END_TEST
START_TEST (test_SpeciesReference_setStoichiometryMath)
{
const ASTNode_t *math = SBML_parseFormula("k3 / k2");
StoichiometryMath_t *stoich = StoichiometryMath_create(2, 4);
StoichiometryMath_setMath(stoich, math);
const StoichiometryMath_t * math1;
char * formula;
SpeciesReference_setStoichiometryMath(SR, stoich);
math1 = SpeciesReference_getStoichiometryMath(SR);
fail_unless( math1 != NULL );
formula = SBML_formulaToString(StoichiometryMath_getMath(math1));
fail_unless( formula != NULL );
fail_unless( !strcmp(formula, "k3 / k2") );
fail_unless( SpeciesReference_isSetStoichiometryMath(SR) );
safe_free(formula);
}
END_TEST
START_TEST (test_StoichiometryMath_setMath)
{
ASTNode_t *math = SBML_parseFormula("lambda(x, x^3)");
const ASTNode_t * math1;
char * formula;
StoichiometryMath_setMath(D, math);
math1 = StoichiometryMath_getMath(D);
fail_unless( math1 != NULL );
formula = SBML_formulaToString(math1);
fail_unless( formula != NULL );
fail_unless( !strcmp(formula, "lambda(x, x^3)") );
fail_unless( StoichiometryMath_getMath(D) != math );
fail_unless( StoichiometryMath_isSetMath(D) );
safe_free(formula);
/* Reflexive case (pathological) */
StoichiometryMath_setMath(D, (ASTNode_t *) StoichiometryMath_getMath(D));
math1 = StoichiometryMath_getMath(D);
fail_unless( math1 != NULL );
formula = SBML_formulaToString(math1);
fail_unless( formula != NULL );
fail_unless( !strcmp(formula, "lambda(x, x^3)") );
safe_free(formula);
StoichiometryMath_setMath(D, NULL);
fail_unless( !StoichiometryMath_isSetMath(D) );
if (StoichiometryMath_getMath(D) != NULL)
{
fail("StoichiometryMath_setMath(D, NULL) did not clear ASTNode.");
}
ASTNode_free(math);
}
END_TEST
START_TEST (test_StoichiometryMath_setMath1)
{
ASTNode_t *math = SBML_parseFormula("2 * k");
int i = StoichiometryMath_setMath(D, math);
fail_unless( i == LIBSBML_OPERATION_SUCCESS);
fail_unless( StoichiometryMath_getMath(D) != math );
fail_unless( StoichiometryMath_isSetMath(D) );
i = StoichiometryMath_setMath(D, NULL);
fail_unless( i == LIBSBML_OPERATION_SUCCESS);
fail_unless( StoichiometryMath_getMath(D) == NULL );
fail_unless( !StoichiometryMath_isSetMath(D) );
ASTNode_free(math);
}
SBML_ODESOLVER_API int drawModel(Model_t *m, char* file, char *format)
{
/** if SOSlib has been compiled without graphviz, the graph will be
written to a text file in graphviz' dot format */
#if !USE_GRAPHVIZ
SolverError_error(WARNING_ERROR_TYPE, SOLVER_ERROR_NO_GRAPHVIZ,
"odeSolver has been compiled without GRAPHIZ. ",
"Graphs are printed to stdout in 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;
SpeciesReference_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");
if ( Reaction_getFast(re) )
{
a = agnodeattr(g, "color", "");
agxset(r, a->index, "red");
a = agnodeattr(g, "fontcolor", "");
agxset(r, a->index, "red");
}
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, SpeciesReference_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 = StoichiometryMath_getMath(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, "arrowhead", "");
agxset(e, a->index, "diamond");
a = agedgeattr(g, "arrowtail", "");
agxset(e, a->index, "odiamond");
}
}
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 = StoichiometryMath_getMath(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, "arrowhead", "");
agxset(e, a->index, "diamond");
a = agedgeattr(g, "arrowtail", "");
agxset(e, a->index, "odiamond");
}
}
}
/* 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;
}
