/*
 *                    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.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.FastaHeaderFormatInterface;
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.BufferedOutputStream;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.util.Collection;
import java.util.LinkedHashMap;

/**
 * The FastaWriter writes a collection of sequences to an outputStream. FastaWriterHelper should be
 * used to write out sequences. Each sequence loaded from a fasta file retains the original Fasta header
 * and that is used when writing to the stream. This behavior can be overwritten by implementing
 * a custom FastaHeaderFormatInterface.
 *
 * @author Scooter Willis <willishf at gmail dot com>
 */
public class FastaWriter<S extends Sequence<?>, C extends Compound> {

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

	OutputStream os;
	Collection<S> sequences;
	FastaHeaderFormatInterface<S, C> headerFormat;
	private int lineLength = 60;
	byte[] lineSep = System.getProperty("line.separator").getBytes();
/**
 * Use default line length of 60
 * @param os
 * @param sequences
 * @param headerFormat
 */
	public FastaWriter(OutputStream os, Collection<S> sequences, FastaHeaderFormatInterface<S, C> headerFormat) {

		this.os = os;
		this.sequences = sequences;
		this.headerFormat = headerFormat;
	}

/**
 * Set custom lineLength
 * @param os
 * @param sequences
 * @param headerFormat
 * @param lineLength
 */

	public FastaWriter(OutputStream os, Collection<S> sequences, FastaHeaderFormatInterface<S, C> headerFormat, int lineLength) {
		this.os = os;
		this.sequences = sequences;
		this.headerFormat = headerFormat;
		this.lineLength = lineLength;
	}

	/**
	 * Allow an override of operating system line separator for programs that needs a specific CRLF or CR or LF option
	 * @param lineSeparator
	 */
	public void setLineSeparator(String lineSeparator){
		lineSep = lineSeparator.getBytes();
	}

	public void process() throws IOException {
	   // boolean closeit = false;



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

			int compoundCount = 0;
			String seq = "";

			seq = sequence.getSequenceAsString();

			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);
			}
		}

	}

	public static void main(String[] args) {
		try {
			FileInputStream is = new FileInputStream("/Users/Scooter/scripps/dyadic/c1-454Scaffolds.faa");


			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.debug(proteinSequences);

			FileOutputStream fileOutputStream = new FileOutputStream("/Users/Scooter/scripps/dyadic/c1-454Scaffolds_temp.faa");

			BufferedOutputStream bo = new BufferedOutputStream(fileOutputStream);
			long start = System.currentTimeMillis();
			FastaWriter<ProteinSequence, AminoAcidCompound> fastaWriter = new FastaWriter<ProteinSequence, AminoAcidCompound>(bo, proteinSequences.values(), new GenericFastaHeaderFormat<ProteinSequence, AminoAcidCompound>());
			fastaWriter.process();
			bo.close();
			long end = System.currentTimeMillis();
			logger.info("Took {} seconds", (end - start));

			fileOutputStream.close();


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

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

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

@@ -3728,1255 +3728,8 @@
 %09%7D%0A%0A
-%09public static void main(String%5B%5D args) %7B%0A%09%09try %7B%0A%09%09%09FileInputStream is = new FileInputStream(%22/Users/Scooter/scripps/dyadic/c1-454Scaffolds.faa%22);%0A%0A%0A%09%09%09FastaReader%3CProteinSequence, AminoAcidCompound%3E fastaReader = new FastaReader%3CProteinSequence, AminoAcidCompound%3E(is, new GenericFastaHeaderParser%3CProteinSequence, AminoAcidCompound%3E(), new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));%0A%09%09%09LinkedHashMap%3CString, ProteinSequence%3E proteinSequences = fastaReader.process();%0A%09%09%09is.close();%0A%0A%0A%09%09  //  logger.debug(proteinSequences);%0A%0A%09%09%09FileOutputStream fileOutputStream = new FileOutputStream(%22/Users/Scooter/scripps/dyadic/c1-454Scaffolds_temp.faa%22);%0A%0A%09%09%09BufferedOutputStream bo = new BufferedOutputStream(fileOutputStream);%0A%09%09%09long start = System.currentTimeMillis();%0A%09%09%09FastaWriter%3CProteinSequence, AminoAcidCompound%3E fastaWriter = new FastaWriter%3CProteinSequence, AminoAcidCompound%3E(bo, proteinSequences.values(), new GenericFastaHeaderFormat%3CProteinSequence, AminoAcidCompound%3E());%0A%09%09%09fastaWriter.process();%0A%09%09%09bo.close();%0A%09%09%09long end = System.currentTimeMillis();%0A%09%09%09logger.info(%22Took %7B%7D seconds%22, (end - start));%0A%0A%09%09%09fileOutputStream.close();%0A%0A%0A%09%09%7D catch (IOException e) %7B%0A%09%09%09logger.warn(%22Exception: %22, e);%0A%09%09%7D%0A%09%7D%0A%0A
 %09/**

remove FastaWriter main