vg::WFATree Class Reference

Classes
struct	ScoreProperties

Public Member Functions
	WFATree (const gbwtgraph::GBWTGraph &graph, const std::string &sequence, pos_t from, pos_t to, const Aligner &aligner, const WFAExtender::ErrorModel &error_model)
std::uint32_t	size () const
uint32_t	parent (std::uint32_t node) const
std::int32_t	gap_extend_penalty (std::uint32_t length) const
std::int32_t	gap_penalty (std::uint32_t length) const
void	extend (std::int32_t score)
std::int32_t	next_score (std::int32_t match_score)
void	next (std::int32_t score)
std::pair< MatchPos, WFAAlignment::Edit >	ins_predecessor (uint32_t node, int32_t score, int32_t diagonal) const
std::pair< MatchPos, WFAAlignment::Edit >	del_predecessor (uint32_t node, int32_t score, int32_t diagonal) const
std::pair< MatchPos, WFAAlignment::Edit >	match_predecessor (uint32_t node, int32_t score, int32_t diagonal) const
void	successor_offset (MatchPos &pos) const
void	predecessor_offset (uint32_t &node, uint32_t &offset) const
void	trim (const Aligner &aligner)

Static Public Member Functions
static bool	is_root (std::uint32_t node)
static bool	no_pos (pos_t pos)

Public Attributes
const gbwtgraph::CachedGBWTGraph	graph
const std::string &	sequence
pos_t	from
pos_t	to
std::vector< WFANode >	nodes
WFAPoint	candidate_point
std::uint32_t	candidate_node
std::int32_t	mismatch
std::int32_t	gap_open
std::int32_t	gap_extend
std::int32_t	score_bound
std::int32_t	max_distance
std::int32_t	min_distance
std::map< std::int32_t, ScoreProperties >	possible_scores

Private Member Functions
void	extend_over (std::int32_t score, std::int32_t diagonal, const std::vector< std::uint32_t > &leaves)
std::vector< std::uint32_t >	get_leaves () const
std::pair< std::int32_t, std::int32_t >	update_diagonal_range (std::pair< std::int32_t, std::int32_t > range, std::int32_t score) const
std::pair< int32_t, int32_t >	get_diagonals (int32_t score)
void	expand_if_necessary (const MatchPos &pos)
MatchPos	find_pos (size_t type, uint32_t node, int32_t score, int32_t diagonal, bool extendable_seq, bool extendable_graph) const
bool	at_dead_end (const MatchPos &pos) const

Static Private Member Functions
static void	adjust_diagonal_range (std::pair< std::int32_t, std::int32_t > &range, std::int32_t diagonal)
static std::pair< int32_t, int32_t >	empty_diagonal_range ()

Constructor & Destructor Documentation

WFATree()

vg::WFATree::WFATree ( const gbwtgraph::GBWTGraph & graph, const std::string & sequence, pos_t from, pos_t to, const Aligner & aligner, const WFAExtender::ErrorModel & error_model )

inline

Member Function Documentation

adjust_diagonal_range()

void vg::WFATree::adjust_diagonal_range ( std::pair< std::int32_t, std::int32_t > & range, std::int32_t diagonal )

inlinestaticprivate

at_dead_end()

bool vg::WFATree::at_dead_end ( const MatchPos & pos ) const

inlineprivate

del_predecessor()

std::pair< MatchPos, WFAAlignment::Edit > vg::WFATree::del_predecessor ( uint32_t node, int32_t score, int32_t diagonal ) const

inline

empty_diagonal_range()

std::pair< int32_t, int32_t > vg::WFATree::empty_diagonal_range ( )

inlinestaticprivate

expand_if_necessary()

void vg::WFATree::expand_if_necessary ( const MatchPos & pos )

inlineprivate

extend()

void vg::WFATree::extend ( std::int32_t score )

inline

extend_over()

void vg::WFATree::extend_over ( std::int32_t score, std::int32_t diagonal, const std::vector< std::uint32_t > & leaves )

inlineprivate

find_pos()

MatchPos vg::WFATree::find_pos ( size_t type, uint32_t node, int32_t score, int32_t diagonal, bool extendable_seq, bool extendable_graph ) const

inlineprivate

gap_extend_penalty()

std::int32_t vg::WFATree::gap_extend_penalty ( std::uint32_t length ) const

inline

gap_penalty()

std::int32_t vg::WFATree::gap_penalty ( std::uint32_t length ) const

inline

get_diagonals()

std::pair< int32_t, int32_t > vg::WFATree::get_diagonals ( int32_t score )

inlineprivate

get_leaves()

std::vector< std::uint32_t > vg::WFATree::get_leaves ( ) const

inlineprivate

ins_predecessor()

std::pair< MatchPos, WFAAlignment::Edit > vg::WFATree::ins_predecessor ( uint32_t node, int32_t score, int32_t diagonal ) const

inline

is_root()

bool vg::WFATree::is_root ( std::uint32_t node )

inlinestatic

match_predecessor()

std::pair< MatchPos, WFAAlignment::Edit > vg::WFATree::match_predecessor ( uint32_t node, int32_t score, int32_t diagonal ) const

inline

next()

void vg::WFATree::next ( std::int32_t score )

inline

next_score()

std::int32_t vg::WFATree::next_score ( std::int32_t match_score )

inline

no_pos()

bool vg::WFATree::no_pos ( pos_t pos )

inlinestatic

parent()

uint32_t vg::WFATree::parent ( std::uint32_t node ) const

inline

predecessor_offset()

void vg::WFATree::predecessor_offset ( uint32_t & node, uint32_t & offset ) const

inline

size()

std::uint32_t vg::WFATree::size ( ) const

inline

successor_offset()

void vg::WFATree::successor_offset ( MatchPos & pos ) const

inline

trim()

void vg::WFATree::trim ( const Aligner & aligner )

inline

update_diagonal_range()

std::pair< std::int32_t, std::int32_t > vg::WFATree::update_diagonal_range ( std::pair< std::int32_t, std::int32_t > range, std::int32_t score ) const

inlineprivate

Member Data Documentation

candidate_node

std::uint32_t vg::WFATree::candidate_node

candidate_point

WFAPoint vg::WFATree::candidate_point

from

pos_t vg::WFATree::from

gap_extend

std::int32_t vg::WFATree::gap_extend

gap_open

std::int32_t vg::WFATree::gap_open

graph

const gbwtgraph::CachedGBWTGraph vg::WFATree::graph

max_distance

std::int32_t vg::WFATree::max_distance

min_distance

std::int32_t vg::WFATree::min_distance

mismatch

std::int32_t vg::WFATree::mismatch

nodes

std::vector<WFANode> vg::WFATree::nodes

possible_scores

std::map<std::int32_t, ScoreProperties> vg::WFATree::possible_scores

score_bound

std::int32_t vg::WFATree::score_bound

sequence

const std::string& vg::WFATree::sequence

to

pos_t vg::WFATree::to

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

• src/gbwt_extender.cpp