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 and Description
IlluminaFastqWriter()

Method Summary

Methods

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.
protected void	validate(Fastq fastq) Validate the specified FASTQ formatted sequence for writing.
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.

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

validate

protected void validate(Fastq fastq)
                 throws IOException

Validate the specified FASTQ formatted sequence for writing.

Parameters:

fastq - FASTQ formatted sequence to validate, will not be null

Throws:

IOException - if the specified FASTQ formatted sequence is not valid for writing

append

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

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

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

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

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

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

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