raptor::raptor_index< data_t > Class Template Reference

Inheritance diagram for raptor::raptor_index< data_t >:

Collaboration diagram for raptor::raptor_index< data_t >:

Public Member Functions
void	append_bin_path (std::vector< std::string > const &path)
std::vector< std::vector< std::string > > const &	bin_path () const
auto const &	config () const
double	fpr () const
data_t &	ibf ()
data_t const &	ibf () const
bool	is_hibf () const
template<seqan3::cereal_input_archive archive_t>
void	load_parameters (archive_t &archive)
void	mark_resized (size_t const ibf_idx)
	Records that the IBF at ibf_idx has been grown beyond the size its layout assigned to it.
size_t	number_of_ibfs () const
	The number of IBFs, including the ones retired by an update.
size_t	number_of_resized_ibfs () const
	The number of IBFs that have been grown beyond the size their layout assigned to them.
raptor_index &	operator= (raptor_index &&)=default
raptor_index &	operator= (raptor_index const &)=default
size_t	original_number_of_ibfs () const
	The number of IBFs the index had when it was built from a layout.
uint8_t	parts () const
	raptor_index (build_arguments const &arguments)
	raptor_index (raptor_index &&)=default
	raptor_index (raptor_index const &)=default
	raptor_index (window const window_size, seqan3::shape const shape, uint8_t const parts, std::vector< std::vector< std::string > > const &bin_path, seqan::hibf::config const &config, data_t &&ibf)
template<seqan3::cereal_archive archive_t>
void	serialize (archive_t &archive)
	Serialisation support function.
seqan3::shape	shape () const
void	sync_resized (bool const value_for_new_ibfs)
	Matches the resize bookkeeping to the current number of IBFs.
bool	was_resized (size_t const ibf_idx) const
	Whether the IBF at ibf_idx has already been grown beyond the size its layout assigned to it.
uint64_t	window_size () const

Static Public Attributes
static constexpr uint32_t	version {3u}

Private Attributes
std::vector< std::vector< std::string > >	bin_path_ {}
seqan::hibf::config	config_ {}
double	fpr_ {}
data_t	ibf_ {}
bool	is_hibf_ {index_structure::is_hibf<data_t>}
size_t	original_number_of_ibfs_ {}
	The number of IBFs the index had when it was built from a layout.
uint8_t	parts_ {}
seqan3::shape	shape_ {}
seqan::hibf::bit_vector	was_resized_ {}
	Whether an IBF has already been grown beyond the size its layout assigned to it. Indexed by IBF index.
uint64_t	window_size_ {}

Member Function Documentation

number_of_ibfs()

template<index_structure::is_valid data_t = index_structure::ibf>

size_t raptor::raptor_index< data_t >::number_of_ibfs ( ) const

inline

The number of IBFs, including the ones retired by an update.

Read from the resize bookkeeping, which raptor::raptor_index::sync_resized keeps as large as ibf_.ibf_vector. Unlike ibf().ibf_vector.size(), this is also available after raptor::raptor_index::load_parameters.

serialize()

template<index_structure::is_valid data_t = index_structure::ibf>

template<seqan3::cereal_archive archive_t>

void raptor::raptor_index< data_t >::serialize ( archive_t & archive )

inline

Serialisation support function.

Template Parameters

archive_t

Type of archive; must satisfy seqan3::cereal_archive.

Parameters

[in]

archive

The archive being serialised from/to.

Attention

These functions are never called directly.

See also

https://docs.seqan.de/seqan/3.2.0/group__io.html#serialisation

Here is the call graph for this function:

sync_resized()

template<index_structure::is_valid data_t = index_structure::ibf>

void raptor::raptor_index< data_t >::sync_resized ( bool const value_for_new_ibfs )

inline

Matches the resize bookkeeping to the current number of IBFs.

Parameters

[in]

value_for_new_ibfs

The value assigned to IBFs added since the last call.

Deriving the size from ibf_.ibf_vector keeps both in sync by construction.

Here is the caller graph for this function:

Member Data Documentation

original_number_of_ibfs_

template<index_structure::is_valid data_t = index_structure::ibf>

size_t raptor::raptor_index< data_t >::original_number_of_ibfs_ {}

private

The number of IBFs the index had when it was built from a layout.

Updating grows the index beyond the layout it was built from. Comparing the current state against this value gives a measure of how far the index has drifted from a proper layout. Must be declared after ibf_, because the constructor reads ibf_.ibf_vector. Reset whenever the index is rebuilt in full.

was_resized_

template<index_structure::is_valid data_t = index_structure::ibf>

seqan::hibf::bit_vector raptor::raptor_index< data_t >::was_resized_ {}

private

Whether an IBF has already been grown beyond the size its layout assigned to it. Indexed by IBF index.

Only meaningful for the HIBF; empty for a plain IBF index. Must be declared after ibf_, because the constructor sizes it from ibf_.ibf_vector. Use raptor::raptor_index::sync_resized to keep the size in sync with the number of IBFs.

---

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

• index.hpp