#include <bitefm.h>

Public Member Functions
	BitEfm ()
int	load_efm_bit (string efm_bit_fname, t_UnsignedInt num_ems, vector< vector< double > > &stoich)
	Load bit-represented elementary flux mode matrix from the given file using the given number of elementary flux modes.
char *	get_buffer ()
int	get_bytes_per_efm ()
int	get_num_reacs ()
t_UnsignedInt	get_num_modes ()
int	fast_is_fes (vector< long > &ineff_efm_indices, set< int > &reacs)
	This method checks if the subset of efficient elementary flux modes which uniquely determines the set of reactions 'reacs' is feasible.
int	is_efm_elem_zero (unsigned long index, int reac, int &is_zero)
	Check if elementary flux mode has zero value for given reaction.
int	read_single_efm (unsigned long index, vector< double > &efm)
	Read indexed elementary mode from the bit-matrix into expanded floating-point column.
int	print_efm (unsigned long index, vector< string > &reacs_names)
int	retain_efm (vector< long > efm_indices2retain, vector< vector< double > > &yields)
	Removes elementary modes not indexed by the given indices array.
int	remove_efm (vector< long > efm_indices2remove, vector< vector< double > > &yields)
	Removes elementary modes indexed by the given indices array.
int	knock_efms (map< string, int > knock_reacs, vector< vector< double > > &yields)
	Given a subset of reactions, removes those elementary modes having non-zero flux for at least one of those reactions.
Private Attributes
char *	buffer
	variable to store bit-represented elementar mode matrix
string	efm_bit_fname
	name of file containing bit-represented elementary mode matrix
vector< vector< double > >	stoich
	stoichiometry matrix
t_UnsignedInt	num_ems
	number of elementary flux modes
t_UnsignedInt	file_length
	length of file containing bit-represented elementary flux modes
int	bytes_per_efm
	number of bytes used to represent single elementary flux modes
int	num_reacs
	number of reactions in the network

Detailed Description

Abstraction of bit-represented elementary flux mode matrix. Methods allow scanning of elementary flux modes and removal of desired modes.

Definition at line 24 of file bitefm.h.

Constructor & Destructor Documentation

BitEfm::BitEfm ( )

Definition at line 15 of file bitefm.cpp.

Member Function Documentation

int BitEfm::fast_is_fes	(	vector< long > &	ineff_efm_indices,
		set< int > &	reacs
	)

This method checks if the subset of efficient elementary flux modes which uniquely determines the set of reactions 'reacs' is feasible.

If the subset of reactions from 'reacs' can be used to collapse all the modes indexed by 'ineff_efm_indices' then the corresponding subset of efficient modes is feasible. Scan the given set of inefficient modes to check if there is a mode not having non-zero flux in the given reaction subset reacs

Parameters:

[in]	ineff_efm_indices	Index of inefficient elementary flux modes
[in]	reacs	subset of reactions available to knockout inefficient modes

Returns:: return 1 if subset is FES, otherwise 0

Definition at line 112 of file bitefm.cpp.

char* BitEfm::get_buffer ( ) [inline]

Definition at line 40 of file bitefm.h.

int BitEfm::get_bytes_per_efm ( ) [inline]

Definition at line 41 of file bitefm.h.

t_UnsignedInt BitEfm::get_num_modes ( )

Definition at line 232 of file bitefm.cpp.

int BitEfm::get_num_reacs ( )

Definition at line 229 of file bitefm.cpp.

int BitEfm::is_efm_elem_zero	(	unsigned long	efm_index,
		int	reac,
		int &	is_zero
	)

Check if elementary flux mode has zero value for given reaction.

Parameters:

[in]	efm_index	Index of elementary flux mode in the EFM matrix
[in]	reac	index of reaction in the elementary mode
[out]	is_zero	Indicator if the mode has non-zero or zero value for given reaction. 0:non-zero value , 1:zero value

Returns:: Indicator of success of method execution

Definition at line 147 of file bitefm.cpp.

int BitEfm::knock_efms	(	map< string, int >	knock_reacs,
		vector< vector< double > > &	yields
	)

Given a subset of reactions, removes those elementary modes having non-zero flux for at least one of those reactions.

Parameters:

[in]	knock_reacs	Reactions which are deleted from network
[out]	yields	updated yields array for target metabolites

Returns:: Indicator of success of method execution

See also:: retain_efm()

Definition at line 336 of file bitefm.cpp.

int BitEfm::load_efm_bit	(	string	efm_bit_fname,
		t_UnsignedInt	num_ems,
		vector< vector< double > > &	stoich
	)

Load bit-represented elementary flux mode matrix from the given file using the given number of elementary flux modes.

Parameters:

[in]	efm_bit_fname	name of file which contains bit-represented elementary mode matrix
[in]	num_ems	number of elementary modes
[in]	stoich	stoichiometry matrix

Returns:: return 1 if subset is FES, otherwise 0

Definition at line 28 of file bitefm.cpp.

int BitEfm::print_efm	(	unsigned long	index,
		vector< string > &	reacs_names
	)

Definition at line 221 of file bitefm.cpp.

int BitEfm::read_single_efm	(	unsigned long	efm_index,
		vector< double > &	efm
	)

Read indexed elementary mode from the bit-matrix into expanded floating-point column.

Parameters:

[in]	efm_index	Index of elementary flux mode in the EFM matrix
[out]	efm	Elementary mode floating-point column

Returns:: Indicator of success of method execution

Definition at line 170 of file bitefm.cpp.

int BitEfm::remove_efm	(	vector< long >	efm_indices2remove,
		vector< vector< double > > &	yields
	)

Removes elementary modes indexed by the given indices array.

Parameters:

[in]	efm_indices2remove	Array of indices of modes which should be removed
[in,out]	yields	Array of yields for target metabolites for the remaining modes

Returns:: Indicator of success of method execution

See also:: retain_efm()

Definition at line 290 of file bitefm.cpp.

int BitEfm::retain_efm	(	vector< long >	efm_indices2retain,
		vector< vector< double > > &	yields
	)

Removes elementary modes not indexed by the given indices array.

Parameters:

[in]	efm_indices2retain	Array of indices of modes which should be retained
[in,out]	yields	Array of yields for target metabolites for the remaining modes

Returns:: Indicator of success of method execution

See also:: remove_efm()

Definition at line 247 of file bitefm.cpp.

Field Documentation

char* BitEfm::buffer [private]

variable to store bit-represented elementar mode matrix

Definition at line 27 of file bitefm.h.

int BitEfm::bytes_per_efm [private]

number of bytes used to represent single elementary flux modes

Definition at line 32 of file bitefm.h.

string BitEfm::efm_bit_fname [private]

name of file containing bit-represented elementary mode matrix

Definition at line 28 of file bitefm.h.

t_UnsignedInt BitEfm::file_length [private]

length of file containing bit-represented elementary flux modes

Definition at line 31 of file bitefm.h.

t_UnsignedInt BitEfm::num_ems [private]

number of elementary flux modes

Definition at line 30 of file bitefm.h.

int BitEfm::num_reacs [private]

number of reactions in the network

Definition at line 33 of file bitefm.h.

vector< vector<double> > BitEfm::stoich [private]

stoichiometry matrix

Definition at line 29 of file bitefm.h.

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

BitEfm Class Reference

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Field Documentation