ReactionPathDiagram Class Reference

Reaction path diagrams (graphs). More...

#include <ReactionPath.h>

Detailed Description

Reaction path diagrams (graphs).

Definition at line 159 of file ReactionPath.h.

Public Member Functions
virtual	~ReactionPathDiagram ()
	Destructor. More...
double	maxFlow ()
	The largest one-way flow value in any path. More...
double	netFlow (size_t k1, size_t k2)
	The net flow from node k1 to node k2. More...
double	flow (size_t k1, size_t k2)
	The one-way flow from node k1 to node k2. More...
bool	hasNode (size_t k)
	True if a node for species k exists. More...
void	writeData (std::ostream &s)
void	exportToDot (std::ostream &s)
	Export the reaction path diagram. More...
void	add (ReactionPathDiagram &d)
SpeciesNode *	node (size_t k)
Path *	path (size_t k1, size_t k2)
Path *	path (size_t n)
size_t	nPaths ()
size_t	nNodes ()
void	addNode (size_t k, const string &nm, double x=0.0)
void	displayOnly (size_t k=npos)
void	linkNodes (size_t k1, size_t k2, size_t rxn, double value, string legend="")
void	include (const string &aaname)
void	exclude (const string &aaname)
void	include (vector< string > &names)
void	exclude (vector< string > &names)
vector< string > &	included ()
vector< string > &	excluded ()
vector< size_t >	species ()
vector< int >	reactions ()
void	findMajorPaths (double threshold, size_t lda, double *a)
void	setFont (const string &font)

Public Attributes
string	title
string	bold_color = "blue"
string	normal_color = "steelblue"
string	dashed_color = "gray"
string	element
string	m_font = "Helvetica"
double	threshold = 0.005
double	bold_min = 0.2
double	dashed_max = 0.0
double	label_min = 0.0
double	x_size = -1.0
double	y_size = -1.0
string	name = "reaction_paths"
string	dot_options = "center=1;"
flow_t	flow_type = NetFlow
double	scale = -1
double	arrow_width = -5.0
bool	show_details = false
double	arrow_hue = 0.6666

Protected Attributes
double	m_flxmax = 0.0
map< size_t, map< size_t, Path * > >	m_paths
map< size_t, SpeciesNode * >	m_nodes
	map of species index to SpeciesNode More...
vector< Path * >	m_pathlist
vector< string >	m_include
vector< string >	m_exclude
vector< size_t >	m_speciesNumber
set< size_t >	m_rxns
	Indices of reactions that are included in the diagram. More...
size_t	m_local = npos

Constructor & Destructor Documentation

~ReactionPathDiagram()

~ReactionPathDiagram ( )

virtual

Destructor.

Deletes all nodes and paths in the diagram.

Definition at line 81 of file ReactionPath.cpp.

Member Function Documentation

maxFlow()

double maxFlow ( )

inline

The largest one-way flow value in any path.

Definition at line 170 of file ReactionPath.h.

netFlow()

double netFlow ( size_t  k1, size_t  k2  )

inline

The net flow from node k1 to node k2.

Definition at line 175 of file ReactionPath.h.

flow()

double flow ( size_t  k1, size_t  k2  )

inline

The one-way flow from node k1 to node k2.

Definition at line 180 of file ReactionPath.h.

hasNode()

bool hasNode ( size_t  k )

inline

True if a node for species k exists.

Definition at line 185 of file ReactionPath.h.

exportToDot()

void exportToDot

(

std::ostream &

s

)

Export the reaction path diagram.

This method writes to stream s the commands for the 'dot' program in the GraphViz package from AT&T. (GraphViz may be downloaded from www.graphviz.org.)

To generate a postscript reaction path diagram from the output of this method saved in file paths.dot, for example, give the command:

dot -Tps paths.dot > paths.ps

To generate a GIF image, replace -Tps with -Tgif

Definition at line 171 of file ReactionPath.cpp.

Member Data Documentation

m_nodes

map<size_t, SpeciesNode*> m_nodes

protected

map of species index to SpeciesNode

Definition at line 285 of file ReactionPath.h.

m_rxns

set<size_t> m_rxns

protected

Indices of reactions that are included in the diagram.

Definition at line 292 of file ReactionPath.h.

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

• ReactionPath.h
• ReactionPath.cpp