Package 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	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	Description
int	getLineLength()
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

getLineLength

public int getLineLength()

Returns:

the lineLength

setLineLength

public void setLineLength(int lineLength)

Parameters:

lineLength - the lineLength to set