void GraphvizAdapterImpl::init(std::string arg0, std::string arg1, std::string arg2) {
init();
const char * const args[] = {
arg0.c_str(),
arg1.c_str(),
arg2.c_str()
};
gvParseArgs(gvc_, sizeof(args)/sizeof(char*), (char**)args);
assert(gvc_);
}
int main(int argc, char **argv)
{
graph_t *prev = NULL;
int r, rc = 0;
Gvc = gvContextPlugins(lt_preloaded_symbols, DEMAND_LOADING);
GvExitOnUsage = 1;
gvParseArgs(Gvc, argc, argv);
#ifndef _WIN32
signal(SIGUSR1, gvToggle);
signal(SIGINT, intr);
#ifndef NO_FPERR
signal(SIGFPE, fperr);
#endif
#endif
if (MemTest) {
while (MemTest--) {
/* Create a test graph */
G = create_test_graph();
/* Perform layout and cleanup */
gvLayoutJobs(Gvc, G); /* take layout engine from command line */
gvFreeLayout(Gvc, G);
agclose (G);
}
}
else if ((G = gvPluginsGraph(Gvc))) {
gvLayoutJobs(Gvc, G); /* take layout engine from command line */
gvRenderJobs(Gvc, G);
}
else {
while ((G = gvNextInputGraph(Gvc))) {
if (prev) {
gvFreeLayout(Gvc, prev);
agclose(prev);
}
gvLayoutJobs(Gvc, G); /* take layout engine from command line */
gvRenderJobs(Gvc, G);
gvFinalize(Gvc);
r = agreseterrors();
rc = MAX(rc,r);
prev = G;
}
}
r = gvFreeContext(Gvc);
return (MAX(rc,r));
}
int main(int argc, char **argv)
{
graph_t *g, *prev = NULL;
GVC_t *gvc;
gvc = gvContext();
gvParseArgs(gvc, argc, argv);
while ((g = gvNextInputGraph(gvc))) {
if (prev) {
gvFreeLayout(gvc, prev);
agclose(prev);
}
gvLayoutJobs(gvc, g);
gvRenderJobs(gvc, g);
prev = g;
}
return (gvFreeContext(gvc));
}
int main(int argc, char **argv)
{
graph_t *prev = NULL;
Gvc = gvNEWcontext(Info, gvUsername());
gvParseArgs(Gvc, argc, argv);
#ifndef WIN32
signal(SIGUSR1, gvToggle);
signal(SIGINT, intr);
#ifndef NO_FPERR
fpinit();
signal(SIGFPE, fperr);
#endif
#endif
if (MemTest) {
while (1) {
/* Create a test graph */
G = create_test_graph();
/* Perform layout and cleanup */
gvLayoutJobs(Gvc, G); /* take layout engine from command line */
gvFreeLayout(Gvc, G);
/* Delete graph */
agclose(G);
}
} else {
while ((G = gvNextInputGraph(Gvc))) {
if (prev) {
gvFreeLayout(Gvc, prev);
agclose(prev);
}
gvLayoutJobs(Gvc, G); /* take layout engine from command line */
gvRenderJobs(Gvc, G);
prev = G;
}
}
return (gvFreeContext(Gvc));
}
int main(int argc, char **argv)
{
Agraph_t *g;
Agnode_t *n, *m;
Agedge_t *e;
GVC_t *gvc;
/* set up a graphviz context */
gvc = gvContext();
/* parse command line args - minimally argv[0] sets layout engine */
gvParseArgs(gvc, argc, argv);
/* Create a simple digraph */
g = agopen("g", AGDIGRAPH);
n = agnode(g, "n");
m = agnode(g, "m");
e = agedge(g, n, m);
/* Set an attribute - in this case one that affects the visible rendering */
agsafeset(n, "color", "red", "");
/* Compute a layout using layout engine from command line args */
gvLayoutJobs(gvc, g);
/* Write the graph according to -T and -o options */
gvRenderJobs(gvc, g);
/* Free layout data */
gvFreeLayout(gvc, g);
/* Free graph structures */
agclose(g);
/* close output file, free context, and return number of errors */
return (gvFreeContext(gvc));
}
SBML_ODESOLVER_API int drawJacoby(cvodeData_t *data, char *file, char *format) {
#if !USE_GRAPHVIZ
SolverError_error(
WARNING_ERROR_TYPE,
SOLVER_ERROR_NO_GRAPHVIZ,
"odeSolver has been compiled without GRAPHIZ functionality. ",
"Graphs are printed to stdout in the graphviz' .dot format.");
drawJacobyTxt(data, file);
#else
int i, j;
GVC_t *gvc;
Agraph_t *g;
Agnode_t *r;
Agnode_t *s;
Agedge_t *e;
Agsym_t *a;
char name[WORDSIZE];
char label[WORDSIZE];
char *output[3];
char *command = "dot";
char *formatopt;
char *outfile;
/* setting name of outfile */
ASSIGN_NEW_MEMORY_BLOCK(outfile, strlen(file)+ strlen(format)+7, char, 0);
sprintf(outfile, "-o%s_jm.%s", file, format);
/* setting output format */
ASSIGN_NEW_MEMORY_BLOCK(formatopt, strlen(format)+3, char, 0);
sprintf(formatopt, "-T%s", format);
/* construct command-line */
output[0] = command;
output[1] = formatopt;
output[2] = outfile;
output[3] = NULL;
/* set up renderer context */
gvc = (GVC_t *) gvContext();
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION < 4
dotneato_initialize(gvc, 3, output);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
parse_args(gvc, 3, output);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3
gvParseArgs(gvc, 3, output);
#endif
g = agopen("G", AGDIGRAPH);
/* avoid overlapping nodes, for graph embedding by neato */
a = agraphattr(g, "overlap", "");
agxset(g, a->index, "scale");
/* set graph label */
if ( Model_isSetName(data->model->m) )
sprintf(label, "%s at time %g", Model_getName(data->model->m),
data->currenttime);
else if ( Model_isSetId(data->model->m) )
sprintf(label, "%s at time %g", Model_getId(data->model->m),
data->currenttime);
else
sprintf(label, "label=\"at time %g\";\n", data->currenttime);
a = agraphattr(g, "label", "");
agxset(g, a->index, label);
/*
Set edges from species A to species B if the
corresponding entry in the jacobian ((d[B]/dt)/d[A])
is not '0'. Set edge color 'red' and arrowhead 'tee'
if negative.
*/
for ( i=0; i<data->model->neq; i++ ) {
for ( j=0; j<data->model->neq; j++ ) {
if ( evaluateAST(data->model->jacob[i][j], data) != 0 ) {
sprintf(name, "%s", data->model->names[j]);
r = agnode(g,name);
agset(r, "label", data->model->names[j]);
sprintf(label, "%s.htm", data->model->names[j]);
a = agnodeattr(g, "URL", "");
agxset(r, a->index, label);
sprintf(name,"%s", data->model->names[i]);
s = agnode(g,name);
agset(s, "label", data->model->names[i]);
sprintf(label, "%s.htm", data->model->names[i]);
a = agnodeattr(g, "URL", "");
agxset(s, a->index, label);
e = agedge(g,r,s);
a = agedgeattr(g, "label", "");
sprintf(name, "%g", evaluateAST(data->model->jacob[i][j], data));
agxset (e, a->index, name);
if ( evaluateAST(data->model->jacob[i][j], data) < 0 ) {
a = agedgeattr(g, "arrowhead", "");
agxset(e, a->index, "tee");
a = agedgeattr(g, "color", "");
agxset(e, a->index, "red");
}
}
}
}
/* Compute a layout */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
gvBindContext(gvc, g);
dot_layout(g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
gvlayout_layout(gvc, g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3
gvLayoutJobs(gvc, g);
#endif
/* Write the graph according to -T and -o options */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
dotneato_write(gvc);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
emit_jobs(gvc, g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3
gvRenderJobs(gvc, g);
#endif
/* Clean out layout data */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
dot_cleanup(g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
gvlayout_cleanup(gvc, g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3
gvFreeLayout(gvc, g);
#endif
/* Free graph structures */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
dot_cleanup(g);
#endif
agclose(g);
/* Clean up output file and errors */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
gvFREEcontext(gvc);
dotneato_eof(gvc);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
dotneato_terminate(gvc);
#elif (GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6) || GRAPHVIZ_MAJOR_VERSION >= 3
gvFreeContext(gvc);
#endif
xfree(formatopt);
xfree(outfile);
#endif
return 1;
}
SBML_ODESOLVER_API int drawModel(Model_t *m, char* file, char *format) {
#if !USE_GRAPHVIZ
SolverError_error(
WARNING_ERROR_TYPE,
SOLVER_ERROR_NO_GRAPHVIZ,
"odeSolver has been compiled without GRAPHIZ functionality. ",
"Graphs are printed to stdout in the graphviz' .dot format.");
drawModelTxt(m, file);
#else
GVC_t *gvc;
Agraph_t *g;
Agnode_t *r;
Agnode_t *s;
Agedge_t *e;
Agsym_t *a;
Species_t *sp;
Reaction_t *re;
const ASTNode_t *math;
SpeciesReference_t *sref;
ModifierSpeciesReference_t *mref;
char *output[4];
char *command = "dot";
char *formatopt;
char *outfile;
int i,j;
int reversible;
char name[WORDSIZE];
char label[WORDSIZE];
/* setting name of outfile */
ASSIGN_NEW_MEMORY_BLOCK(outfile, strlen(file)+ strlen(format)+7, char, 0);
sprintf(outfile, "-o%s_rn.%s", file, format);
/* setting output format */
ASSIGN_NEW_MEMORY_BLOCK(formatopt, strlen(format)+3, char, 0);
sprintf(formatopt, "-T%s", format);
/* construct command-line */
output[0] = command;
output[1] = formatopt;
output[2] = outfile;
output[3] = NULL;
/* set up renderer context */
gvc = (GVC_t *) gvContext();
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION < 4
dotneato_initialize(gvc, 3, output);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
parse_args(gvc, 3, output);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3
gvParseArgs(gvc, 3, output);
#endif
g = agopen("G", AGDIGRAPH);
/* avoid overlapping nodes, for graph embedding by neato */
a = agraphattr(g, "overlap", "");
agxset(g, a->index, "scale");
for ( i=0; i<Model_getNumReactions(m); i++ ) {
re = Model_getReaction(m,i);
reversible = Reaction_getReversible(re);
sprintf(name, "%s", Reaction_getId(re));
r = agnode(g,name);
a = agnodeattr(g, "shape", "ellipse");
agxset(r, a->index, "box");
sprintf(label, "%s", Reaction_isSetName(re) ?
Reaction_getName(re) : Reaction_getId(re));
agset(r, "label", label);
sprintf(label, "%s.htm", Reaction_getId(re));
a = agnodeattr(g, "URL", "");
agxset(r, a->index, label);
for ( j=0; j<Reaction_getNumModifiers(re); j++ ) {
mref = Reaction_getModifier(re,j);
sp = Model_getSpeciesById(m, ModifierSpeciesReference_getSpecies(mref));
sprintf(name,"%s", Species_getId(sp));
s = agnode(g,name);
sprintf(label, "%s", Species_isSetName(sp) ?
Species_getName(sp) : Species_getId(sp));
agset(s, "label", label);
if ( Species_getBoundaryCondition(sp) ) {
a = agnodeattr(g, "color", "");
agxset(s, a->index, "blue");
}
if ( Species_getConstant(sp) ) {
a = agnodeattr(g, "color", "");
agxset(s, a->index, "green4");
}
sprintf(label, "%s.htm", Species_getId(sp));
a = agnodeattr(g, "URL", "");
agxset(s, a->index, label);
e = agedge(g,s,r);
a = agedgeattr(g, "style", "");
agxset(e, a->index, "dashed");
a = agedgeattr(g, "arrowhead", "");
agxset(e, a->index, "odot");
}
for ( j=0; j<Reaction_getNumReactants(re); j++ ) {
sref = Reaction_getReactant(re,j);
sp = Model_getSpeciesById(m, SpeciesReference_getSpecies(sref));
sprintf(name,"%s", Species_getId(sp));
s = agnode(g, name);
sprintf(label, "%s", Species_isSetName(sp) ?
Species_getName(sp) : Species_getId(sp));
agset(s, "label", label);
if ( Species_getBoundaryCondition(sp) ) {
a = agnodeattr(g, "color", "");
agxset(s, a->index, "blue");
}
if ( Species_getConstant(sp) ) {
a = agnodeattr(g, "color", "");
agxset(s, a->index, "green4");
}
sprintf(label, "%s.htm", Species_getId(sp));
a = agnodeattr(g, "URL", "");
agxset(s, a->index, label);
e = agedge(g,s,r);
a = agedgeattr(g, "label", "");
if ( (SpeciesReference_isSetStoichiometryMath(sref)) ) {
math = SpeciesReference_getStoichiometryMath(sref);
if ( (strcmp(SBML_formulaToString(math),"1") !=
0) ) {
agxset (e, a->index, SBML_formulaToString(math));
}
}
else {
if ( SpeciesReference_getStoichiometry(sref) != 1 ) {
sprintf(name, "%g", SpeciesReference_getStoichiometry(sref));
agxset (e, a->index, name);
}
}
if ( reversible == 1 ) {
a = agedgeattr(g, "arrowtail", "");
agxset(e, a->index, "onormal");
}
}
for ( j=0; j<Reaction_getNumProducts(re); j++ ) {
sref = Reaction_getProduct(re,j);
sp = Model_getSpeciesById(m, SpeciesReference_getSpecies(sref));
sprintf(name,"%s", Species_getId(sp));
s = agnode(g,name);
sprintf(label, "%s", Species_isSetName(sp) ?
Species_getName(sp) : Species_getId(sp));
agset(s, "label", label);
if ( Species_getBoundaryCondition(sp) ) {
a = agnodeattr(g, "color", "");
agxset(s, a->index, "blue");
}
if ( Species_getConstant(sp) ) {
a = agnodeattr(g, "color", "");
agxset(s, a->index, "green4");
}
sprintf(label, "%s.htm", Species_getId(sp));
a = agnodeattr(g, "URL", "");
agxset(s, a->index, label);
e = agedge(g,r,s);
a = agedgeattr(g, "label", "");
if ( SpeciesReference_isSetStoichiometryMath(sref) ) {
math = SpeciesReference_getStoichiometryMath(sref);
if ( (strcmp(SBML_formulaToString(math),"1") !=
0) ) {
agxset (e, a->index, SBML_formulaToString(math));
}
}
else {
if ( SpeciesReference_getStoichiometry(sref) != 1 ) {
sprintf(name, "%g",SpeciesReference_getStoichiometry(sref));
agxset (e, a->index,name);
}
}
if ( reversible == 1 ) {
a = agedgeattr(g, "arrowtail", "");
agxset(e, a->index, "onormal");
}
}
}
/* Compute a layout */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
gvBindContext(gvc, g);
dot_layout(g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
gvlayout_layout(gvc, g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3
gvLayoutJobs(gvc, g);
#endif
/* Write the graph according to -T and -o options */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
dotneato_write(gvc);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
emit_jobs(gvc, g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3
gvRenderJobs(gvc, g);
#endif
/* Clean out layout data */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
dot_cleanup(g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
gvlayout_cleanup(gvc, g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3
gvFreeLayout(gvc, g);
#endif
/* Free graph structures */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
dot_cleanup(g);
#else
agclose(g);
#endif
/* Clean up output file and errors */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
gvFREEcontext(gvc);
dotneato_eof(gvc);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
dotneato_terminate(gvc);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3
gvFreeContext(gvc);
#endif
xfree(formatopt);
xfree(outfile);
#endif
return 1;
}
/*
* Print in Graphviz format
*/
void
FA_dump_dot_fn(struct FA *fa, const char *ofname, int inc_step)
{
struct FA_State *st_from = NULL;
struct FA_State *st_to = NULL;
struct FA_State *st = NULL;
GVC_t *gvc = NULL;
graph_t *g = NULL;
Agedge_t *e = NULL;
Agnode_t *e_from = NULL;
Agnode_t *e_to = NULL;
Agnode_t *state0 = NULL;
Agnode_t **nodes = NULL;
Agnode_t *node = NULL;
char *argv[4] = { NULL };
char buf[4096];
int argc;
int i;
int ri, ci, ai;
FA_ASSERT(fa);
ASSERT(ofname != NULL);
ASSERT(inc_step == FA_INSERT_EXT ||
inc_step == FA_INSERT_NOTHING);
memset(buf, 0, sizeof(buf));
if (inc_step == FA_INSERT_EXT)
(void)snprintf(buf, sizeof(buf) - 1, "-o%s.%d", ofname,
fa->simstep);
else
(void)snprintf(buf, sizeof(buf) - 1, "-o%s", ofname);
argv[0] = strdup("FLViz.exe");
argv[1] = strdup(buf);
argv[2] = strdup("-Tsvg");
argv[3] = NULL;
argc = (sizeof(argv) / sizeof(argv[0])) - 1;
gvc = gvContext();
ASSERT(gvc != NULL);
gvParseArgs(gvc, argc, argv);
memset(buf, 0, sizeof(buf));
snprintf(buf, sizeof(buf) - 1, "flvizstep%d", fa->simstep);
g = agopen(buf, AGDIGRAPHSTRICT);
/* Ustawianie atrybutów dla grafu */
agraphattr(g, "size", "8,8");
agraphattr(g, "rankdir", "LR");
/* Stan 0 */
state0 = agnode(g, "state0");
agsafeset(state0, "label", "", "");
agsafeset(state0, "width", "0.1", "");
agsafeset(state0, "height", "0.1", "");
agsafeset(state0, "shape", "box", "");
agsafeset(state0, "style", "filled", "");
agsafeset(state0, "fillcolor", "white", "");
agsafeset(state0, "color", "white", "");
nodes = (Agnode_t **)calloc(sizeof(Agnode_t *), fa->nstates);
ASSERT(nodes != NULL);
for (i = 0; i < fa->nstates; i++) {
st = &fa->states[i];
node = agnode(g, st->name);
agsafeset(node, "label", st->name, "");
agsafeset(node, "width", "0.5", "");
agsafeset(node, "height", "0.5", "");
agsafeset(node, "shape", "circle", "");
if (st->flag & FA_STATE_LAST)
agsafeset(node, "shape", "doublecircle", "");
agsafeset(node, "style", "filled", "");
agsafeset(node, "fillcolor", "gray", "");
if (st->flag & FA_STATE_CURR)
agsafeset(node, "fillcolor", "green", "");
st->obj = node;
nodes[i] = node;
}
e = agedge(g, state0, (Agnode_t *)fa->states[0].obj);
agsafeset(e, "label", "START", "");
if (fa->trans_from == fa->state0 && fa->trans_to == &fa->states[0])
agsafeset(e, "color", "green", "");
for (ri = 0; ri < fa->nstates; ri++) {
st_from = fa->transt[ri][0];
e_from = (Agnode_t *)st_from->obj;
for (ai = 0; ai < fa->nalpha; ai++) {
ci = ai + 1;
st_to = fa->transt[ri][ci];
if (st_to == NULL)
continue;
e_to = (Agnode_t *)st_to->obj;
e = agedge(g, e_from, e_to);
agsafeset(e, "label", fa->alpha[ai].word, "");
if (fa->trans_from == st_from && fa->trans_to == st_to)
agsafeset(e, "color", "green", "");
}
}
/* Compute a layout using layout engine from command line args */
gvLayoutJobs(gvc, g);
/* Write the graph according to -T and -o options */
gvRenderJobs(gvc, g);
gvFreeLayout(gvc, g);
agclose(g);
gvFreeContext(gvc);
fa->simstep++;
}
