#include <enumeffknocks.h>

Public Member Functions
	EnumEffKnocks ()
	Default constructor.
	EnumEffKnocks (MetabolicNetwork *metab_network)
	Constructor with instance of class MetabolicNetwork as argument.
void	enum_ufes ()
	Enumerate all maximal feasible efficient elementary flux mode subsets for the given algorithm options and inputs.
void	enum_ufes_from_single (long ind)
	Enumerate MFES subsets starting from single growth-efficient elementary flux mode indexed by 'eff_efm_index'.
void	enum_erk ()
void	enum_erk_direct ()
void	enum_erk_from_single_ufes (UFES ufes)
double	get_erk_enum_time ()
double	get_ufes_enum_time ()
map< string, UFES > &	get_ufes_map ()
map< string, RK > &	get_erk_map ()
void	set_erk_enum_time (double new_erk_enum_time)
void	set_ufes_enum_time (double new_ufes_enum_time)
bool	can_collapse_ineff_modes (vector< int > reac_knockout)
void	print_ufes (string ufes_fname)
void	print_erk (string erk_fname)
int	reacs_for_knock (UFES ufes, vector< int > &avail_reacs)
int	is_fes (vector< long > efm_indices)
long	collapse_ems (RK rk, vector< long > ems_to_collapse, vector< long > &uncollapsed_ems)
int	is_all_ems_collapsed (RK rk, vector< long > ems_to_collapse)
int	compute_ranks_vector (UFES v, long range_start, long range_end, multimap< int, long > &ranked_efms)
int	compute_ranks_vector_bitwise (UFES v, long range_start, long range_end, multimap< int, long > &ranked_efms, vector< unsigned char > &bit_sets_table256)
int	compute_rank (vector< long > efm_indices, long cand_efm_index)
int	compute_reac_rank (map< int, string > reac_knocks, int reac, vector< long > &uncollapsed_ems)
double	rank_reac_for_direct_enumeration (map< int, string > reac_knocks, int reac, vector< long > &remain_ineff_efm_indices, vector< long > &remain_eff_efm_indices)
int	communicate_ufes_map ()
	Distribute and merge the generate MFES subsets across compute nodes.
int	communicate_erk_map ()
	Communicate, exchange and merge generated collections of efficient reaction knockout subsets.
Private Attributes
int	max_rk_length
	maximal length of efficient reaction knockout subset
int	max_rk_cands
	maximal number of candidates considered for knockout at every search step
MetabolicNetwork *	metab_network
	pointer to associated metabolic network object
map< string, UFES >	ufes_map
	hash map to store unique maximal feasible elementary mode subsets
map< string, RK >	erk_map
	hash map to store unique efficient reaction knockout subsets
string	erk_fname
double	portion_time
double	erk_enum_time
double	ufes_enum_time
Static Private Attributes
static const int	max_ufes_length = 100

Detailed Description

Implementation of algorithms for direct and indirect knockout subset enumerations

Definition at line 18 of file enumeffknocks.h.

Constructor & Destructor Documentation

EnumEffKnocks::EnumEffKnocks ( )

Default constructor.

Definition at line 28 of file enumeffknocks.cpp.

EnumEffKnocks::EnumEffKnocks ( MetabolicNetwork * metab_network )

Constructor with instance of class MetabolicNetwork as argument.

Parameters:

[in] metab_network pre-initialized metabolic network object

Definition at line 36 of file enumeffknocks.cpp.

Member Function Documentation

bool EnumEffKnocks::can_collapse_ineff_modes ( vector< int > reac_knockout )

Definition at line 747 of file enumeffknocks.cpp.

long EnumEffKnocks::collapse_ems	(	RK	rk,
		vector< long >	ems_to_collapse,
		vector< long > &	uncollapsed_ems
	)

Definition at line 1112 of file enumeffknocks.cpp.

int EnumEffKnocks::communicate_erk_map ( )

Communicate, exchange and merge generated collections of efficient reaction knockout subsets.

Returns:: return indicator of success of execution

Definition at line 305 of file enumeffknocks.cpp.

int EnumEffKnocks::communicate_ufes_map ( )

Distribute and merge the generate MFES subsets across compute nodes.

Returns:: return indicator of success of execution

Definition at line 194 of file enumeffknocks.cpp.

int EnumEffKnocks::compute_rank	(	vector< long >	efm_indices,
		long	cand_efm_index
	)

Definition at line 756 of file enumeffknocks.cpp.

int EnumEffKnocks::compute_ranks_vector	(	UFES	v,
		long	range_start,
		long	range_end,
		multimap< int, long > &	ranked_efms
	)

Definition at line 1135 of file enumeffknocks.cpp.

int EnumEffKnocks::compute_ranks_vector_bitwise	(	UFES	v,
		long	range_start,
		long	range_end,
		multimap< int, long > &	ranked_efms,
		vector< unsigned char > &	bit_sets_table256
	)

Definition at line 1174 of file enumeffknocks.cpp.

int EnumEffKnocks::compute_reac_rank	(	map< int, string >	reac_knocks,
		int	reac,
		vector< long > &	uncollapsed_ems
	)

Definition at line 902 of file enumeffknocks.cpp.

void EnumEffKnocks::enum_erk ( )

Definition at line 413 of file enumeffknocks.cpp.

void EnumEffKnocks::enum_erk_direct ( )

Definition at line 465 of file enumeffknocks.cpp.

void EnumEffKnocks::enum_erk_from_single_ufes ( UFES ufes )

Definition at line 611 of file enumeffknocks.cpp.

void EnumEffKnocks::enum_ufes ( )

Enumerate all maximal feasible efficient elementary flux mode subsets for the given algorithm options and inputs.

For every growth-efficient elementary flux mode a method for enumeration of MFES is invoked.

Returns:: no return value

See also:: enum_ufes_from_single()

Definition at line 53 of file enumeffknocks.cpp.

void EnumEffKnocks::enum_ufes_from_single ( long eff_efm_index )

Enumerate MFES subsets starting from single growth-efficient elementary flux mode indexed by 'eff_efm_index'.

Parameters:

[in] eff_efm_index index of starting growth-efficient elementary flux mode

Returns:: returns no value

Definition at line 91 of file enumeffknocks.cpp.

double EnumEffKnocks::get_erk_enum_time ( ) [inline]

Definition at line 42 of file enumeffknocks.h.

map<string,RK>& EnumEffKnocks::get_erk_map ( ) [inline]

Definition at line 45 of file enumeffknocks.h.

double EnumEffKnocks::get_ufes_enum_time ( ) [inline]

Definition at line 43 of file enumeffknocks.h.

map<string,UFES>& EnumEffKnocks::get_ufes_map ( ) [inline]

Definition at line 44 of file enumeffknocks.h.

int EnumEffKnocks::is_all_ems_collapsed	(	RK	rk,
		vector< long >	ems_to_collapse
	)

Definition at line 1083 of file enumeffknocks.cpp.

int EnumEffKnocks::is_fes ( vector< long > efm_indices )

Definition at line 1048 of file enumeffknocks.cpp.

void EnumEffKnocks::print_erk ( string erk_fname )

Definition at line 938 of file enumeffknocks.cpp.

void EnumEffKnocks::print_ufes ( string ufes_fname )

Definition at line 794 of file enumeffknocks.cpp.

double EnumEffKnocks::rank_reac_for_direct_enumeration	(	map< int, string >	reac_knocks,
		int	reac,
		vector< long > &	remain_ineff_efm_indices,
		vector< long > &	remain_eff_efm_indices
	)