/*
* Eoulsan development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public License version 2.1 or
* later and CeCILL-C. This should be distributed with the code.
* If you do not have a copy, see:
*
* http://www.gnu.org/licenses/lgpl-2.1.txt
* http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt
*
* Copyright for this code is held jointly by the Genomic platform
* of the Institut de Biologie de l'École normale supérieure and
* the individual authors. These should be listed in @author doc
* comments.
*
* For more information on the Eoulsan project and its aims,
* or to join the Eoulsan Google group, visit the home page
* at:
*
* http://outils.genomique.biologie.ens.fr/eoulsan
*
*/
package fr.ens.biologie.genomique.eoulsan.bio.io;
import static fr.ens.biologie.genomique.eoulsan.bio.io.BioCharsets.FASTA_CHARSET;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.OutputStream;
import java.io.Writer;
import fr.ens.biologie.genomique.eoulsan.Globals;
import fr.ens.biologie.genomique.eoulsan.bio.Sequence;
import fr.ens.biologie.genomique.eoulsan.util.FileUtils;
/**
* This class implements a Fasta writer.
* @since 1.0
* @author Laurent Jourdren
*/
public class FastaWriter implements SequenceWriter {
private final Writer writer;
/**
* Write the current entry.
* @throws IOException if an error occurs while writing data
*/
@Override
public void write(final Sequence sequence) throws IOException {
if (sequence == null) {
return;
}
this.writer.write(sequence.toFasta(Globals.FASTA_FILE_WIDTH));
}
/**
* Close the writer.
* @throws IOException if an error occurs while closing the writer
*/
@Override
public void close() throws IOException {
this.writer.close();
}
//
// Constructors
//
/**
* Public constructor.
* @param writer Writer to use
*/
public FastaWriter(final Writer writer) {
if (writer == null) {
throw new NullPointerException("The writer is null.");
}
this.writer = writer;
}
/**
* Public constructor.
* @param os OutputStream to use
*/
public FastaWriter(final OutputStream os) throws FileNotFoundException {
this.writer = FileUtils.createFastBufferedWriter(os, FASTA_CHARSET);
}
/**
* Public constructor.
* @param outputFile file to use
*/
public FastaWriter(final File outputFile) throws IOException {
this.writer = FileUtils.createFastBufferedWriter(outputFile, FASTA_CHARSET);
}
/**
* Public constructor.
* @param outputFilename name of the file to use
*/
public FastaWriter(final String outputFilename) throws IOException {
this.writer =
FileUtils.createFastBufferedWriter(outputFilename, FASTA_CHARSET);
}
}