static void attr_set(char *name, char *value)
{
Agsym_t *ap = NULL;
char *defval = "";
if (In_decl && (G->root == G)) defval = value;
switch (Current_class) {
case TAG_NODE:
ap = agfindattr(G->proto->n,name);
if (ap == NULL)
ap = agnodeattr(AG.parsed_g,name,defval);
else if (ap->fixed && In_decl)
return;
agxset(N,ap->index,value);
break;
case TAG_EDGE:
ap = agfindattr(G->proto->e,name);
if (ap == NULL)
ap = agedgeattr(AG.parsed_g,name,defval);
else if (ap->fixed && In_decl)
return;
agxset(E,ap->index,value);
break;
case 0: /* default */
case TAG_GRAPH:
ap = agfindattr(G,name);
if (ap == NULL)
ap = agraphattr(AG.parsed_g,name,defval);
else if (ap->fixed && In_decl)
return;
agxset(G,ap->index,value);
break;
}
}
/* constrainY:
* See constrainX.
*/
static void constrainY(graph_t* g, nitem* nlist, int nnodes, intersectfn ifn,
int ortho)
{
Dt_t *list = dtopen(&constr, Dtobag);
nitem *p = nlist;
graph_t *cg;
int i;
for (i = 0; i < nnodes; i++) {
p->val = p->pos.y;
dtinsert(list, p);
p++;
}
if (ortho)
cg = mkConstraintG(g, list, ifn, distY);
else
cg = mkNConstraintG(g, list, ifn, distY);
rank(cg, 2, INT_MAX);
#ifdef DEBUG
{
Agsym_t *mlsym = agedgeattr(cg, "minlen", "");
Agsym_t *rksym = agnodeattr(cg, "rank", "");
char buf[100];
node_t *n;
edge_t *e;
for (n = agfstnode(cg); n; n = agnxtnode(cg, n)) {
sprintf(buf, "%d", ND_rank(n));
agxset(n, rksym->index, buf);
for (e = agfstedge(cg, n); e; e = agnxtedge(cg, e, n)) {
sprintf(buf, "%d", ED_minlen(e));
agxset(e, mlsym->index, buf);
}
}
}
#endif
p = nlist;
for (i = 0; i < nnodes; i++) {
int newpos, oldpos, delta;
oldpos = p->pos.y;
newpos = ND_rank(p->cnode);
delta = newpos - oldpos;
p->pos.y = newpos;
p->bb.LL.y += delta;
p->bb.UR.y += delta;
p++;
}
closeGraph(cg);
dtclose(list);
}
char *setv(Agedge_t *e, char *attr, char *val)
{
Agraph_t *g;
Agsym_t *a;
if (!e || !attr || !val)
return NULL;
g = e->tail->graph->root;
a = agfindattr(g->proto->e, attr);
if (!a)
a = agedgeattr(g, attr, empty_string);
myagxset(e, a, val);
return val;
}
/* setAttr:
* Sets object's name attribute to the given value.
* Creates the attribute if not already set.
*/
static Agsym_t *setAttr(graph_t * g, void *obj, char *name, char *value,
Agsym_t * ap)
{
if (ap == NULL) {
switch (agobjkind(obj)) {
case AGGRAPH:
ap = agraphattr(g, name, "");
break;
case AGNODE:
ap = agnodeattr(g, name, "");
break;
case AGEDGE:
ap = agedgeattr(g, name, "");
break;
}
}
agxset(obj, ap->index, value);
return ap;
}
int agsafeset(void* obj, char* name, char* value, char* def)
{
Agsym_t* a = agfindattr(obj, name);
if (a == NULL) {
if (!def) def = "";
switch (TAG_OF(obj)) {
case TAG_GRAPH:
a = agraphattr(((Agraph_t*)obj)->root, name, def);
break;
case TAG_NODE:
a = agnodeattr(((Agnode_t*)obj)->graph, name, def);
break;
case TAG_EDGE:
a = agedgeattr(((Agedge_t*)obj)->head->graph, name, def);
break;
}
}
return agxset(obj, a->index, value);
}
static inline Agsym_t* _agedgeattr(Agraph_t* object, QString attr, QString value){
setlocale(LC_NUMERIC,"en_US.UTF-8");
return agedgeattr(object, const_cast<char *>(qPrintable(attr)),const_cast<char *>(qPrintable(value)));
}
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;
}
main(int argc, char *argv[])
{
Agraph_t **gs;
Agraph_t **ccs;
Agraph_t *g;
Agraph_t *gp;
char *fname;
FILE *fp;
int cnt;
int i;
init(argc, argv);
if (!Files) {
fprintf(stderr, "No input files given\n");
exit(1);
}
PSinputscale = POINTS_PER_INCH;
if (doComps) {
if (verbose)
fprintf(stderr, "do Comps\n");
while (fname = *Files++) {
fp = fopen(fname, "r");
if (!fp) {
fprintf(stderr, "Could not open %s\n", fname);
continue;
}
g = agread(fp);
fclose(fp);
if (!g) {
fprintf(stderr, "Could not read graph\n");
continue;
}
printf("%s %d nodes %d edges %sconnected\n",
g->name, agnnodes(g), agnedges(g),
(isConnected(g) ? "" : "not "));
gs = ccomps(g, &cnt, "abc");
for (i = 0; i < cnt; i++) {
gp = gs[i];
printf(" %s %d nodes %d edges\n", gp->name, agnnodes(gp),
agnedges(gp));
}
}
} else {
gs = N_GNEW(nFiles, Agraph_t *);
cnt = 0;
while (fname = Files[cnt]) {
fp = fopen(fname, "r");
if (!fp) {
fprintf(stderr, "Could not open %s\n", fname);
exit(1);
}
g = agread(fp);
fclose(fp);
if (!g) {
fprintf(stderr, "Could not read graph\n");
exit(1);
}
if (!single) {
graph_init(g);
ptest_initGraph(g);
}
initPos(g);
/* if (Verbose) dumpG (g); */
gs[cnt++] = g;
}
if (single) {
Agraph_t *root;
Agnode_t *n;
Agnode_t *np;
Agnode_t *tp;
Agnode_t *hp;
Agedge_t *e;
Agedge_t *ep;
root = agopen("root", 0);
agedgeattr(root, "pos", "");
for (i = 0; i < cnt; i++) {
g = gs[i];
for (n = agfstnode(g); n; n = agnxtnode(g, n)) {
if (agfindnode(root, n->name)) {
fprintf(stderr,
"Error: node %s in graph %d (%s) previously added\n",
n->name, i, Files[i]);
exit(1);
}
np = agnode(root, n->name);
ND_pos(np)[0] = ND_pos(n)[0];
ND_pos(np)[1] = ND_pos(n)[1];
ND_coord_i(np).x = ND_coord_i(n).x;
ND_coord_i(np).y = ND_coord_i(n).y;
}
for (n = agfstnode(g); n; n = agnxtnode(g, n)) {
tp = agfindnode(root, n->name);
for (e = agfstout(g, n); e; e = agnxtout(g, e)) {
hp = agfindnode(root, e->head->name);
ep = agedge(root, tp, hp);
ED_spl(ep) = ED_spl(e);
}
}
}
graph_init(root);
ptest_initGraph(root);
ccs = ccomps(root, &cnt, 0);
packGraphs(cnt, ccs, root, margin, doEdges);
if (!doEdges)
copyPos(root);
else
State = GVSPLINES;
attach_attrs(root);
for (i = 0; i < cnt; i++) {
agdelete(root, ccs[i]);
}
agwrite(root, stdout);
} else {
packGraphs(cnt, gs, 0, margin, doEdges);
if (doEdges)
State = GVSPLINES;
for (i = 0; i < cnt; i++) {
if (!doEdges)
copyPos(gs[i]);
attach_attrs(gs[i]);
agwrite(gs[i], stdout);
}
}
}
}
static inline Agsym_t* _agedgeattr(Agraph_t* object, QString attr, QString value){
setlocale(LC_NUMERIC,"en_US.UTF-8"); // Débug séparateur de décimales en version française
return agedgeattr(object, const_cast<char *>(qPrintable(attr)),const_cast<char *>(qPrintable(value)));
}