org.biojava.bio.program.fastq
Interface FastqWriter

All Known Implementing Classes:
IlluminaFastqWriter, SangerFastqWriter, SolexaFastqWriter

public interface FastqWriter

Writer for FASTQ formatted sequences.


Method Summary
<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