vg
tools for working with variation graphs
Classes | Public Member Functions | Static Public Member Functions | Public Attributes | Private Member Functions | Static Private Member Functions | List of all members
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()

static 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()

static 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()

static 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()

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