com.milaboratory.core.io.sequence.fastq

Class SingleFastqWriter

java.lang.Object

com.milaboratory.core.io.sequence.fastq.SingleFastqWriter

All Implemented Interfaces:

SequenceWriter<SingleRead>, SingleSequenceWriter, AutoCloseable

public final class SingleFastqWriter
extends Object
implements SingleSequenceWriter

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_BUFFER_SIZE

Constructor Summary

Constructors

Constructor and Description
SingleFastqWriter(File file)
SingleFastqWriter(File file, QualityFormat qualityFormat, CompressionType ct)
SingleFastqWriter(OutputStream outputStream)
SingleFastqWriter(OutputStream outputStream, QualityFormat qualityFormat, CompressionType ct)
SingleFastqWriter(OutputStream outputStream, QualityFormat qualityFormat, CompressionType ct, int bufferSize)
SingleFastqWriter(String fileName)
SingleFastqWriter(String fileName, QualityFormat qualityFormat, CompressionType ct)

Method Summary

Methods

Modifier and Type	Method and Description
void	close() Closes this writer
void	flush() Writes all buffers to the underlying stream
void	write(SingleRead read) Writes corresponding subtype of SequenceRead

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

DEFAULT_BUFFER_SIZE

public static final int DEFAULT_BUFFER_SIZE

See Also:

Constant Field Values

Constructor Detail

SingleFastqWriter

public SingleFastqWriter(String fileName)
                  throws IOException

Throws:

IOException

SingleFastqWriter

public SingleFastqWriter(File file)
                  throws IOException

Throws:

IOException

SingleFastqWriter

public SingleFastqWriter(OutputStream outputStream)
                  throws IOException

Throws:

IOException

SingleFastqWriter

public SingleFastqWriter(File file,
                 QualityFormat qualityFormat,
                 CompressionType ct)
                  throws IOException

Throws:

IOException

SingleFastqWriter

public SingleFastqWriter(String fileName,
                 QualityFormat qualityFormat,
                 CompressionType ct)
                  throws IOException

Throws:

IOException

SingleFastqWriter

public SingleFastqWriter(OutputStream outputStream,
                 QualityFormat qualityFormat,
                 CompressionType ct)
                  throws IOException

Throws:

IOException

SingleFastqWriter

public SingleFastqWriter(OutputStream outputStream,
                 QualityFormat qualityFormat,
                 CompressionType ct,
                 int bufferSize)
                  throws IOException

Throws:

IOException

Method Detail

write

public void write(SingleRead read)

Description copied from interface: SequenceWriter

Writes corresponding subtype of SequenceRead

Specified by:

write in interface SequenceWriter<SingleRead>

Parameters:

read - read

flush

public void flush()

Description copied from interface: SequenceWriter

Writes all buffers to the underlying stream

Specified by:

flush in interface SequenceWriter<SingleRead>

close

public void close()

Description copied from interface: SequenceWriter

Closes this writer

Specified by:

close in interface SequenceWriter<SingleRead>

Specified by:

close in interface AutoCloseable