Reaction path diagrams (graphs).
More...
#include <ReactionPath.h>
Reaction path diagrams (graphs).
Definition at line 159 of file ReactionPath.h.
|
| virtual | ~ReactionPathDiagram () |
| | Destructor.
|
| |
| double | maxFlow () |
| | The largest one-way flow value in any path.
|
| |
| double | netFlow (size_t k1, size_t k2) |
| | The net flow from node k1 to node k2.
|
| |
| double | flow (size_t k1, size_t k2) |
| | The one-way flow from node k1 to node k2.
|
| |
| bool | hasNode (size_t k) |
| | True if a node for species k exists.
|
| |
| void | writeData (std::ostream &s) |
| |
| void | exportToDot (std::ostream &s) |
| | Export the reaction path diagram.
|
| |
| 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) |
| |
◆ ~ReactionPathDiagram()
Destructor.
Deletes all nodes and paths in the diagram.
Definition at line 81 of file ReactionPath.cpp.
◆ maxFlow()
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 |
◆ 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()
◆ writeData()
| void writeData |
( |
std::ostream & |
s | ) |
|
◆ 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
double dot(InputIter x_begin, InputIter x_end, InputIter2 y_begin)
Function that calculates a templated inner product.
To generate a GIF image, replace -Tps with -Tgif
Definition at line 171 of file ReactionPath.cpp.
◆ add()
◆ node()
◆ path() [1/2]
| Path * path |
( |
size_t |
k1, |
|
|
size_t |
k2 |
|
) |
| |
|
inline |
◆ path() [2/2]
◆ nPaths()
◆ nNodes()
◆ addNode()
| void addNode |
( |
size_t |
k, |
|
|
const string & |
nm, |
|
|
double |
x = 0.0 |
|
) |
| |
◆ displayOnly()
| void displayOnly |
( |
size_t |
k = npos | ) |
|
|
inline |
◆ linkNodes()
| void linkNodes |
( |
size_t |
k1, |
|
|
size_t |
k2, |
|
|
size_t |
rxn, |
|
|
double |
value, |
|
|
string |
legend = "" |
|
) |
| |
◆ include() [1/2]
| void include |
( |
const string & |
aaname | ) |
|
|
inline |
◆ exclude() [1/2]
| void exclude |
( |
const string & |
aaname | ) |
|
|
inline |
◆ include() [2/2]
| void include |
( |
vector< string > & |
names | ) |
|
|
inline |
◆ exclude() [2/2]
| void exclude |
( |
vector< string > & |
names | ) |
|
|
inline |
◆ included()
| vector< string > & included |
( |
| ) |
|
|
inline |
◆ excluded()
| vector< string > & excluded |
( |
| ) |
|
|
inline |
◆ species()
| vector< size_t > species |
( |
| ) |
|
◆ reactions()
| vector< int > reactions |
( |
| ) |
|
◆ findMajorPaths()
| void findMajorPaths |
( |
double |
threshold, |
|
|
size_t |
lda, |
|
|
double * |
a |
|
) |
| |
◆ setFont()
| void setFont |
( |
const string & |
font | ) |
|
|
inline |
◆ title
◆ bold_color
| string bold_color = "blue" |
◆ normal_color
| string normal_color = "steelblue" |
◆ dashed_color
| string dashed_color = "gray" |
◆ element
◆ m_font
| string m_font = "Helvetica" |
◆ threshold
◆ bold_min
◆ dashed_max
◆ label_min
◆ x_size
◆ y_size
◆ name
| string name = "reaction_paths" |
◆ dot_options
| string dot_options = "center=1;" |
◆ flow_type
| flow_t flow_type = NetFlow |
◆ scale
◆ arrow_width
| double arrow_width = -5.0 |
◆ show_details
| bool show_details = false |
◆ arrow_hue
| double arrow_hue = 0.6666 |
◆ m_flxmax
◆ m_paths
| map<size_t, map<size_t, Path*> > m_paths |
|
protected |
◆ m_nodes
◆ m_pathlist
◆ m_include
◆ m_exclude
◆ m_speciesNumber
| vector<size_t> m_speciesNumber |
|
protected |
◆ m_rxns
Indices of reactions that are included in the diagram.
Definition at line 292 of file ReactionPath.h.
◆ m_local
The documentation for this class was generated from the following files:
1.9.7