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;
}
}
static void
attach_phase_attrs (Agraph_t * g, int maxphase)
{
Agsym_t* rk = agnodeattr(g,"rank","");
Agsym_t* order = agnodeattr(g,"order","");
Agnode_t* n;
char buf[BUFSIZ];
for (n = agfstnode(g); n; n = agnxtnode(g,n)) {
if (maxphase >= 1) {
sprintf(buf, "%d", ND_rank(n));
ag_xset(n,rk,buf);
}
if (maxphase >= 2) {
sprintf(buf, "%d", ND_order(n));
ag_xset(n,order,buf);
}
}
}
void dotneato_initialize(int argc, char** argv, char *str)
{
char *rest,c;
int i,nfiles;
aginit();
nfiles = 0;
for (i = 1; i < argc; i++)
if (argv[i][0] != '-') nfiles++;
Files = N_NEW(nfiles + 1, char *);
Files[nfiles++] = str;
nfiles = 0;
CmdName = argv[0];
for (i = 1; i < argc; i++) {
if (argv[i][0] == '-') {
rest = &(argv[i][2]);
switch (c = argv[i][1]) {
case 'G': global_def(rest,agraphattr); break;
case 'N': global_def(rest,agnodeattr); break;
case 'E': global_def(rest,agedgeattr); break;
case 'T': Output_lang = lang_select(rest); break;
case 'V':
fprintf(stderr,"%s version %s (%s)\n",
Info[0], Info[1], Info[2]);
exit (0);
break;
case 'l':
use_library(rest[0]?rest:(*argv[i+1]!='-'?argv[++i]:NULL));
break;
case 'n':
Nop = TRUE;
if (isdigit(*rest)) Nop = atoi (rest);
break;
case 'o':
Output_file = file_select(rest[0]?rest:argv[++i]);
break;
case 's':
PSinputscale = (rest[0]?atof(rest):POINTS_PER_INCH);
break;
case 'v': Verbose = TRUE; break;
case 'x': Reduce = TRUE; break;
default:
fprintf(stderr,"%s: option -%c unrecognized\n",CmdName,c);
}
}
else
Files[nfiles++] = argv[i];
}
if (Output_file == NULL) Output_file = stdout;
/* set persistent attributes here */
agnodeattr(NULL,"label",NODENAME_ESC);
}
/* 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);
}
int main(int argc, char** argv)
{
Agraph_t *g;
Agnode_t *n,*m;
Agedge_t *e;
Agsym_t *a;
GVC_t *gvc;
/* set up renderer context */
gvc = gvContext();
/* Accept -T and -o options like dot.
* Input files are ignored in this demo. */
dotneato_initialize(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 */
if (!(a = agfindattr(g->proto->n, "color")))
a = agnodeattr(g, "color", "");
agxset(n, a->index, "red");
/* bind graph to GV context - currently must be done before layout */
gvBindContext(gvc,g);
/* Compute a layout */
neato_layout(g);
/* twopi_layout(g); */
/* dot_layout(g); */
/* Write the graph according to -T and -o options */
dotneato_write(gvc);
/* Clean out layout data */
/* neato_cleanup(g); */
/* twopi_cleanup(g); */
/* dot_cleanup(g); */
/* Free graph structures */
agclose(g);
/* Clean up output file and errors */
dotneato_terminate(gvc);
return 1;
}
char *setv(Agnode_t *n, char *attr, char *val)
{
Agraph_t *g;
Agsym_t *a;
if (!n || !attr || !val)
return NULL;
g = n->graph->root;
a = agfindattr(g->proto->n, attr);
if (!a)
a = agnodeattr(g, attr, empty_string);
myagxset(n, a, val);
return val;
}
GVC_t *gvContextPlugins(const lt_symlist_t *builtins, int demand_loading)
{
GVC_t *gvc;
#ifndef WITH_CGRAPH
aginit();
agnodeattr(NULL, "label", NODENAME_ESC);
#else
agattr(NULL, AGNODE, "label", NODENAME_ESC);
#endif
gvc = gvNEWcontext(builtins, demand_loading);
gvconfig(gvc, FALSE); /* configure for available plugins */
return gvc;
}
GVC_t *gvContext(void)
{
GVC_t *gvc;
#ifndef WITH_CGRAPH
aginit();
agnodeattr(NULL, "label", NODENAME_ESC);
#else
agattr(NULL, AGNODE, "label", NODENAME_ESC);
#endif
/* default to no builtins, demand loading enabled */
gvc = gvNEWcontext(NULL, TRUE);
gvconfig(gvc, FALSE); /* configure for available plugins */
return gvc;
}
gboolean
cls_node_collapse (ClsNode *cls_node)
{
Agsym_t *sym;
if (cls_node->expansion_status == CLS_NODE_COLLAPSED)
return FALSE;
if (!(sym = agfindattr(cls_node->graph->proto->n, "label")))
sym = agnodeattr(cls_node->graph, "label", "");
agxset(cls_node->agnode, sym->index, cls_node->sym_name);
cls_node->expansion_status = CLS_NODE_COLLAPSED;
return TRUE;
}
/* 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;
}
char *setv(Agnode_t *n, char *attr, char *val)
{
Agraph_t *g;
Agsym_t *a;
if (!n || !attr || !val)
return NULL;
if (AGTYPE(n) == AGRAPH) { // protonode
g = (Agraph_t*)n;
a = agattr(g, AGNODE, attr, val); // create default attribute in psuodo protonode
// FIXME? - deal with html in "label" attributes
return val;
}
g = agroot(agraphof(n));
a = agattr(g, AGNODE, attr, NULL);
if (!a)
a = agnodeattr(g, attr, emptystring);
myagxset(n, a, val);
return val;
}
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);
}
void dotneato_initialize(GVC_t *gvc, int argc, char** argv)
{
char *rest,c, *val;
int i,v,nfiles;
/* establish if we are running in a CGI environment */
HTTPServerEnVar=getenv("SERVER_NAME");
/* establish Gvfilepath, if any */
Gvfilepath = getenv("GV_FILE_PATH");
aginit();
nfiles = 0;
for (i = 1; i < argc; i++)
if (argv[i][0] != '-') nfiles++;
Files = N_NEW(nfiles + 1, char *);
nfiles = 0;
if (!CmdName) setCmdName (argv[0]);
for (i = 1; i < argc; i++) {
if (argv[i][0] == '-') {
rest = &(argv[i][2]);
switch (c = argv[i][1]) {
case 'G':
if (*rest) global_def(rest,agraphattr);
else {
fprintf(stderr,"Missing argument for -G flag\n");
dotneato_usage (1);
}
break;
case 'N':
if (*rest) global_def(rest,agnodeattr);
else {
fprintf(stderr,"Missing argument for -N flag\n");
dotneato_usage (1);
}
break;
case 'E':
if (*rest) global_def(rest,agedgeattr);
else {
fprintf(stderr,"Missing argument for -E flag\n");
dotneato_usage (1);
}
break;
case 'T':
val = getFlagOpt (argc, argv, &i);
if (!val) {
fprintf(stderr,"Missing argument for -T flag\n");
dotneato_usage (1);
}
gvrender_output_langname_job(gvc, val);
break;
case 'V':
fprintf(stderr,"%s version %s (%s)\n",
gvc->info[0], gvc->info[1], gvc->info[2]);
exit (0);
break;
case 'l':
val = getFlagOpt (argc, argv, &i);
if (!val) {
fprintf(stderr,"Missing argument for -l flag\n");
dotneato_usage (1);
}
use_library(val);
break;
case 'o':
val = getFlagOpt (argc, argv, &i);
gvrender_output_filename_job(gvc, val);
break;
case 'q':
if (*rest) {
v = atoi(rest);
if (v <= 0) {
fprintf (stderr, "Invalid parameter \"%s\" for -q flag - ignored\n", rest);
}
else if (v == 1) agseterr (AGERR);
else agseterr (AGMAX);
}
else agseterr (AGERR);
break;
case 's':
if (*rest) {
PSinputscale = atof(rest);
if (PSinputscale <= 0) {
fprintf (stderr, "Invalid parameter \"%s\" for -s flag\n", rest);
dotneato_usage (1);
}
}
else PSinputscale = POINTS_PER_INCH;
break;
case 'v':
Verbose = TRUE;
if (isdigit(*rest)) Verbose = atoi (rest);
break;
case 'y': y_invert = TRUE; break;
case '?': dotneato_usage (0); break;
default:
fprintf(stderr, "%s: option -%c unrecognized\n\n",
CmdName,c);
dotneato_usage (1);
}
}
else
Files[nfiles++] = argv[i];
}
/* if no -Txxx, then set default format */
if (!gvc->jobs || !gvc->jobs->output_langname) {
gvrender_output_langname_job(gvc, "dot");
}
/* need to set Output_lang now based on the first -Txxx,
* so that CodeGen->textsize picks up an appropriate routine
* otherwise node sizing can be wrong for any or all of the products.
*/
/* FIXME */
Output_lang = lang_select(gvc, gvc->jobs->output_langname, 0);
/* set persistent attributes here (if not already set from command line options) */
if (! (agfindattr(agprotograph()->proto->n, "label")))
agnodeattr(NULL,"label",NODENAME_ESC);
}
void dotneato_args_initialize(GVC_t * gvc, int argc, char **argv)
{
char *rest, c, *val;
int i, v, nfiles;
/* establish if we are running in a CGI environment */
HTTPServerEnVar = getenv("SERVER_NAME");
/* establish Gvfilepath, if any */
Gvfilepath = getenv("GV_FILE_PATH");
/* configure for available plugins and codegens */
gvconfig(gvc, gvc->common.config);
if (gvc->common.config)
exit (0);
gvc->common.cmdname = dotneato_basename(argv[0]);
i = gvlayout_select(gvc, gvc->common.cmdname);
if (i == NO_SUPPORT)
gvlayout_select(gvc, "dot");
/* feed the globals */
Verbose = gvc->common.verbose;
CmdName = gvc->common.cmdname;
aginit();
nfiles = 0;
for (i = 1; i < argc; i++)
if (argv[i] && argv[i][0] != '-')
nfiles++;
gvc->input_filenames = N_NEW(nfiles + 1, char *);
nfiles = 0;
for (i = 1; i < argc; i++) {
if (argv[i] && argv[i][0] == '-') {
rest = &(argv[i][2]);
switch (c = argv[i][1]) {
case 'G':
if (*rest)
global_def(rest, agraphattr);
else {
fprintf(stderr, "Missing argument for -G flag\n");
dotneato_usage(1);
}
break;
case 'N':
if (*rest)
global_def(rest, agnodeattr);
else {
fprintf(stderr, "Missing argument for -N flag\n");
dotneato_usage(1);
}
break;
case 'E':
if (*rest)
global_def(rest, agedgeattr);
else {
fprintf(stderr, "Missing argument for -E flag\n");
dotneato_usage(1);
}
break;
case 'T':
val = getFlagOpt(argc, argv, &i);
if (!val) {
fprintf(stderr, "Missing argument for -T flag\n");
dotneato_usage(1);
exit(1);
}
v = gvjobs_output_langname(gvc, val);
if (!v) {
fprintf(stderr, "Format: \"%s\" not recognized. Use one of:%s\n",
val, gvplugin_list(gvc, API_device, val));
exit(1);
}
break;
case 'K':
val = getFlagOpt(argc, argv, &i);
if (!val) {
fprintf(stderr, "Missing argument for -K flag\n");
dotneato_usage(1);
exit(1);
}
v = gvlayout_select(gvc, val);
if (v == NO_SUPPORT) {
fprintf(stderr, "Layout type: \"%s\" not recognized. Use one of:%s\n",
val, gvplugin_list(gvc, API_layout, val));
exit(1);
}
break;
case 'V':
fprintf(stderr, "%s - %s version %s (%s)\n",
gvc->common.cmdname, gvc->common.info[0],
gvc->common.info[1], gvc->common.info[2]);
exit(0);
break;
case 'l':
val = getFlagOpt(argc, argv, &i);
if (!val) {
fprintf(stderr, "Missing argument for -l flag\n");
dotneato_usage(1);
}
use_library(gvc, val);
break;
case 'o':
val = getFlagOpt(argc, argv, &i);
if (! gvc->common.auto_outfile_names)
gvjobs_output_filename(gvc, val);
break;
case 'q':
if (*rest) {
v = atoi(rest);
if (v <= 0) {
fprintf(stderr,
"Invalid parameter \"%s\" for -q flag - ignored\n",
rest);
} else if (v == 1)
agseterr(AGERR);
else
agseterr(AGMAX);
} else
agseterr(AGERR);
break;
case 's':
if (*rest) {
PSinputscale = atof(rest);
if (PSinputscale <= 0) {
fprintf(stderr,
"Invalid parameter \"%s\" for -s flag\n",
rest);
dotneato_usage(1);
}
} else
PSinputscale = POINTS_PER_INCH;
break;
case 'x':
Reduce = TRUE;
break;
case 'y':
Y_invert = TRUE;
break;
case '?':
dotneato_usage(0);
break;
default:
fprintf(stderr, "%s: option -%c unrecognized\n\n", gvc->common.cmdname,
c);
dotneato_usage(1);
}
} else if (argv[i])
gvc->input_filenames[nfiles++] = argv[i];
}
/* if no -Txxx, then set default format */
if (!gvc->jobs || !gvc->jobs->output_langname) {
v = gvjobs_output_langname(gvc, "dot");
assert(v); /* "dot" should always be available as an output format */
}
/* set persistent attributes here (if not already set from command line options) */
if (!(agfindattr(agprotograph()->proto->n, "label")))
agnodeattr(NULL, "label", NODENAME_ESC);
}
static inline Agsym_t* _agnodeattr(Agraph_t* object, QString attr, QString value){
setlocale(LC_NUMERIC,"en_US.UTF-8");
return agnodeattr(object, const_cast<char *>(qPrintable(attr)),const_cast<char *>(qPrintable(value)));
}
/* init:
*/
static void init(int argc, char *argv[], pack_info* pinfo)
{
int c, len;
char buf[BUFSIZ];
char* bp;
agnodeattr(NULL, "label", NODENAME_ESC);
pinfo->mode = l_clust;
pinfo->margin = CL_OFFSET;
pinfo->doSplines = TRUE; /* Use edges in packing */
pinfo->fixed = 0;
pinfo->sz = 0;
opterr = 0;
while ((c = getopt(argc, argv, ":na:gvum:s:o:G:")) != -1) {
switch (c) {
case 'a':
len = strlen(optarg) + 2;
if (len > BUFSIZ)
bp = N_GNEW(len, char);
else
bp = buf;
sprintf (bp, "a%s\n", optarg);
parsePackModeInfo (bp, pinfo->mode, pinfo);
if (bp != buf)
free (bp);
break;
case 'n':
parsePackModeInfo ("node", pinfo->mode, pinfo);
break;
case 's':
gname = optarg;
break;
case 'g':
parsePackModeInfo ("graph", pinfo->mode, pinfo);
break;
case 'm':
setUInt(&pinfo->margin, optarg);
break;
case 'o':
outfp = openFile(optarg, "w");
break;
case 'u':
pinfo->mode = l_undef;
break;
case 'G':
if (*optarg)
setNameValue(optarg);
else
fprintf(stderr,
"gvpack: option -G missing argument - ignored\n");
break;
case 'v':
verbose = 1;
Verbose = 1;
break;
case ':':
fprintf(stderr, "gvpack: option -%c missing argument - ignored\n", optopt);
break;
case '?':
if (optopt == '?')
usage(0);
else
fprintf(stderr,
"gvpack: option -%c unrecognized - ignored\n", optopt);
break;
}
}
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;
}
gboolean
cls_node_expand (ClsNode *cls_node, ClsNodeExpansionType expansion_type)
{
Agsym_t *sym;
GString *label;
gint max_label_items = 0;
gint real_items_length = 0;
gint var_order = -1000;
gint method_order = 0;
IAnjutaSymbol *node_sym;
IAnjutaIterable *iter;
GError *err = NULL;
if (cls_node->expansion_status == expansion_type ||
expansion_type == CLS_NODE_COLLAPSED)
return FALSE;
node_sym =
IANJUTA_SYMBOL (ianjuta_symbol_query_search_id (cls_node->plugin->query_id,
cls_node->klass_id,
&err));
if (err)
{
g_warning ("Symbol ID query failed: %s", err->message);
g_error_free (err);
err = NULL;
}
if (!node_sym)
return FALSE;
if (!(sym = agfindattr(cls_node->graph->proto->n, "shape")))
sym = agnodeattr(cls_node->graph, "shape", "");
agxset (cls_node->agnode, sym->index, "record");
if (!(sym = agfindattr(cls_node->graph->proto->n, "label")))
sym = agnodeattr(cls_node->graph, "label", "");
label = g_string_new ("");
g_string_printf (label, "{%s", cls_node->sym_name);
/* get members from the passed symbol node */
iter = ianjuta_symbol_query_search_members (cls_node->plugin->query_members,
node_sym, &err);
if (err)
{
g_warning ("Class members query failed: %s", err->message);
g_error_free (err);
err = NULL;
}
real_items_length = ianjuta_iterable_get_length (iter, NULL);
/* set the max number of items to draw */
if (real_items_length <= NODE_HALF_DISPLAY_ELEM_NUM ||
expansion_type == CLS_NODE_FULL_EXPANDED)
{
max_label_items = real_items_length;
cls_node->expansion_status = CLS_NODE_FULL_EXPANDED;
}
else
{
max_label_items = NODE_HALF_DISPLAY_ELEM_NUM;
cls_node->expansion_status = CLS_NODE_SEMI_EXPANDED;
}
g_hash_table_remove_all (cls_node->members);
if (iter && real_items_length > 0)
{
gint i = 0;
/* First member variables */
do
{
const gchar *name, *args, *type_name;
IAnjutaSymbol *symbol;
GdkPixbuf *icon;
symbol = IANJUTA_SYMBOL (iter);
name = g_strdup (ianjuta_symbol_get_string (symbol,
IANJUTA_SYMBOL_FIELD_NAME,
NULL));
args = ianjuta_symbol_get_string (symbol,
IANJUTA_SYMBOL_FIELD_SIGNATURE,
NULL);
icon = (GdkPixbuf*) ianjuta_symbol_get_icon (symbol, NULL);
if (!args) /* Member variables */
{
ClsNodeItem *cls_item = g_new0 (ClsNodeItem, 1);
type_name = ianjuta_symbol_get_string (symbol, IANJUTA_SYMBOL_FIELD_TYPE_NAME, NULL);
cls_item->cls_node = cls_node;
cls_item->label = g_strconcat (name, " : ", type_name, NULL);
cls_item->order = var_order++;
if (icon)
g_object_ref (icon);
cls_item->icon = icon;
g_hash_table_insert (cls_node->members,
g_strdup (cls_item->label),
cls_item);
g_string_append_printf (label, "|%s", cls_item->label);
/* Setup file and line */
cls_item->type_name = g_strdup (type_name);
cls_item->line = ianjuta_symbol_get_int (symbol,
IANJUTA_SYMBOL_FIELD_FILE_POS,
NULL);
cls_item->file = ianjuta_symbol_get_file (symbol, NULL);
}
else /* Member methods */
{
ClsNodeItem *cls_item;
gchar *method_key = g_strconcat (name, args, NULL);
cls_item = g_hash_table_lookup (cls_node->members, method_key);
if (cls_item) /* We found an entry for this method */
{
IAnjutaSymbolType sym_type
= ianjuta_symbol_get_sym_type (symbol, NULL);
if (!(sym_type & IANJUTA_SYMBOL_TYPE_PROTOTYPE))
{
/* This one is method, so take this one instead */
g_free (cls_item->args);
cls_item->args = g_strdup (args);
if (cls_item->file) g_object_unref (cls_item->file);
cls_item->file = NULL;
/* Setup file and line */
cls_item->line = ianjuta_symbol_get_int (symbol,
IANJUTA_SYMBOL_FIELD_FILE_POS,
NULL);
cls_item->file = ianjuta_symbol_get_file (symbol, NULL);
}
}
else /* We did not find a member entry, create a new one */
{
ClsNodeItem *cls_item = g_new0 (ClsNodeItem, 1);
type_name = ianjuta_symbol_get_string (symbol,
IANJUTA_SYMBOL_FIELD_RETURNTYPE,
NULL);
cls_item->cls_node = cls_node;
if (type_name)
{
if (strlen (args) > 2)
cls_item->label = g_strconcat (name, "(...)",
" : ", type_name,
NULL);
else
cls_item->label = g_strconcat (name, "()", " : ",
type_name, NULL);
}
else
{
if (strlen (args) > 2)
cls_item->label = g_strconcat (name, "(...)", NULL);
else
cls_item->label = g_strconcat (name, "()", NULL);
}
cls_item->args = g_strdup (args);
cls_item->type_name = g_strdup (type_name);
cls_item->order = method_order++;
if (icon)
g_object_ref (icon);
cls_item->icon = icon;
g_string_append_printf (label, "|%s", cls_item->label);
g_hash_table_insert (cls_node->members, method_key,
cls_item);
/* Setup file and line */
cls_item->line = ianjuta_symbol_get_int (symbol,
IANJUTA_SYMBOL_FIELD_FILE_POS,
NULL);
cls_item->file = ianjuta_symbol_get_file (symbol, NULL);
}
}
i++;
}
while (ianjuta_iterable_next (iter, NULL) && i < max_label_items);
}
if (iter)
g_object_unref (iter);
if (cls_node->expansion_status == CLS_NODE_SEMI_EXPANDED &&
real_items_length > NODE_HALF_DISPLAY_ELEM_NUM)
{
g_string_append_printf (label, "|%s", NODE_SHOW_ALL_MEMBERS_STR);
}
g_string_append_printf (label, "}");
agxset(cls_node->agnode, sym->index, label->str);
/* set the margin for icons */
if (!(sym = agfindattr(cls_node->graph->proto->n, "margin")))
sym = agnodeattr(cls_node->graph, "margin", "0.11,0.055");
agxset(cls_node->agnode, sym->index, "0.3,0.03");
g_string_free (label, TRUE);
return TRUE;
}
/*----------------------------------------------------------------------------
* add a node to an Agraph. Check also if the node is yet in the hash_table so
* that we can build the label of the node with the class-data.
*/
static ClsNode*
cls_inherit_create_node (AnjutaClassInheritance *plugin,
const IAnjutaSymbol *node_sym)
{
ClsNode *cls_node;
Agsym_t *sym;
gint font_size;
const gchar *font_name;
#define FONT_SIZE_STR_LEN 16
gchar font_size_str[FONT_SIZE_STR_LEN];
cls_node = g_new0 (ClsNode, 1);
cls_node->graph = plugin->graph;
cls_node->canvas = plugin->canvas;
cls_node->plugin = plugin;
cls_node->sym_manager =
anjuta_shell_get_interface (ANJUTA_PLUGIN (plugin)->shell,
IAnjutaSymbolManager, NULL);
cls_node->sym_name =
g_strdup (ianjuta_symbol_get_string (IANJUTA_SYMBOL (node_sym),
IANJUTA_SYMBOL_FIELD_NAME,
NULL));
cls_node->klass_id =
ianjuta_symbol_get_int (IANJUTA_SYMBOL (node_sym),
IANJUTA_SYMBOL_FIELD_ID,
NULL);
cls_node->members =
g_hash_table_new_full (g_str_hash, g_str_equal,
(GDestroyNotify) g_free,
(GDestroyNotify) cls_node_item_free);
cls_node->expansion_status = CLS_NODE_COLLAPSED;
cls_node->drawn_expansion_status = CLS_NODE_COLLAPSED;
cls_node->edges_to =
g_hash_table_new_full (g_direct_hash, g_direct_equal,
NULL, (GDestroyNotify)cls_node_edge_free);
cls_node->edges_from = g_hash_table_new (g_direct_hash, g_direct_equal);
/* let's add the node to the graph */
if ((cls_node->agnode = agnode (cls_node->graph,
cls_node->sym_name)) == NULL)
{
cls_node_free (cls_node);
return NULL;
}
/* set the font */
if (!(sym = agfindattr(plugin->graph->proto->n, "fontname")))
sym = agnodeattr(plugin->graph, "fontname", "");
font_name =
pango_font_description_get_family (plugin->canvas->style->font_desc);
agxset(cls_node->agnode, sym->index, (char*)font_name);
/* set the font-size */
if (!(sym = agfindattr(plugin->graph->proto->n, "fontsize")))
sym = agnodeattr(plugin->graph, "fontsize", "");
font_size =
pango_font_description_get_size (plugin->canvas->style->font_desc)/
PANGO_SCALE;
/* The above font size in points is with real screen DPI, but graphviz
* rendering is done at fixed INCH_TO_PIXELS_CONVERSION_FACTOR dpi. So
* convert to the right font size points for graphviz.
*/
font_size =
font_size * gdk_screen_get_resolution (gdk_screen_get_default ())
/ INCH_TO_PIXELS_CONVERSION_FACTOR;
snprintf (font_size_str, FONT_SIZE_STR_LEN, "%d", font_size);
agxset(cls_node->agnode, sym->index, font_size_str);
if (!(sym = agfindattr(plugin->graph->proto->n, "ratio")))
sym = agnodeattr(plugin->graph, "ratio", "");
agxset(cls_node->agnode, sym->index, "expand");
/* Set an attribute - in this case one that affects the visible rendering */
if (!(sym = agfindattr(plugin->graph->proto->n, "shape")))
sym = agnodeattr(plugin->graph, "shape", "");
agxset(cls_node->agnode, sym->index, "box");
if (!(sym = agfindattr(plugin->graph->proto->n, "label")))
sym = agnodeattr(plugin->graph, "label", "");
agxset(cls_node->agnode, sym->index, cls_node->sym_name);
return cls_node;
}
static void color(Agraph_t * g)
{
int nn, i, j, cnt;
Agnode_t *n, *v, **nlist;
Agedge_t *e;
char *p;
double x, y, maxrank = 0.0;
double sum[NC], d, lowsat, highsat;
if (agfindattr(g->proto->n, "pos") == NULL) {
fprintf(stderr,
"graph must be run through 'dot' before 'gvcolor'\n");
exit(1);
}
if (agfindattr(g->proto->n, "style") == NULL)
agnodeattr(g, "style", "filled");
if ((p = agget(g, "Defcolor")))
setcolor(p, Defcolor);
if ((p = agget(g, "rankdir")) && (p[0] == 'L'))
LR = 1;
if ((p = agget(g, "flow")) && (p[0] == 'b'))
Forward = 0;
if ((p = agget(g, "saturation"))) {
if (sscanf(p, "%lf,%lf", &lowsat, &highsat) == 2) {
MinRankSaturation = lowsat;
MaxRankSaturation = highsat;
AdjustSaturation = 1;
}
}
/* assemble the sorted list of nodes and store the initial colors */
nn = agnnodes(g);
nlist = (Agnode_t **) malloc(nn * sizeof(Agnode_t *));
i = 0;
for (n = agfstnode(g); n; n = agnxtnode(g, n)) {
nlist[i++] = n;
if ((p = agget(n, "color")))
setcolor(p, ND_x(n));
p = agget(n, "pos");
sscanf(p, "%lf,%lf", &x, &y);
ND_relrank(n) = (LR ? x : y);
if (maxrank < ND_relrank(n))
maxrank = ND_relrank(n);
}
if (LR != Forward)
for (i = 0; i < nn; i++) {
n = nlist[i];
ND_relrank(n) = maxrank - ND_relrank(n);
}
qsort((void *) nlist, (size_t) nn, sizeof(Agnode_t *),
(int (*)(const void *, const void *)) cmpf);
/* this is the pass that pushes the colors through the edges */
for (i = 0; i < nn; i++) {
n = nlist[i];
/* skip nodes that were manually colored */
cnt = 0;
for (j = 0; j < NC; j++)
if (ND_x(n)[j] != 0.0)
cnt++;
if (cnt > 0)
continue;
for (j = 0; j < NC; j++)
sum[j] = 0.0;
cnt = 0;
for (e = agfstedge(g, n); e; e = agnxtedge(g, e, n)) {
v = e->head;
if (v == n)
v = e->tail;
d = ND_relrank(v) - ND_relrank(n) - 0.01;
if (d < 0) {
double t = 0.0;
for (j = 0; j < NC; j++) {
t += ND_x(v)[j];
sum[j] += ND_x(v)[j];
}
if (t > 0.0)
cnt++;
}
}
if (cnt)
for (j = 0; j < NC; j++)
ND_x(n)[j] = sum[j] / cnt;
}
/* apply saturation adjustment and convert color to string */
for (i = 0; i < nn; i++) {
double h, s, b, t;
char buf[64];
n = nlist[i];
t = 0.0;
for (j = 0; j < NC; j++)
t += ND_x(n)[j];
if (t > 0.0) {
h = ND_x(n)[0];
if (AdjustSaturation) {
s = ND_relrank(n) / maxrank;
if (!Forward)
s = 1.0 - s;
s = MinRankSaturation
+ s * (MaxRankSaturation - MinRankSaturation);
} else
s = 1.0;
s = s * ND_x(n)[1];
b = ND_x(n)[2];
} else {
h = Defcolor[0];
s = Defcolor[1];
b = Defcolor[2];
}
sprintf(buf, "%f %f %f", h, s, b);
agset(n, "color", buf);
}
}
static inline Agsym_t* _agnodeattr(Agraph_t* object, QString attr, QString value){
setlocale(LC_NUMERIC,"en_US.UTF-8"); // Débug séparateur de décimales en version française
return agnodeattr(object, const_cast<char *>(qPrintable(attr)),const_cast<char *>(qPrintable(value)));
}
