JASS::instream_document_fasta Class Reference

Child class of instream for creating documents from FASTA genome sequence files. More...

#include <instream_document_fasta.h>

Inheritance diagram for JASS::instream_document_fasta:

Collaboration diagram for JASS::instream_document_fasta:

Public Member Functions
	instream_document_fasta (const instream_document_fasta &previous)=delete
	Copy constructor (not available). More...
	instream_document_fasta (std::shared_ptr< instream > &source)
	Constructor. More...
virtual	~instream_document_fasta ()
	Destructor.
virtual void	read (document &buffer)
	Read the next document from the source instream into document. More...
Public Member Functions inherited from JASS::instream
	instream (std::shared_ptr< instream > &source, std::shared_ptr< allocator > &memory)
	Constructor. More...
	instream (std::shared_ptr< instream > &source)
	Constructor. More...
	instream (void)
	Constructor.
virtual	~instream ()
	Destructor. More...
size_t	fetch (void *buffer, size_t bytes)
	fetch() generates a document object, sets its contents to the passed buffer, calls read() and returns the number of bytes of data read More...

Static Public Member Functions
static void	unittest (void)
	Unit test this class.

Protected Member Functions
	instream_document_fasta (std::shared_ptr< instream > &source, size_t buffer_size)
	Protected constructor used to set the size of the internal buffer in the unittest. More...
void	fetch (void *buffer, size_t bytes)
	Fetch another block of data from the source. More...

Protected Attributes
size_t	buffer_size
	Size of the disk read buffer. Normally 16MB.
uint8_t *	buffer
	Pointer to the interal buffer from which documents are extracted. Filled by calling source.read()
uint8_t *	buffer_end
	Pointer to the end of the buffer (used to prevent read past EOF).
size_t	buffer_used
	The number of bytes of buffer that have already been used from buffer (buffer + buffer_used is a pointer to the unused data in buffer)
Protected Attributes inherited from JASS::instream
std::shared_ptr< instream >	source
	If this object is reading from another instream then this is that instream.
std::shared_ptr< allocator >	memory
	Any and all memory allocation must happen using this object.

Detailed Description

Child class of instream for creating documents from FASTA genome sequence files.

See the Wikipedia article on the FASTA file format here: https://en.wikipedia.org/wiki/FASTA_format

Constructor & Destructor Documentation

instream_document_fasta() [1/3]

JASS::instream_document_fasta::instream_document_fasta ( std::shared_ptr< instream > &  source, size_t  buffer_size  )

protected

Protected constructor used to set the size of the internal buffer in the unittest.

Parameters

source	[in] The instream responsible for providing data to this class.
buffer_size	[in] The size of the internal buffer filled from source.

instream_document_fasta() [2/3]

JASS::instream_document_fasta::instream_document_fasta ( const instream_document_fasta &  previous )

delete

Copy constructor (not available).

Parameters

previous

[in] The instance to copy.

instream_document_fasta() [3/3]

JASS::instream_document_fasta::instream_document_fasta

(

std::shared_ptr< instream > &

source

)

Constructor.

Parameters

source

[in] The instream responsible for providing data to this class.

Member Function Documentation

fetch()

void JASS::instream_document_fasta::fetch ( void *  buffer, size_t  bytes  )

inlineprotected

Fetch another block of data from the source.

Parameters

buffer	[out] Write bytes amount of data into this memory location.
bytes	[in] Read this amount of data from the source.

read()

void JASS::instream_document_fasta::read ( document &  buffer )

virtual

Read the next document from the source instream into document.

Parameters

buffer

[out] The next document in the source instream.

Implements JASS::instream.

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The documentation for this class was generated from the following files:

• source/instream_document_fasta.h
• source/instream_document_fasta.cpp