org.biojava.bio.program.fastq

Interface FastqWriter

All Known Implementing Classes:

IlluminaFastqWriter, SangerFastqWriter, SolexaFastqWriter

public interface FastqWriter

Writer for FASTQ formatted sequences.

Since:

1.7.1

Method Summary

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

Method Detail

append

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

Append the specified FASTQ formatted sequences to the specified appendable.

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

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

Append the specified FASTQ formatted sequences to the specified appendable.

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

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

Write the specified FASTQ formatted sequences to the specified file.

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

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

Write the specified FASTQ formatted sequences to the specified file.

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

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

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

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

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

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

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