headerFormat;
	private int lineLength = 60;
/**
 *
 * @param os
 * @param sequences
 * @param headerFormat
 * @param showExonUppercase
 */
	public FastaGeneWriter(OutputStream os, Collection<GeneSequence> sequences, FastaHeaderFormatInterface<GeneSequence, NucleotideCompound> headerFormat, boolean showExonUppercase) {
		this(os, sequences, headerFormat, showExonUppercase, 60);
	}
/**
 *
 * @param os
 * @param sequences
 * @param headerFormat
 * @param showExonUppercase
 * @param lineLength
 */
	public FastaGeneWriter(OutputStream os, Collection<GeneSequence> sequences, FastaHeaderFormatInterface<GeneSequence, NucleotideCompound> headerFormat, boolean showExonUppercase, int lineLength) {
		this.os = os;
		this.sequences = sequences;
		this.headerFormat = headerFormat;
		this.lineLength = lineLength;
		this.showExonUppercase = showExonUppercase;
	}
/**
 *
 * @throws Exception
 */
	public void process() throws Exception {
		byte[] lineSep = System.getProperty("line.separator").getBytes();

		for (GeneSequence sequence : sequences) {
			String header = headerFormat.getHeader(sequence);
			os.write('>');
			os.write(header.getBytes());
			os.write(lineSep);

			int compoundCount = 0;
			String seq = "";
			//GeneSequence currently has a strand attribute to indicate direction

			seq = sequence.getSequence5PrimeTo3Prime().getSequenceAsString();
			if (showExonUppercase) {
				StringBuilder sb = new StringBuilder(seq.toLowerCase());
				int geneBioBegin = sequence.getBioBegin();
				int geneBioEnd = sequence.getBioEnd();
				for (ExonSequence exonSequence : sequence.getExonSequences()) {
					int featureBioBegin = 0;
					int featureBioEnd = 0;
					if (sequence.getStrand() != Strand.NEGATIVE) {
						featureBioBegin = exonSequence.getBioBegin() - geneBioBegin;
						featureBioEnd = exonSequence.getBioEnd() - geneBioBegin;
					} else {
						featureBioBegin = geneBioEnd - exonSequence.getBioEnd();
						featureBioEnd = geneBioEnd - exonSequence.getBioBegin();
					}
					if (featureBioBegin < 0 || featureBioEnd < 0 || featureBioEnd > sb.length() || featureBioBegin > sb.length()) {
						logger.warn("Bad Feature, Accession: {}, Sequence Strand: {}, Gene Begin: {}, Gene End: {}, Exon Begin: {}, Exon End: {}", sequence.getAccession().toString(), sequence.getStrand(), geneBioBegin, geneBioEnd, exonSequence.getBioBegin(), exonSequence.getBioEnd());
					} else {
						for (int i = featureBioBegin; i <= featureBioEnd; i++) {
							char ch = sb.charAt(i);
							//probably not the fastest but the safest way if language is not standard ASCII
							String temp = String.valueOf(ch);
							ch = temp.toUpperCase().charAt(0);
							sb.setCharAt(i, ch);
						}
					}
				}
				seq = sb.toString();
			}

			for (int i = 0; i < seq.length(); i++) {
				os.write(seq.charAt(i));
				compoundCount++;
				if (compoundCount == lineLength) {
					os.write(lineSep);
					compoundCount = 0;
				}

			}


			//If we had sequence which was a reciprocal of line length
			//then don't write the line terminator as this has already written
			//it
			if ((sequence.getLength() % getLineLength()) != 0) {
				os.write(lineSep);
			}
		}
	}

	/**
	 * @return the lineLength
	 */
	public int getLineLength() {
		return lineLength;
	}

	/**
	 * @param lineLength the lineLength to set
	 */
	public void setLineLength(int lineLength) {
		this.lineLength = lineLength;
	}

	public static void main(String[] args) {

		try {
			ArrayList<GeneSequence> sequences = new ArrayList<GeneSequence>();
			ChromosomeSequence seq1 = new ChromosomeSequence("ATATATATATATATATATATATATATATATATACGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCATATATATATATATATATATATACGCGCGCGCGCGCGCGCATATATATATATATATATATATATATATATATACGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCATATATATATATATATATATATACGCGCGCGCGCGCGCGC");
			GeneSequence gene1 = seq1.addGene(new AccessionID("gene1"), 1, 20, Strand.POSITIVE);

			gene1.addExon(new AccessionID("t1_1_10"), 1, 10);
			gene1.addExon(new AccessionID("t1_12_15"), 12, 15);
			GeneSequence gene2 = seq1.addGene(new AccessionID("gene2"), 1, 20, Strand.NEGATIVE);

			gene2.addExon(new AccessionID("t2_1_10"), 1, 10);
			gene2.addExon(new AccessionID("t2_12_15"), 12, 15);
			sequences.add(gene1);
			sequences.add(gene2);


			FastaGeneWriter fastaWriter = new FastaGeneWriter(System.out, sequences, new GenericFastaHeaderFormat<GeneSequence, NucleotideCompound>(), true);
			fastaWriter.process();


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