net.sf.jfasta.impl

Class FASTAFileWriter

java.lang.Object

net.sf.kerner.utils.io.buffered.AbstractBufferedWriter

net.sf.jfasta.impl.FASTAFileWriter

All Implemented Interfaces:

Closeable, AutoCloseable, net.sf.kerner.utils.io.buffered.GenericBufferedWriter, net.sf.kerner.utils.io.ObjectWriter<FASTAElement>

public class FASTAFileWriter
extends net.sf.kerner.utils.io.buffered.AbstractBufferedWriter
implements net.sf.kerner.utils.io.ObjectWriter<FASTAElement>

A FASTAFileWriter writes FASTAElements and FASTAFiles to

• a File
• a Writer
• an OutputStream

Example:

 TODO example
 

last reviewed: 2013-04-29

FASTAFileWriter is thread save.

Version:

2010-11-30

Author:

Alexander Kerner

Field Summary

Fields inherited from class net.sf.kerner.utils.io.buffered.AbstractBufferedWriter

writer

Constructor Summary

Constructors

Constructor and Description
FASTAFileWriter(File file) Creates a FASTAFileWriter that writes to a file.
FASTAFileWriter(OutputStream stream) Creates a FASTAFileWriter that writes to a stream.
FASTAFileWriter(Writer writer) Creates a FASTAFileWriter that writes to a writer.

Method Summary

Methods

Modifier and Type	Method and Description
void	write(FASTAElement e) Writes a FASTAElement.
void	write(FASTAFile e) Writes a FASTAFile at once.

Methods inherited from class net.sf.kerner.utils.io.buffered.AbstractBufferedWriter

close, flush

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

FASTAFileWriter

public FASTAFileWriter(File file)
                throws IOException

Creates a FASTAFileWriter that writes to a file.

Parameters:

file - file to write to

Throws:

IOException - if file is not accessible

FASTAFileWriter

public FASTAFileWriter(OutputStream stream)

Creates a FASTAFileWriter that writes to a stream.

Parameters:

stream - output stream to write to

FASTAFileWriter

public FASTAFileWriter(Writer writer)

Creates a FASTAFileWriter that writes to a writer.

Parameters:

writer - writer to write to

Method Detail

write

public void write(FASTAElement e)
           throws IOException

Writes a FASTAElement.

Note: For big FASTA elements, prepare for equivalent memory usage.

Specified by:

write in interface net.sf.kerner.utils.io.ObjectWriter<FASTAElement>

Throws:

IOException

write

public void write(FASTAFile e)
           throws IOException

Writes a FASTAFile at once.

Note: For big FASTA files, use write(FASTAElement) instead and write FASTA file element by element.

Parameters:

e - FASTA file to write

Throws:

IOException - if writing fails