nvbio::io::SequenceDataStorage< system_tag > Struct Template Reference

Detailed description

template< typename system_tag>
struct nvbio::io::SequenceDataStorage< system_tag >

A concrete SequenceData storage implementation in host/device memory

Definition at line 436 of file sequence.h.

#include <sequence.h>

Inheritance diagram for nvbio::io::SequenceDataStorage< system_tag >:

Public Types
typedef SequenceData	SequenceDataBase
typedef SequenceDataView	plain_view_type
typedef ConstSequenceDataView	const_plain_view_type
typedef nvbio::vector < system_tag, uint32 > ::iterator	index_iterator
typedef nvbio::vector < system_tag, uint32 > ::iterator	sequence_storage_iterator
typedef nvbio::vector < system_tag, char >::iterator	qual_storage_iterator
typedef nvbio::vector < system_tag, char >::iterator	name_storage_iterator
typedef nvbio::vector < system_tag, uint32 > ::const_iterator	const_index_iterator
typedef nvbio::vector < system_tag, uint32 > ::const_iterator	const_sequence_storage_iterator
typedef nvbio::vector < system_tag, char > ::const_iterator	const_qual_storage_iterator
typedef nvbio::vector < system_tag, char > ::const_iterator	const_name_storage_iterator
Public Types inherited from nvbio::io::SequenceData
typedef SequenceDataView	plain_view_type
typedef ConstSequenceDataView	const_plain_view_type

Public Methods
	SequenceDataStorage ()
template<typename other_tag >
	SequenceDataStorage (const SequenceDataStorage< other_tag > &other)
template<typename IndexIterator , typename SequenceStorageIterator , typename QualStorageIterator , typename NameStorageIterator >
	SequenceDataStorage (const SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator > &other)
	SequenceDataStorage (const SequenceData &other)
template<typename other_tag >
SequenceDataStorage &	operator= (const SequenceDataStorage< other_tag > &other)
template<typename IndexIterator , typename SequenceStorageIterator , typename QualStorageIterator , typename NameStorageIterator >
SequenceDataStorage &	operator= (const SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator > &other)
	operator plain_view_type ()
	operator const_plain_view_type () const
void	reserve (const uint32 n_seqs, const uint32 n_bps)
NVBIO_FORCEINLINE index_iterator	name_index ()
NVBIO_FORCEINLINE index_iterator	sequence_index ()
NVBIO_FORCEINLINE name_storage_iterator	name_stream ()
NVBIO_FORCEINLINE sequence_storage_iterator	sequence_storage ()
NVBIO_FORCEINLINE qual_storage_iterator	qual_stream ()
NVBIO_FORCEINLINE const_index_iterator	name_index () const
NVBIO_FORCEINLINE const_index_iterator	sequence_index () const
NVBIO_FORCEINLINE const_name_storage_iterator	name_stream () const
NVBIO_FORCEINLINE const_sequence_storage_iterator	sequence_storage () const
NVBIO_FORCEINLINE const_qual_storage_iterator	qual_stream () const
Public Methods inherited from nvbio::io::SequenceData
virtual	~SequenceData ()
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

Public Members
nvbio::vector< system_tag, uint32 >	m_sequence_vec
nvbio::vector< system_tag, uint32 >	m_sequence_index_vec
nvbio::vector< system_tag, char >	m_qual_vec
nvbio::vector< system_tag, char >	m_name_vec
nvbio::vector< system_tag, uint32 >	m_name_index_vec

Member Typedef Documentation

template<typename system_tag>

typedef nvbio::vector<system_tag,uint32>::const_iterator nvbio::io::SequenceDataStorage< system_tag >::const_index_iterator

Definition at line 448 of file sequence.h.

template<typename system_tag>

typedef nvbio::vector<system_tag,char>::const_iterator nvbio::io::SequenceDataStorage< system_tag >::const_name_storage_iterator

Definition at line 451 of file sequence.h.

template<typename system_tag>

typedef ConstSequenceDataView nvbio::io::SequenceDataStorage< system_tag >::const_plain_view_type

Definition at line 441 of file sequence.h.

template<typename system_tag>

typedef nvbio::vector<system_tag,char>::const_iterator nvbio::io::SequenceDataStorage< system_tag >::const_qual_storage_iterator

Definition at line 450 of file sequence.h.

template<typename system_tag>

typedef nvbio::vector<system_tag,uint32>::const_iterator nvbio::io::SequenceDataStorage< system_tag >::const_sequence_storage_iterator

Definition at line 449 of file sequence.h.

template<typename system_tag>

typedef nvbio::vector<system_tag,uint32>::iterator nvbio::io::SequenceDataStorage< system_tag >::index_iterator

Definition at line 443 of file sequence.h.

template<typename system_tag>

typedef nvbio::vector<system_tag,char>::iterator nvbio::io::SequenceDataStorage< system_tag >::name_storage_iterator

Definition at line 446 of file sequence.h.

template<typename system_tag>

typedef SequenceDataView nvbio::io::SequenceDataStorage< system_tag >::plain_view_type

Definition at line 440 of file sequence.h.

template<typename system_tag>

typedef nvbio::vector<system_tag,char>::iterator nvbio::io::SequenceDataStorage< system_tag >::qual_storage_iterator

Definition at line 445 of file sequence.h.

template<typename system_tag>

typedef nvbio::vector<system_tag,uint32>::iterator nvbio::io::SequenceDataStorage< system_tag >::sequence_storage_iterator

Definition at line 444 of file sequence.h.

template<typename system_tag>

typedef SequenceData nvbio::io::SequenceDataStorage< system_tag >::SequenceDataBase

Definition at line 438 of file sequence.h.

Constructor & Destructor Documentation

template<typename system_tag>

nvbio::io::SequenceDataStorage< system_tag >::SequenceDataStorage ( )

inline

constructor

Definition at line 455 of file sequence.h.

template<typename system_tag>

template<typename other_tag >

nvbio::io::SequenceDataStorage< system_tag >::SequenceDataStorage ( const SequenceDataStorage< other_tag > &  other)

inline

copy constructor

Definition at line 460 of file sequence.h.

template<typename system_tag>

template<typename IndexIterator , typename SequenceStorageIterator , typename QualStorageIterator , typename NameStorageIterator >

nvbio::io::SequenceDataStorage< system_tag >::SequenceDataStorage ( const SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator > &  other)

inline

copy constructor

Definition at line 473 of file sequence.h.

template<typename system_tag >

nvbio::io::SequenceDataStorage< system_tag >::SequenceDataStorage

(

const SequenceData &

other)

copy constructor

Definition at line 760 of file sequence.h.

Member Function Documentation

template<typename system_tag>

NVBIO_FORCEINLINE index_iterator nvbio::io::SequenceDataStorage< system_tag >::name_index ( )

inline

Definition at line 573 of file sequence.h.

template<typename system_tag>

NVBIO_FORCEINLINE const_index_iterator nvbio::io::SequenceDataStorage< system_tag >::name_index ( ) const

inline

Definition at line 579 of file sequence.h.

template<typename system_tag>

NVBIO_FORCEINLINE name_storage_iterator nvbio::io::SequenceDataStorage< system_tag >::name_stream ( )

inline

Definition at line 575 of file sequence.h.

template<typename system_tag>

NVBIO_FORCEINLINE const_name_storage_iterator nvbio::io::SequenceDataStorage< system_tag >::name_stream ( ) const

inline

Definition at line 581 of file sequence.h.

template<typename system_tag>

nvbio::io::SequenceDataStorage< system_tag >::operator const_plain_view_type ( ) const

inlinevirtual

convert to a const plain_view

Reimplemented from nvbio::io::SequenceData.

Definition at line 546 of file sequence.h.

template<typename system_tag>

nvbio::io::SequenceDataStorage< system_tag >::operator plain_view_type ( )

inlinevirtual

convert to a plain_view

Reimplemented from nvbio::io::SequenceData.

Definition at line 534 of file sequence.h.

template<typename system_tag>

template<typename other_tag >

SequenceDataStorage& nvbio::io::SequenceDataStorage< system_tag >::operator= ( const SequenceDataStorage< other_tag > &  other)

inline

assignment operator

Definition at line 486 of file sequence.h.

template<typename system_tag>

template<typename IndexIterator , typename SequenceStorageIterator , typename QualStorageIterator , typename NameStorageIterator >

SequenceDataStorage& nvbio::io::SequenceDataStorage< system_tag >::operator= ( const SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator > &  other)

inline

assignment operator, from a view object NOTE: if the view contains raw pointers, this method works if only if the pointers refer to host data. If the view refers to device data instead, it must provide proper device iterators.

Definition at line 509 of file sequence.h.

template<typename system_tag>

NVBIO_FORCEINLINE qual_storage_iterator nvbio::io::SequenceDataStorage< system_tag >::qual_stream ( )

inline

Definition at line 577 of file sequence.h.

template<typename system_tag>

NVBIO_FORCEINLINE const_qual_storage_iterator nvbio::io::SequenceDataStorage< system_tag >::qual_stream ( ) const

inline

Definition at line 583 of file sequence.h.

template<typename system_tag>

void nvbio::io::SequenceDataStorage< system_tag >::reserve ( const uint32  n_seqs, const uint32  n_bps  )

inline

Definition at line 559 of file sequence.h.

template<typename system_tag>

NVBIO_FORCEINLINE index_iterator nvbio::io::SequenceDataStorage< system_tag >::sequence_index ( )

inline

Definition at line 574 of file sequence.h.

template<typename system_tag>

NVBIO_FORCEINLINE const_index_iterator nvbio::io::SequenceDataStorage< system_tag >::sequence_index ( ) const

inline

Definition at line 580 of file sequence.h.

template<typename system_tag>

NVBIO_FORCEINLINE sequence_storage_iterator nvbio::io::SequenceDataStorage< system_tag >::sequence_storage ( )

inline

Definition at line 576 of file sequence.h.

template<typename system_tag>

NVBIO_FORCEINLINE const_sequence_storage_iterator nvbio::io::SequenceDataStorage< system_tag >::sequence_storage ( ) const

inline

Definition at line 582 of file sequence.h.

Member Data Documentation

template<typename system_tag>

nvbio::vector<system_tag,uint32> nvbio::io::SequenceDataStorage< system_tag >::m_name_index_vec

Definition at line 589 of file sequence.h.

template<typename system_tag>

nvbio::vector<system_tag,char> nvbio::io::SequenceDataStorage< system_tag >::m_name_vec

Definition at line 588 of file sequence.h.

template<typename system_tag>

nvbio::vector<system_tag,char> nvbio::io::SequenceDataStorage< system_tag >::m_qual_vec

Definition at line 587 of file sequence.h.

template<typename system_tag>

nvbio::vector<system_tag,uint32> nvbio::io::SequenceDataStorage< system_tag >::m_sequence_index_vec

Definition at line 586 of file sequence.h.

template<typename system_tag>

nvbio::vector<system_tag,uint32> nvbio::io::SequenceDataStorage< system_tag >::m_sequence_vec

Definition at line 585 of file sequence.h.

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The documentation for this struct was generated from the following file:

• E:/git/nvbio/nvbio/io/sequence/sequence.h