org.biojava.bio.program.fastq

Interface FastqWriter

All Known Implementing Classes:

IlluminaFastqWriter, SangerFastqWriter, SolexaFastqWriter

public interface FastqWriter

Writer for FASTQ formatted sequences.

Method Summary

Methods

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

Method Detail

append

<T extends java.lang.Appendable> T append(T appendable,
                                        Fastq... fastq)
                                      throws java.io.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:

java.io.IOException - if an IO error occurs

append

<T extends java.lang.Appendable> T append(T appendable,
                                        java.lang.Iterable<Fastq> fastq)
                                      throws java.io.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:

java.io.IOException - if an IO error occurs

write

void write(java.io.File file,
         Fastq... fastq)
           throws java.io.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:

java.io.IOException - if an IO error occurs

write

void write(java.io.File file,
         java.lang.Iterable<Fastq> fastq)
           throws java.io.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:

java.io.IOException - if an IO error occurs

write

void write(java.io.OutputStream outputStream,
         Fastq... fastq)
           throws java.io.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:

java.io.IOException - if an IO error occurs

write

void write(java.io.OutputStream outputStream,
         java.lang.Iterable<Fastq> fastq)
           throws java.io.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:

java.io.IOException - if an IO error occurs