Package org.biojava.bio.program.fastq

Class IlluminaFastqWriter

java.lang.Object

org.biojava.bio.program.fastq.IlluminaFastqWriter

All Implemented Interfaces:

FastqWriter

public final class IlluminaFastqWriter
extends Object

Writer for FastqVariant.FASTQ_ILLUMINA formatted sequences.

Since:

1.7.1

Constructor Summary

Constructors

Constructor	Description
IlluminaFastqWriter()

Method Summary

Modifier and Type	Method	Description
<T extends Appendable> T	append(T appendable, Iterable<Fastq> fastq)	Append the specified FASTQ formatted sequences to the specified appendable.
<T extends Appendable> T	append(T appendable, Fastq... fastq)	Append the specified FASTQ formatted sequences to the specified appendable.
protected Fastq	convert(Fastq fastq)	Convert the specified FASTQ formatted sequence if necessary.
void	write(File file, Iterable<Fastq> fastq)	Write the specified FASTQ formatted sequences to the specified file.
void	write(File file, Fastq... fastq)	Write the specified FASTQ formatted sequences to the specified file.
void	write(OutputStream outputStream, Iterable<Fastq> fastq)	Write the specified FASTQ formatted sequences to the specified output stream.
void	write(OutputStream outputStream, Fastq... fastq)	Write the specified FASTQ formatted sequences to the specified output stream.

Methods inherited from class java.lang.Object

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

Constructor Detail

IlluminaFastqWriter

public IlluminaFastqWriter()

Method Detail

convert

protected Fastq convert(Fastq fastq)

Convert the specified FASTQ formatted sequence if necessary.

Parameters:

fastq - FASTQ formatted sequence to convert, must not be null

Returns:

the specified FASTQ formatted sequence or a new FASTA formatted sequence if conversion is necessary

append

public final <T extends Appendable> T append(T appendable,
                                             Fastq... fastq)
                                      throws IOException

Description copied from interface: FastqWriter

Append the specified FASTQ formatted sequences to the specified appendable.

Specified by:

append in interface FastqWriter

Type Parameters:

T - extends Appendable

Parameters:

appendable - appendable to append the specified FASTQ formatted sequences to, must not be null

fastq - variable number of FASTQ formatted sequences to append, must not be null

Returns:

the specified appendable with the specified FASTQ formatted sequences appended

Throws:

IOException - if an I/O error occurs

append

public final <T extends Appendable> T append(T appendable,
                                             Iterable<Fastq> fastq)
                                      throws IOException

Description copied from interface: FastqWriter

Append the specified FASTQ formatted sequences to the specified appendable.

Specified by:

append in interface FastqWriter

Type Parameters:

T - extends Appendable

Parameters:

appendable - appendable to append the specified FASTQ formatted sequences to, must not be null

fastq - zero or more FASTQ formatted sequences to append, must not be null

Returns:

the specified appendable with the specified FASTQ formatted sequences appended

Throws:

IOException - if an I/O error occurs

write

public final void write(File file,
                        Fastq... fastq)
                 throws IOException

Description copied from interface: FastqWriter

Write the specified FASTQ formatted sequences to the specified file.

Specified by:

write in interface FastqWriter

Parameters:

file - file to write to, must not be null

fastq - variable number of FASTQ formatted sequences to write, must not be null

Throws:

IOException - if an I/O error occurs

write

public final void write(File file,
                        Iterable<Fastq> fastq)
                 throws IOException

Description copied from interface: FastqWriter

Write the specified FASTQ formatted sequences to the specified file.

Specified by:

write in interface FastqWriter

Parameters:

file - file to write to, must not be null

fastq - zero or more FASTQ formatted sequences to write, must not be null

Throws:

IOException - if an I/O error occurs

write

public final void write(OutputStream outputStream,
                        Fastq... fastq)
                 throws IOException

Description copied from interface: FastqWriter

Write the specified FASTQ formatted sequences to the specified output stream.

Specified by:

write in interface FastqWriter

Parameters:

outputStream - output stream to write to, must not be null

fastq - variable number of FASTQ formatted sequences to write, must not be null

Throws:

IOException - if an I/O error occurs

write

public final void write(OutputStream outputStream,
                        Iterable<Fastq> fastq)
                 throws IOException

Description copied from interface: FastqWriter

Write the specified FASTQ formatted sequences to the specified output stream.

Specified by:

write in interface FastqWriter

Parameters:

outputStream - output stream to write to, must not be null

fastq - zero or more FASTQ formatted sequences to write, must not be null

Throws:

IOException - if an I/O error occurs