org.biojava3.sequencing.io.fastq
Class SolexaFastqWriter

java.lang.Object
  extended by org.biojava3.sequencing.io.fastq.SolexaFastqWriter
All Implemented Interfaces:
FastqWriter

public final class SolexaFastqWriter
extends Object

Writer for FastqVariant.FASTQ_SOLEXA formatted sequences.

Since:
3.0.3

Constructor Summary
SolexaFastqWriter()
           
 
Method Summary
<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

SolexaFastqWriter

public SolexaFastqWriter()
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