Detailed description

: Base abstract class to encapsulate a sequence data object. This class is meant to be a base for either host, shared or device memory objects, and provides almost no interface, except for virtual methods to obtain a plain view of the class itself.

Definition at line 414 of file sequence.h.

#include <sequence.h>

Inheritance diagram for nvbio::io::SequenceData:

Public Types
typedef SequenceDataView	plain_view_type

typedef ConstSequenceDataView	const_plain_view_type

Public Methods
virtual	~SequenceData ()

virtual	operator plain_view_type ()

virtual	operator const_plain_view_type () const

Public Methods inherited from nvbio::io::SequenceDataInfo
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE	SequenceDataInfo ()

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE Alphabet	alphabet () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	size () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	bps () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	words () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	qs () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	name_stream_len () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool	has_qualities () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	max_sequence_len () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	min_sequence_len () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	avg_sequence_len () const

Additional Inherited Members
Public Members inherited from nvbio::io::SequenceDataInfo
Alphabet	m_alphabet
	the alphabet More...

uint32	m_n_seqs
	number of reads in this struct More...

uint32	m_name_stream_len
	the length (in bytes) of the name_stream buffer More...

uint32	m_sequence_stream_len
	the length of sequence_stream in base pairs More...

uint32	m_sequence_stream_words
	the number of words in sequence_stream More...

uint32	m_has_qualities
	has qualities More...

uint32	m_min_sequence_len
	statistics on the reads More...

uint32	m_max_sequence_len
	statistics on the reads More...

uint32	m_avg_sequence_len
	statistics on the reads More...