END_TEST
START_TEST (test_Reaction_setId)
{
const char *id = "J1";
Reaction_setId(R, id);
fail_unless( !strcmp(Reaction_getId(R), id) );
fail_unless( Reaction_isSetId(R) );
if (Reaction_getId(R) == id)
{
fail("Reaction_setId(...) did not make a copy of string.");
}
/* Reflexive case (pathological) */
Reaction_setId(R, Reaction_getId(R));
fail_unless( !strcmp(Reaction_getId(R), id) );
Reaction_setId(R, NULL);
fail_unless( !Reaction_isSetId(R) );
if (Reaction_getId(R) != NULL)
{
fail("Reaction_setId(R, NULL) did not clear string.");
}
}
void prepare_reversible_fast_reaction(Model_t *m, myReaction *re[], mySpecies *sp[], myParameter *param[], myCompartment *comp[], double sim_time, double dt, double *time, myInitialAssignment *initAssign[], char *time_variant_target_id[], unsigned int num_of_time_variant_targets, timeVariantAssignments *timeVarAssign, allocated_memory *mem, copied_AST *cp_AST){
unsigned int i;
unsigned int num_of_reactions = Model_getNumReactions(m);
ASTNode_t *node, *cp_node1, *cp_node2;
myASTNode *myNode = NULL;
myASTNode *copied_myAST[MAX_COPIED_AST];
unsigned int num_of_copied_myAST = 0;
for(i=0; i<num_of_reactions; i++){
if(re[i]->is_fast && re[i]->is_reversible){
node = (ASTNode_t*)KineticLaw_getMath(Reaction_getKineticLaw(re[i]->origin));
node = ASTNode_deepCopy(node);
TRACE(("original math of %s: ", Reaction_getId(re[i]->origin)));
check_AST(node, NULL);
/* alter_tree_structure(m, &node, cp_AST); */
alter_tree_structure(m, &node, NULL, 0, cp_AST);
set_local_para_as_value(node, Reaction_getKineticLaw(re[i]->origin));
TRACE(("alterated math of %s : ", Reaction_getId(re[i]->origin)));
check_AST(node, NULL);
cp_node1 = ASTNode_deepCopy(node);
cp_node2 = ASTNode_deepCopy(node);
/* get products numerator */
myNode = (myASTNode*)malloc(sizeof(myASTNode));
copied_myAST[num_of_copied_myAST++] = myNode;
myNode->origin = cp_node1;
myNode->parent = NULL;
myNode->left = NULL;
myNode->right = NULL;
myASTNode_create(myNode, cp_node1, copied_myAST, &num_of_copied_myAST);
re[i]->products_equili_numerator = (equation*)malloc(sizeof(equation));
TRACE(("target_id is %s\n", Species_getId(re[i]->reactants[0]->mySp->origin)));
check_AST(cp_node1, NULL);
_prepare_reversible_fast_reaction(m, myNode, re[i], sp, param, comp, re, sim_time, dt, time, initAssign, time_variant_target_id, num_of_time_variant_targets, timeVarAssign, (char*)Species_getId(re[i]->reactants[0]->mySp->origin), 0, mem);
/* get reactants numerator */
myNode = (myASTNode*)malloc(sizeof(myASTNode));
copied_myAST[num_of_copied_myAST++] = myNode;
myNode->origin = cp_node2;
myNode->parent = NULL;
myNode->left = NULL;
myNode->right = NULL;
re[i]->reactants_equili_numerator = (equation*)malloc(sizeof(equation));
myASTNode_create(myNode, cp_node2, copied_myAST, &num_of_copied_myAST);
TRACE(("target_id is %s\n", Species_getId(re[i]->products[0]->mySp->origin)));
check_AST(cp_node2, NULL);
_prepare_reversible_fast_reaction(m, myNode, re[i], sp, param, comp, re, sim_time, dt, time, initAssign, time_variant_target_id, num_of_time_variant_targets, timeVarAssign, (char*)Species_getId(re[i]->products[0]->mySp->origin), 1, mem);
myASTNode_free(copied_myAST, num_of_copied_myAST);
}
}
}
/**
* \fn void SBML_score(Model_t *mod, pEspeces molecules, pScore result, double *reactions_ratio, int nbReactions, int nbEspeces)
* \author Amine Ghozlane
* \brief Alloc memory and initialize the struct Especes
* \param mod Model of the SBML file
* \param molecules Struct Especes
* \param result Struct Score
* \param reactions_ratio List of computed reaction ratio
* \param nbReactions Number of reactions
* \param nbEspeces Number of molecules
*/
void SBML_score(Model_t *mod, pEspeces molecules, pScore result, double *reactions_ratio, int nbReactions, int nbEspeces)
{
/* Fonction de score */
int i, resultat=OK;
Reaction_t *react=NULL;
const char *kf=NULL;
KineticLaw_t *kl=NULL;
/* Enregistre le score des especes */
Especes_scoreSpecies(molecules, nbEspeces, result->name, result->quantite);
/* Enregistre le ratio des reactions */
for (i = 0; i < (nbReactions); i++) {
react = Model_getReaction(mod, i);
if(result->name[nbEspeces+i]==NULL){
result->name[nbEspeces+i]=(char*)malloc(((int)strlen((char *)Reaction_getId(react))+1)*sizeof(char));
assert(result->name[nbEspeces+i]!=NULL);
strcpy(result->name[nbEspeces+i],(char *)Reaction_getId(react));
}
/* Recherche si la reaction est etudiee*/
resultat = SBML_findReaction(result->reaction, result->name[nbEspeces+i], result->nb_reaction);
/* Recuperation de la loi cinetique sur la */
kl = Reaction_getKineticLaw(react);
/* Reaction dont on recherche le bon ratio*/
if(resultat!=OK) result->quantite[nbEspeces+i]=reactions_ratio[resultat];
else if(KineticLaw_isSetFormula(kl)){
kf = KineticLaw_getFormula(kl);
result->quantite[nbEspeces+i]=SBML_evalExpression(kf);
}
else { /*Sinon on n'utilise pas ces informations*/
fprintf(stderr,"SBML equation are taken into account, use instead the parameter file\n");
exit(EXIT_FAILURE);
}
}
}
END_TEST
START_TEST (test_Reaction_setId2)
{
int i = Reaction_setId(R, "cell");
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( Reaction_isSetId(R) );
fail_unless( !strcmp(Reaction_getId(R), "cell" ));
i = Reaction_setId(R, NULL);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( !Reaction_isSetId(R) );
}
/**
* \fn void SBML_setReactions(Model_t *mod, pEspeces molecules, pScore result, double *reactions_ratio, int nbReactions, int nbEspeces)
* \author Amine Ghozlane
* \brief Alloc memory and initialize the struct Especes
* \param mod Model of the SBML file
* \param molecules Struct Especes
* \param result Struct Score
* \param reactions_ratio List of computed reaction ratio
* \param nbReactions Number of reaction
* \param nbEspeces Number of molecules
*/
void SBML_setReactions(Model_t *mod, pEspeces molecules, pScore result, double *reactions_ratio, int nbReactions, int nbEspeces)
{
/* Initialisation les reactions auquelles participent chaque espece */
int ref = 0, i, j, resultat=OK;
SpeciesReference_t *reactif=NULL;
Species_t *especeId=NULL;
Reaction_t *react=NULL;
const char *kf=NULL;
/*const ASTNode_t *km;*/
KineticLaw_t *kl=NULL;
/* Recherche les reactions ou apparaissent chaque espece */
for (i = 0; i < nbReactions; i++) {
react = Model_getReaction(mod, i);
/* Recherche si la reaction est etudiee */
resultat = SBML_findReaction(result->reaction,Reaction_getId(react), result->nb_reaction);
/* Etude des reactifs */
for (j = 0; j < (int)Reaction_getNumReactants(react); j++) {
/* Recuperation d'un reactif */
reactif = Reaction_getReactant(react, j);
/* Recuperation du nom de l'espece */
especeId = Model_getSpeciesById(mod, SpeciesReference_getSpecies(reactif));
/* Recherche la reference de cette molecule dans la struture molecule */
ref = Especes_find(molecules, Species_getId(especeId), nbEspeces);
/* Recuperation de la loi cinetique sur la */
kl = Reaction_getKineticLaw(react);
/* Reaction dont on recherche le bon ratio */
if(resultat!=OK){
Especes_allocReactions(molecules, ref, react, reactions_ratio[resultat]);
}
/* Si la loi cinetique est au format : formule on recupere le ratio en question */
else if (KineticLaw_isSetFormula(kl)) {
kf = KineticLaw_getFormula(kl);
Especes_allocReactions(molecules, ref, react, SBML_evalExpression(kf));
} else { /* Sinon on n'utilise pas ces informations */
/*km = KineticLaw_getMath(kl);*/
fprintf(stderr,"SBML equation are taken into account, use instead the parameter file\n");
/*exit(EXIT_FAILURE);*/
}
}
}
}
void
printReactionMath (unsigned int n, Reaction_t *r)
{
char *formula;
KineticLaw_t *kl;
if (Reaction_isSetKineticLaw(r))
{
kl = Reaction_getKineticLaw(r);
if ( KineticLaw_isSetMath(kl) )
{
formula = SBML_formulaToDot( KineticLaw_getMath(kl) );
fprintf(fout, "subgraph cluster%u {\n", noClusters);
fprintf(fout, "label=\"Reaction: %s\";\n%s\n", Reaction_getId(r), formula);
free(formula);
noClusters++;
}
}
}
int
main (int argc, char* argv[])
{
unsigned int i,j,errors;
const char* filename;
SBMLDocument_t* document;
Model_t* m;
if (argc != 2)
{
printf("\nUsage: printNotes filename\n\n");
return 1;
}
filename = argv[1];
document = readSBML(filename);
errors = SBMLDocument_getNumErrors( document);
printf("\n%s\n\n", filename);
if(errors > 0)
{
SBMLDocument_printErrors(document, stderr);
SBMLDocument_free(document);
return errors;
}
/* Model */
m = SBMLDocument_getModel(document);
printNotes((SBase_t*)m, Model_getId(m));
for(i=0; i < Model_getNumReactions(m); i++)
{
Reaction_t* re = Model_getReaction( m, i);
printNotes((SBase_t*)re, Reaction_getId(re));
/* SpeciesReference (Reactant) */
for(j=0; j < Reaction_getNumReactants( re); j++)
{
SpeciesReference_t* rt = Reaction_getReactant(re, j);
if (SBase_isSetNotes((SBase_t*) rt)) printf(" ");
printNotes((SBase_t*)rt, SpeciesReference_getSpecies( rt ) );
}
/* SpeciesReference (Product) */
for(j=0; j < Reaction_getNumProducts( re ); j++)
{
SpeciesReference_t* rt = Reaction_getProduct( re, j);
if (SBase_isSetNotes((SBase_t*) rt)) printf(" ");
printNotes((SBase_t*)rt, SpeciesReference_getSpecies( rt ) );
}
/* ModifierSpeciesReference (Modifiers) */
for(j=0; j < Reaction_getNumModifiers( re ); j++)
{
SpeciesReference_t* md = Reaction_getModifier(re, j);
if (SBase_isSetNotes((SBase_t*) md)) printf(" ");
printNotes((SBase_t*)md, SpeciesReference_getSpecies( md ) );
}
/* KineticLaw */
if(Reaction_isSetKineticLaw( re ))
{
KineticLaw_t* kl = Reaction_getKineticLaw( re );
if (SBase_isSetNotes((SBase_t*) kl)) printf(" ");
printNotes((SBase_t*)kl, "");
/* Parameter */
for(j=0; j < KineticLaw_getNumParameters( kl ); j++)
{
Parameter_t* pa = KineticLaw_getParameter( kl, j);
if (SBase_isSetNotes((SBase_t*) pa)) printf(" ");
printNotes((SBase_t*)pa, Parameter_getId(pa));
}
}
}
/* Species */
for(i=0; i < Model_getNumSpecies(m); i++)
{
Species_t* sp = Model_getSpecies(m, i);
printNotes((SBase_t*)sp, Species_getId(sp));
}
/* Compartments */
for(i=0; i < Model_getNumCompartments( m ); i++)
{
Compartment_t* sp = Model_getCompartment(m, i);
printNotes((SBase_t*)sp, Compartment_getId(sp));
}
/* FunctionDefinition */
for(i=0; i < Model_getNumFunctionDefinitions(m); i++)
{
FunctionDefinition_t* sp = Model_getFunctionDefinition(m, i);
printNotes((SBase_t*)sp, FunctionDefinition_getId(sp));
}
/* UnitDefinition */
for(i=0; i < Model_getNumUnitDefinitions(m); i++)
{
UnitDefinition_t* sp = Model_getUnitDefinition( m, i);
printNotes((SBase_t*)sp, UnitDefinition_getId(sp));
}
/* Parameter */
for(i=0; i < Model_getNumParameters( m ); i++)
{
Parameter_t* sp = Model_getParameter( m, i);
printNotes((SBase_t*)sp, Parameter_getId(sp));
}
/* Rule */
for(i=0; i < Model_getNumReactions( m ); i++)
{
Rule_t* sp = Model_getRule(m, i);
printNotes((SBase_t*)sp, "");
}
/* InitialAssignment */
for(i=0; i < Model_getNumInitialAssignments(m); i++)
{
InitialAssignment_t* sp = Model_getInitialAssignment(m, i);
printNotes((SBase_t*)sp, "");
}
/* Event */
for(i=0; i < Model_getNumEvents(m); i++)
{
Event_t* sp = Model_getEvent(m, i);
printNotes((SBase_t*)sp, Event_getId(sp));
/* Trigger */
if(Event_isSetTrigger( sp ))
{
Trigger_t* tg = Event_getTrigger(sp);
if (SBase_isSetNotes( (SBase_t*) tg)) printf( " " );
printNotes((SBase_t*)tg, "");
}
/* Delay */
if(Event_isSetDelay(sp))
{
Delay_t* dl = Event_getDelay(sp);
if (SBase_isSetNotes( (SBase_t*) dl)) printf( " " );
printNotes((SBase_t*) dl, "");
}
/* EventAssignment */
for(j=0; j < Event_getNumEventAssignments(sp); j++)
{
EventAssignment_t* ea = Event_getEventAssignment(sp, j);
if (SBase_isSetNotes( (SBase_t*) ea)) printf( " " );
printNotes((SBase_t*)ea, "");
}
}
/* SpeciesType */
for(i=0; i < Model_getNumSpeciesTypes(m); i++)
{
SpeciesType_t* sp = Model_getSpeciesType(m, i);
printNotes((SBase_t*)sp, SpeciesType_getId(sp));
}
/* Constraints */
for(i=0; i < Model_getNumConstraints(m); i++)
{
Constraint_t* sp = Model_getConstraint(m, i);
printNotes((SBase_t*)sp, "");
}
SBMLDocument_free( document );
return errors;
}
static int
drawModelTxt(Model_t *m, char *file) {
Species_t *s;
Reaction_t *re;
const ASTNode_t *math;
SpeciesReference_t *sref;
ModifierSpeciesReference_t *mref;
int i,j;
int reversible;
char filename[WORDSIZE];
FILE *f;
sprintf(filename, "%s.dot", file);
f = fopen(filename, "w");
fprintf(f ,"digraph reactionnetwork {\n");
fprintf(f ,"label=\"%s\";\n",
Model_isSetName(m) ?
Model_getName(m) : (Model_isSetId(m) ? Model_getId(m) : "noId") );
fprintf(f ,"overlap=scale;\n");
for ( i=0; i<Model_getNumReactions(m); i++ ) {
re = Model_getReaction(m,i);
reversible = Reaction_getReversible(re);
for ( j=0; j<Reaction_getNumModifiers(re); j++ ) {
mref = Reaction_getModifier(re,j);
fprintf(f ,"%s->%s [style=dashed arrowhead=odot];\n",
ModifierSpeciesReference_getSpecies(mref), Reaction_getId(re));
}
for ( j=0; j<Reaction_getNumReactants(re); j++ ) {
sref = Reaction_getReactant(re,j);
fprintf(f ,"%s->%s [label=\"",
SpeciesReference_getSpecies(sref), Reaction_getId(re));
if ( (SpeciesReference_isSetStoichiometryMath(sref)) ) {
math = SpeciesReference_getStoichiometryMath(sref);
if ( (strcmp(SBML_formulaToString(math),"1") !=
0) ) {
fprintf(f ,"%s", SBML_formulaToString(math));
}
}
else {
if ( SpeciesReference_getStoichiometry(sref) != 1) {
fprintf(f ,"%g",SpeciesReference_getStoichiometry(sref));
}
}
if ( reversible == 1 ) {
fprintf(f ,"\" arrowtail=onormal];\n");
}
else {
fprintf(f ,"\" ];\n");
}
}
for ( j=0; j<Reaction_getNumProducts(re); j++ ) {
sref = Reaction_getProduct(re,j);
fprintf(f ,"%s->%s [label=\"",
Reaction_getId(re), SpeciesReference_getSpecies(sref));
if ( (SpeciesReference_isSetStoichiometryMath(sref)) ) {
math = SpeciesReference_getStoichiometryMath(sref);
if ( (strcmp(SBML_formulaToString(math),"1") !=
0) ) {
fprintf(f ,"%s ", SBML_formulaToString(math));
}
}
else {
if ( SpeciesReference_getStoichiometry(sref) != 1) {
fprintf(f ,"%g ",SpeciesReference_getStoichiometry(sref));
}
}
if ( reversible == 1 ) {
fprintf(f ,"\" arrowtail=onormal];\n");
}
else {
fprintf(f ,"\" ];\n");
}
}
}
for ( i=0; i<Model_getNumReactions(m); i++ ) {
re = Model_getReaction(m,i);
fprintf(f ,"%s [label=\"%s\" shape=box];\n",
Reaction_getId(re),
Reaction_isSetName(re) ?
Reaction_getName(re) : Reaction_getId(re));
}
for ( i=0; i<Model_getNumSpecies(m); i++) {
s = Model_getSpecies(m, i);
fprintf(f ,"%s [label=\"%s\"];",
Species_getId(s),
Species_isSetName(s) ? Species_getName(s) : Species_getId(s));
}
fprintf(f ,"}\n");
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;
}
static int printXMGReactionTimeCourse ( cvodeData_t *data )
{
int i, j, k, n;
double maxY, minY, result;
Model_t *m;
Reaction_t *r;
KineticLaw_t *kl;
ASTNode_t **kls;
odeModel_t *om = data->model;
cvodeResults_t *results = data->results;
maxY = 0.0;
minY = 0.0;
fprintf(stderr,
"Printing time development of reaction fluxes to XMGrace!\n");
if ( om->m == NULL ) {
fprintf(stderr, "Error: No reaction model availabe\n");
return 1;
}
else m = om->m;
if ( openXMGrace(data) > 0 ) {
fprintf(stderr, "Error: Couldn't open XMGrace\n");
return 1;
}
GracePrintf("yaxis label \"%s\"", "flux [substance/time]");
if ( Model_isSetName(m) )
GracePrintf("subtitle \"%s, %s\"", Model_getName(m),
"reaction flux time courses");
else if ( Model_isSetId(m) )
GracePrintf("subtitle \"%s, %s\"", Model_getId(m),
"reaction flux time courses");
else
GracePrintf("subtitle \"model has no name, %s/id\"",
"reaction flux time courses");
/* print legend */
for ( i=0; i<Model_getNumReactions(m); i++ ) {
r = Model_getReaction(m, i);
if ( Reaction_isSetName(r) )
GracePrintf("g0.s%d legend \"%s: %s \"\n", i+1,
Reaction_getId(r), Reaction_getName(r));
else
GracePrintf("g0.s%d legend \"%s \"\n", i+1, Reaction_getId(r));
}
GracePrintf("legend 1.155, 0.85");
GracePrintf("legend font 8");
GracePrintf("legend char size 0.6");
if(!(kls = (ASTNode_t **)calloc(Model_getNumReactions(m),
sizeof(ASTNode_t *))))
fprintf(stderr, "failed!\n");
for ( i=0; i<Model_getNumReactions(m); i++ ) {
r = Model_getReaction(m, i);
kl = Reaction_getKineticLaw(r);
kls[i] = copyAST(KineticLaw_getMath(kl));
AST_replaceNameByParameters(kls[i], KineticLaw_getListOfParameters(kl));
AST_replaceConstants(m, kls[i]);
}
/* evaluate flux for each time point and print to XMGrace */
for ( i=0; i<=results->nout; i++ ) {
n = 1;
/* set time and variable values to values at time[k] */
data->currenttime = results->time[i];
for ( j=0; j<data->model->neq; j++ )
data->value[j] = results->value[j][i];
/* evaluate kinetic law expressions */
for ( j=0; j<Model_getNumReactions(m); j++ ) {
result = evaluateAST(kls[j], data);
if ( result > maxY ) {
maxY = result;
GracePrintf("world ymax %g", 1.25*maxY);
}
if ( result < minY ) {
minY = result;
GracePrintf("world ymin %g", 1.25*minY);
}
GracePrintf("g0.s%d point %g, %g",
n, results->time[i], result);
n++;
}
}
GracePrintf("yaxis tick major %g", 1.25*(fabs(maxY)+fabs(minY))/10);
GracePrintf("redraw");
closeXMGrace(data, "flux");
/* free temporary ASTNodes */
for ( i=0; i<Model_getNumReactions(m); i++ )
ASTNode_free(kls[i]);
free(kls);
return 0;
}
void printReactionTimeCourse(cvodeData_t *data, Model_t *m, FILE *f)
{
int i, j;
cvodeResults_t *results;
Reaction_t *r;
KineticLaw_t *kl;
ASTNode_t **kls;
if ( data == NULL || data->results == NULL ) {
Warn(stderr, "No results, please integrate first.\n");
return;
}
#if USE_GRACE
if ( Opt.Xmgrace == 1 ) {
printXMGReactionTimeCourse(data);
return;
}
#endif
results = data->results;
if ( Opt.PrintMessage )
fprintf(stderr,
"\nPrinting time course of the reactions (kinetic laws).\n\n");
if(!(kls =
(ASTNode_t **)calloc(Model_getNumReactions(m),
sizeof(ASTNode_t *)))) {
fprintf(stderr, "failed!\n");
}
fprintf(f, "#t ");
for ( i=0; i<Model_getNumReactions(m); i++ ) {
r = Model_getReaction(m, i);
kl = Reaction_getKineticLaw(r);
kls[i] = copyAST(KineticLaw_getMath(kl));
AST_replaceNameByParameters(kls[i], KineticLaw_getListOfParameters(kl));
AST_replaceConstants(m, kls[i]);
fprintf(f, "%s ", Reaction_getId(r));
}
fprintf(f, "\n");
fprintf(f, "##REACTION RATES\n");
for ( i=0; i<=results->nout; ++i ) {
fprintf(f, "%g ", results->time[i]);
data->currenttime = results->time[i];
for ( j=0; j<data->model->neq; j++ ) {
data->value[j] = results->value[j][i];
}
for ( j=0; j<Model_getNumReactions(m); j++ ) {
fprintf(f, "%g ", evaluateAST(kls[j], data));
}
fprintf(f, "\n");
}
fprintf(f, "##REACTION RATES\n");
fprintf(f, "#t ");
for ( i=0; i<Model_getNumReactions(m); i++ ) {
r = Model_getReaction(m, i);
fprintf(f, "%s ", Reaction_getId(r));
ASTNode_free(kls[i]);
}
free(kls);
fprintf(f, "\n");
fflush(f);
#if !USE_GRACE
if ( Opt.Xmgrace == 1 ) {
fprintf(stderr,
"odeSolver has been compiled without XMGRACE functionality.\n");
fprintf(stderr,
"The requested data have been printed to stdout instead.\n");
}
#endif
}
void printReactions(Model_t *m, FILE *f)
{
int i,j,k;
Reaction_t *r;
SpeciesReference_t *sref;
KineticLaw_t *kl;
Rule_t *rl;
AssignmentRule_t *asr;
AlgebraicRule_t *alr;
RateRule_t *rr;
Event_t *e;
EventAssignment_t *ea;
Parameter_t *p;
FunctionDefinition_t *fd;
SBMLTypeCode_t type;
const ASTNode_t *math;
math = NULL;
fprintf(f, "\n");
for(i=0;i<Model_getNumParameters(m);i++){
if(i==0)
fprintf(f, "# Global parameters:\n");
p = Model_getParameter(m,i);
if(Parameter_isSetId(p))
fprintf(f, "%s ", Parameter_getId(p));
if(Parameter_isSetName(p))
fprintf(f, "(%s) ", Parameter_getName(p));
if(Parameter_isSetValue(p))
fprintf(f, "= %g; ", Parameter_getValue(p));
if(Parameter_isSetUnits(p))
fprintf(f, "[%s]; ", Parameter_getUnits(p));
if(!Parameter_getConstant(p))
fprintf(f, "(variable);");
fprintf(f, "\n");
if ( i==Model_getNumParameters(m)-1 )
fprintf(f, "\n");
}
fprintf(f, "# Reactions:\n");
for ( i=0; i<Model_getNumReactions(m); i++ ) {
r = Model_getReaction(m,i);
fprintf(f, "%s: %s",
Reaction_isSetName(r) ? Reaction_getName(r) : Reaction_getId(r),
Reaction_getFast(r) ? "(fast)" : "");
for ( k=0; k<Reaction_getNumReactants(r); k++ ) {
sref = Reaction_getReactant(r,k);
if ( SpeciesReference_isSetStoichiometryMath(sref) )
fprintf(f, "%s ",
SBML_formulaToString(\
SpeciesReference_getStoichiometryMath(sref)));
else
if ( SpeciesReference_getStoichiometry(sref) != 1. )
fprintf(f, "%g ", SpeciesReference_getStoichiometry(sref));
fprintf(f, "%s", SpeciesReference_getSpecies(sref));
if(k+1<Reaction_getNumReactants(r))
fprintf(f, "%s", " + ");
}
fprintf(f, "%s", Reaction_getReversible(r) ? " <-> " : " -> ");
for ( k=0; k<Reaction_getNumProducts(r); k++ ) {
sref = Reaction_getProduct(r,k);
if ( SpeciesReference_isSetStoichiometryMath(sref) )
fprintf(f, "%s ",
SBML_formulaToString(\
SpeciesReference_getStoichiometryMath(sref)));
else
if ( SpeciesReference_getStoichiometry(sref) != 1. )
fprintf(f, "%g ", SpeciesReference_getStoichiometry(sref));
fprintf(f, "%s", SpeciesReference_getSpecies(sref));
if(k+1<Reaction_getNumProducts(r))
fprintf(f, "%s", " + ");
}
fprintf(f, "; ");
if(Reaction_isSetKineticLaw(r)){
kl = Reaction_getKineticLaw(r);
math = KineticLaw_getMath(kl);
fprintf(f, "%s;", SBML_formulaToString(math));
for(k=0;k<KineticLaw_getNumParameters(kl);k++){
p = KineticLaw_getParameter(kl,k);
fprintf(f, " %s", Parameter_getId(p));
if(Parameter_isSetName(p))
fprintf(f, " (%s)", Parameter_getName(p));
if(Parameter_isSetValue(p))
fprintf(f, " = %g", Parameter_getValue(p));
if(Parameter_isSetUnits(p))
fprintf(f, " [%s]", Parameter_getUnits(p));
if ( !Parameter_getConstant(p) )
fprintf(f, " (variable)");
fprintf(f, ";");
}
/* fprintf(f, "\n"); */
}else
fprintf(f, "# no rate law is set for this reaction.");
fprintf(f, "\n");
}
for(i=0;i<Model_getNumRules(m);i++){
rl = Model_getRule(m,i);
if ( i == 0 ) {
fprintf(f, "# Rules:\n");
}
type = SBase_getTypeCode((SBase_t *)rl);
if ( type == SBML_RATE_RULE ) {
rr = (RateRule_t *) rl;
fprintf(f, " rateRule: d%s/dt = ", RateRule_getVariable(rr));
}
if ( type == SBML_ALGEBRAIC_RULE ) {
alr = (AlgebraicRule_t *) rl;
fprintf(f, " algebraicRule: 0 = ");
}
if ( type == SBML_ASSIGNMENT_RULE ) {
asr = (AssignmentRule_t *) rl;
fprintf(f, " assignmentRule (%s): %s = ",
RuleType_toString(AssignmentRule_getType(asr)),
AssignmentRule_getVariable(asr));
}
if(!Rule_isSetMath(rl)){
if(Rule_isSetFormula(rl)){
Rule_setMathFromFormula(rl);
}
}
if(Rule_isSetMath(rl))
fprintf(f, "%s\n", SBML_formulaToString(Rule_getMath(rl)));
}
fprintf(f, "\n");
for(i=0;i<Model_getNumEvents(m);i++){
if(i==0)
fprintf(f, "# Events:\n");
e = Model_getEvent(m,i);
if(Event_isSetId(e))
fprintf(f, "%s: ", Event_getId(e));
if(Event_isSetName(e))
fprintf(f, "(%s) ", Event_getName(e));
if(Event_isSetTrigger(e)) {
math = Event_getTrigger(e);
fprintf(f, "trigger: %s\n", SBML_formulaToString(math));
}
if(Event_isSetDelay(e))
fprintf(f, "delay: %s;\n", SBML_formulaToString(Event_getDelay(e)));
if(Event_isSetTimeUnits(e))
fprintf(f, "time Units: %s;\n", Event_getTimeUnits(e));
for(k=0;k<Event_getNumEventAssignments(e);k++){
ea = Event_getEventAssignment(e,k);
if(EventAssignment_isSetVariable(ea))
fprintf(f, " event: %s = %s;\n",
EventAssignment_getVariable(ea),
EventAssignment_isSetMath(ea) ?
SBML_formulaToString(EventAssignment_getMath(ea)) :
"# no math set;\n");
}
if(i==Model_getNumEvents(m)-1)
fprintf(f, "\n");
}
for ( i=0; i<Model_getNumFunctionDefinitions(m); i++ ) {
if ( i==0 ) fprintf(f, "# Functions:\n");
fd = Model_getFunctionDefinition(m,i);
if ( FunctionDefinition_isSetName(fd) )
fprintf(f, "%s: ", FunctionDefinition_getName(fd));
if(FunctionDefinition_isSetId(fd) && FunctionDefinition_isSetMath(fd)){
fprintf(f, "%s( ", FunctionDefinition_getId(fd));
math = FunctionDefinition_getMath(fd);
for(j=0;j<ASTNode_getNumChildren(math)-1;j++){
fprintf(f, "%s", SBML_formulaToString(ASTNode_getChild(math, j)));
if(j<ASTNode_getNumChildren(math)-2)
fprintf(f, ", ");
if(j==ASTNode_getNumChildren(math)-2)
fprintf(f, ") = ");
}
fprintf(f, "%s;", SBML_formulaToString(ASTNode_getRightChild(math)));
}
fprintf(f, "\n");
}
}