vg::MEMChainModel Class Reference

#include <cluster.hpp>

Public Member Functions
	MEMChainModel (const vector< size_t > &aln_lengths, const vector< vector< MaximalExactMatch > > &matches, const function< int64_t(pos_t)> &approx_position, const function< unordered_map< path_handle_t, vector< pair< size_t, bool > > >(pos_t)> &path_position, const function< double(const MaximalExactMatch &, const MaximalExactMatch &)> &transition_weight, int band_width=10, int position_depth=1, int max_connections=20)
void	score (const unordered_set< MEMChainModelVertex * > &exclude)
MEMChainModelVertex *	max_vertex (void)
vector< vector< MaximalExactMatch > >	traceback (int alt_alns, bool paired, bool debug)
void	display (ostream &out)
void	display_dot (ostream &out, vector< MEMChainModelVertex * > vertex_trace)
void	clear_scores (void)

Public Attributes
vector< MEMChainModelVertex >	model
unordered_map< path_handle_t, map< int64_t, vector< vector< MEMChainModelVertex >::iterator > > >	positions
set< vector< MEMChainModelVertex >::iterator >	redundant_vertexes

Constructor & Destructor Documentation

MEMChainModel()

vg::MEMChainModel::MEMChainModel	(	const vector< size_t > &	aln_lengths,
		const vector< vector< MaximalExactMatch > > &	matches,
		const function< int64_t(pos_t)> &	approx_position,
		const function< unordered_map< path_handle_t, vector< pair< size_t, bool > > >(pos_t)> &	path_position,
		const function< double(const MaximalExactMatch &, const MaximalExactMatch &)> &	transition_weight,
		int	band_width = 10,
		int	position_depth = 1,
		int	max_connections = 20 )

Member Function Documentation

clear_scores()

void vg::MEMChainModel::clear_scores

(

void

)

display()

void vg::MEMChainModel::display

(

ostream &

out

)

display_dot()

void vg::MEMChainModel::display_dot	(	ostream &	out,
		vector< MEMChainModelVertex * >	vertex_trace )

max_vertex()

MEMChainModelVertex * vg::MEMChainModel::max_vertex

(

void

)

score()

void vg::MEMChainModel::score

(

const unordered_set< MEMChainModelVertex * > &

exclude

)

traceback()

vector< vector< MaximalExactMatch > > vg::MEMChainModel::traceback	(	int	alt_alns,
		bool	paired,
		bool	debug )

Member Data Documentation

model

vector<MEMChainModelVertex> vg::MEMChainModel::model

positions

unordered_map<path_handle_t, map<int64_t, vector<vector<MEMChainModelVertex>::iterator> > > vg::MEMChainModel::positions

redundant_vertexes

set<vector<MEMChainModelVertex>::iterator> vg::MEMChainModel::redundant_vertexes

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

• src/cluster.hpp
• src/cluster.cpp