Detailed description

template< Alphabet SEQUENCE_ALPHABET_T, typename SequenceDataT = ConstSequenceDataView>
struct nvbio::io::SequenceDataAccess< SEQUENCE_ALPHABET_T, SequenceDataT >

: An interface class to access a referenced sequence data object.

: This class is templated over the a SequenceDataT type which needs to provide the core iterators to access itself

Template Parameters

SEQUENCE_ALPHABET_T	the alphabet used to access the data
SequenceDataT	the type of the underlying sequence data; must provide the following interface:

interface SequenceDataT : public SequenceDataInfo
{
    typedef ...                   index_iterator;               // the index iterator
    typedef ...         sequence_storage_iterator;              // the read storage iterator
    typedef ...             qual_storage_iterator;              // the qualities iterator
    typedef ...             name_storage_iterator;              // the names string iterator
    typedef ...                    const_index_iterator;        // the index iterator
    typedef ...         const_sequence_storage_iterator;        // the read storage iterator
    typedef ...             const_qual_storage_iterator;        // the qualities iterator
    typedef ...             const_name_storage_iterator;        // the names string iterator
    NVBIO_HOST_DEVICE const_index_iterator            name_index()          const;
    NVBIO_HOST_DEVICE const_index_iterator            sequence_index()      const;
    NVBIO_HOST_DEVICE const_name_storage_iterator     name_stream()         const;
    NVBIO_HOST_DEVICE const_sequence_storage_iterator sequence_storage()    const;
    NVBIO_HOST_DEVICE const_qual_storage_iterator     qual_stream()         const;
};

Definition at line 80 of file sequence_access.h.

#include <sequence_access.h>

Public Types
typedef SequenceDataT::const_index_iterator	index_iterator
	the index iterator More...

typedef SequenceDataT::const_sequence_storage_iterator	sequence_storage_iterator
	the read storage iterator More...

typedef SequenceDataT::const_qual_storage_iterator	qual_storage_iterator
	the qualities iterator More...

typedef SequenceDataT::const_name_storage_iterator	name_storage_iterator
	the names string iterator More...

typedef SequenceDataViewCore < index_iterator, sequence_storage_iterator, qual_storage_iterator, name_storage_iterator >	sequence_reference
	the sequence reference More...

typedef PackedStream < sequence_storage_iterator, uint8, SEQUENCE_BITS, SEQUENCE_BIG_ENDIAN >	sequence_stream_type
	the packed read-stream type More...

typedef vector_view < sequence_stream_type >	sequence_string
	the read string type More...

typedef vector_view < qual_storage_iterator >	qual_string
	the quality string type More...

typedef vector_view < name_storage_iterator >	name_string
	the name string type More...

typedef ConcatenatedStringSet < sequence_stream_type, index_iterator >	sequence_string_set_type
	string-set type More...

typedef ConcatenatedStringSet < qual_storage_iterator, index_iterator >	qual_string_set_type
	quality string-set type More...

typedef ConcatenatedStringSet < name_storage_iterator, index_iterator >	name_string_set_type
	name string-set type More...

Public Methods
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	name_stream_len () 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

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE index_iterator	name_index () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE index_iterator	sequence_index () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE name_storage_iterator	name_stream () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE sequence_storage_iterator	sequence_storage () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE qual_storage_iterator	qual_stream () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE	SequenceDataAccess (const SequenceDataT &data)

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint2	get_range (const uint32 i) const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE sequence_stream_type	sequence_stream () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE sequence_string_set_type	sequence_string_set () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE sequence_string	get_read (const uint32 i) const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE qual_string	get_quals (const uint32 i) const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE name_string	get_name (const uint32 i) const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE qual_string_set_type	qual_string_set () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE name_string_set_type	name_string_set () const

Public Members
const sequence_reference	m_data

Static Public Members
static const Alphabet	SEQUENCE_ALPHABET = SEQUENCE_ALPHABET_T
	alphabet type More...

static const uint32	SEQUENCE_BITS = SequenceDataTraits<SEQUENCE_ALPHABET>::SEQUENCE_BITS
	symbol size More...

static const bool	SEQUENCE_BIG_ENDIAN = SequenceDataTraits<SEQUENCE_ALPHABET>::SEQUENCE_BIG_ENDIAN
	endianness More...

static const uint32	SEQUENCE_SYMBOLS_PER_WORD = SequenceDataTraits<SEQUENCE_ALPHABET>::SEQUENCE_SYMBOLS_PER_WORD
	number of symbols per word More...