org.biojava.nbio.core.sequence.io

Class FastaWriter<S extends Sequence<?>,C extends Compound>

java.lang.Object

org.biojava.nbio.core.sequence.io.FastaWriter<S,C>

public class FastaWriter<S extends Sequence<?>,C extends Compound>
extends Object

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

Constructor Summary

Constructors

Constructor and Description
FastaWriter(OutputStream os, Collection<S> sequences, FastaHeaderFormatInterface<S,C> headerFormat) Use default line length of 60
FastaWriter(OutputStream os, Collection<S> sequences, FastaHeaderFormatInterface<S,C> headerFormat, int lineLength) Set custom lineLength

Method Summary

Modifier and Type	Method and Description
int	getLineLength()
static void	main(String[] args)
void	process()
void	setLineLength(int lineLength)
void	setLineSeparator(String lineSeparator) Allow an override of operating system line separator for programs that needs a specific CRLF or CR or LF option

Methods inherited from class java.lang.Object

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

Constructor Detail

FastaWriter

public FastaWriter(OutputStream os,
                   Collection<S> sequences,
                   FastaHeaderFormatInterface<S,C> headerFormat)

Use default line length of 60

Parameters:

os -

sequences -

headerFormat -

FastaWriter

public FastaWriter(OutputStream os,
                   Collection<S> sequences,
                   FastaHeaderFormatInterface<S,C> headerFormat,
                   int lineLength)

Set custom lineLength

Parameters:

os -

sequences -

headerFormat -

lineLength -

Method Detail

setLineSeparator

public void setLineSeparator(String lineSeparator)

Allow an override of operating system line separator for programs that needs a specific CRLF or CR or LF option

Parameters:

lineSeparator -

process

public void process()
             throws IOException

Throws:

IOException

main

public static void main(String[] args)

getLineLength

public int getLineLength()

Returns:

the lineLength

setLineLength

public void setLineLength(int lineLength)

Parameters:

lineLength - the lineLength to set