bbq Implementation Documentation

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bbq Namespace Reference

bbq is the namespace that contains all classes except for those used for reading parameters etc. More...

Classes
class	bit_multi_set
	This class provides and advanced (but also rather inefficient) way of handling sets, which is a major part of the algorithms underlying bbq. More...
class	footprint_detector
	The class footprint_detector exists for rather historical reasons. More...
class	uint64_bitset
	This class provides one possible way of handling sets, which is a major part of the algorithms underlying bbq. More...
class	uint_bitset
	This class provides one possible way of handling sets, which is a major part of the algorithms underlying bbq. More...
class	variable_bitset
	This class provides one possible way of handling sets, which is a major part of the algorithms underlying bbq. More...
class	weighted_bit_multi_set
	This class provides the most advanced (but also most inefficient) way of handling sets, which is a major part of the algorithms underlying bbq. More...
class	weighted_footprint_detector
	Class weighted_footprint_detector implements most crucial parts of the algorithms underlying bbq, including computation of the interval arrangements and finding best intersections between cells. More...
class	weighted_variable_bitset
	This class provides one possible way of handling sets, which is a major part of the algorithms underlying bbq. More...
Typedefs
typedef std::list< std::triple< int, int, bool > >	match_list
	each list entry is coposed of a
typedef std::map< std::string, std::list< int > >	group_to_index_list
typedef weighted_footprint_detector< weighted_variable_bitset >	w_set_footprint_detector
typedef weighted_footprint_detector< bit_multi_set >	w_mset_footprint_detector
typedef weighted_footprint_detector< weighted_bit_multi_set >	w_wmset_footprint_detector
typedef std::triple< int, int, int >	cluster_triple
	A cluster triple is a triplet (p,e,j), where p is the position, e the edit distance and j the fragment index of an occurence in some T_i.
typedef std::set< cluster_triple >	cluster_set
typedef std::list< std::pair< int, float > >	open_interval_list
typedef variable_bitset	bit_set
typedef std::triple< int, int, bool >	match_list_triple
	match_list_triple.first = segment or group index j, 0 <= j <= k match_list_triple.second = position within the cluster match_list_triple.third = 3' occurence (true) or 5' occurence (false) - indicates whether to print the symbol above or below the corresponding line.
typedef std::list< match_list_triple >	ps_match_list
	a list of matches...
Functions
std::ostream &	operator<< (std::ostream &o, const weighted_variable_bitset &I)
std::ostream &	operator<< (std::ostream &o, const weighted_bit_multi_set &I)
std::ostream &	operator<< (std::ostream &o, const uint_bitset &I)
std::ostream &	operator<< (std::ostream &o, const uint64_bitset &I)
std::ostream &	operator<< (std::ostream &o, const variable_bitset &I)
std::ostream &	operator<< (std::ostream &o, const bit_multi_set &I)
void	print_ps_header (std::ostream &o)
void	print_ps_footer (std::ostream &o)
void	print_cluster (int ypos, std::string name, int beg, int end, int L, ps_match_list ml, std::ostream &o)
void	print_label (int xpos, int ypos, int j, std::string name, std::ostream &o)
int	get_col (int j)
int	get_sh (int j)
template<class w_bit_set> void	print_cluster_members (int ypos, w_bit_set &C, std::ostream &o)
float	get_pos (int x, int L)

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Detailed Description

bbq is the namespace that contains all classes except for those used for reading parameters etc.

in main.cpp

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Typedef Documentation

typedef variable_bitset bbq::bit_set

typedef std::set<cluster_triple> bbq::cluster_set

typedef std::triple< int,int,int > bbq::cluster_triple

A cluster triple is a triplet (p,e,j), where p is the position, e the edit distance and j the fragment index of an occurence in some T_i.

typedef std::map<std::string,std::list<int> > bbq::group_to_index_list

typedef std::list< std::triple<int,int,bool> > bbq::match_list

each list entry is coposed of a

typedef std::triple<int,int,bool> bbq::match_list_triple

match_list_triple.first = segment or group index j, 0 <= j <= k match_list_triple.second = position within the cluster match_list_triple.third = 3' occurence (true) or 5' occurence (false) - indicates whether to print the symbol above or below the corresponding line.

typedef std::list< std::pair<int,float> > bbq::open_interval_list

typedef std::list< match_list_triple > bbq::ps_match_list

a list of matches...

typedef weighted_footprint_detector<bit_multi_set> bbq::w_mset_footprint_detector

typedef weighted_footprint_detector<weighted_variable_bitset> bbq::w_set_footprint_detector

typedef weighted_footprint_detector<weighted_bit_multi_set> bbq::w_wmset_footprint_detector

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Function Documentation

int bbq::get_col (  int  j  )

float get_pos (  int  x, int  L )

int bbq::get_sh (  int  j  )

std::ostream& operator<< (  std::ostream &  o, const bit_multi_set &  I )

std::ostream& operator<< (  std::ostream &  o, const variable_bitset &  I )

std::ostream& operator<< (  std::ostream &  o, const uint64_bitset &  I )

std::ostream& operator<< (  std::ostream &  o, const uint_bitset &  I )

std::ostream& operator<< (  std::ostream &  o, const weighted_bit_multi_set &  I )

std::ostream& operator<< (  std::ostream &  o, const weighted_variable_bitset &  I )

void bbq::print_cluster (  int  ypos, std::string  name, int  beg, int  end, int  L, ps_match_list  ml, std::ostream &  o )

template<class w_bit_set> void print_cluster_members (  int  ypos, w_bit_set &  C, std::ostream &  o )

void bbq::print_label (  int  xpos, int  ypos, int  j, std::string  name, std::ostream &  o )

void bbq::print_ps_footer (  std::ostream &  o  )

void bbq::print_ps_header (  std::ostream &  o  )

bbq Implementation Documentation
Axel Mosig, Bioinformatics, University of Leipzig