int
main (int argc, char* argv[])
{
if (argc != 2)
{
cout << endl << "Usage: printNotes filename" << endl << endl;
return 1;
}
unsigned int i,j;
const char* filename = argv[1];
SBMLDocument* document;
SBMLReader reader;
document = reader.readSBML(filename);
unsigned int errors = document->getNumErrors();
cout << endl;
cout << "filename: " << filename << endl;
cout << endl;
if(errors > 0)
{
document->printErrors(cerr);
delete document;
return errors;
}
/* Model */
Model* m = document->getModel();
printNotes(m);
for(i=0; i < m->getNumReactions(); i++)
{
Reaction* re = m->getReaction(i);
printNotes(re);
/* SpeciesReference (Reacatant) */
for(j=0; j < re->getNumReactants(); j++)
{
SpeciesReference* rt = re->getReactant(j);
if (rt->isSetNotes()) cout << " ";
printNotes(rt, (rt->isSetSpecies() ? rt->getSpecies() : std::string("")) );
}
/* SpeciesReference (Product) */
for(j=0; j < re->getNumProducts(); j++)
{
SpeciesReference* rt = re->getProduct(j);
if (rt->isSetNotes()) cout << " ";
printNotes(rt, (rt->isSetSpecies() ? rt->getSpecies() : std::string("")) );
}
/* ModifierSpeciesReference (Modifier) */
for(j=0; j < re->getNumModifiers(); j++)
{
ModifierSpeciesReference* md = re->getModifier(j);
if (md->isSetNotes()) cout << " ";
printNotes(md, (md->isSetSpecies() ? md->getSpecies() : std::string("")) );
}
/* Kineticlaw */
if(re->isSetKineticLaw())
{
KineticLaw* kl = re->getKineticLaw();
if (kl->isSetNotes()) cout << " ";
printNotes(kl);
/* Parameter */
for(j=0; j < kl->getNumParameters(); j++)
{
Parameter* pa = kl->getParameter(j);
if (pa->isSetNotes()) cout << " ";
printNotes(pa);
}
}
}
/* Species */
for(i=0; i < m->getNumSpecies(); i++)
{
Species* sp = m->getSpecies(i);
printNotes(sp);
}
/* Compartment */
for(i=0; i < m->getNumCompartments(); i++)
{
Compartment* sp = m->getCompartment(i);
printNotes(sp);
}
/* FunctionDefinition */
for(i=0; i < m->getNumFunctionDefinitions(); i++)
{
FunctionDefinition* sp = m->getFunctionDefinition(i);
printNotes(sp);
}
/* UnitDefinition */
for(i=0; i < m->getNumUnitDefinitions(); i++)
{
UnitDefinition* sp = m->getUnitDefinition(i);
printNotes(sp);
}
/* Parameter */
for(i=0; i < m->getNumParameters(); i++)
{
Parameter* sp = m->getParameter(i);
printNotes(sp);
}
/* Rule */
for(i=0; i < m->getNumRules(); i++)
{
Rule* sp = m->getRule(i);
printNotes(sp);
}
/* InitialAssignment */
for(i=0; i < m->getNumInitialAssignments(); i++)
{
InitialAssignment* sp = m->getInitialAssignment(i);
printNotes(sp);
}
/* Event */
for(i=0; i < m->getNumEvents(); i++)
{
Event* sp = m->getEvent(i);
printNotes(sp);
/* Trigger */
if(sp->isSetTrigger())
{
const Trigger* tg = sp->getTrigger();
if (tg->isSetNotes()) cout << " ";
printNotes(const_cast<Trigger*>(tg));
}
/* Delay */
if(sp->isSetDelay())
{
const Delay* dl = sp->getDelay();
if (dl->isSetNotes()) cout << " ";
printNotes(const_cast<Delay*>(dl));
}
/* EventAssignment */
for(j=0; j < sp->getNumEventAssignments(); j++)
{
EventAssignment* ea = sp->getEventAssignment(j);
if (ea->isSetNotes()) cout << " ";
printNotes(ea);
}
}
/* SpeciesType */
for(i=0; i < m->getNumSpeciesTypes(); i++)
{
SpeciesType* sp = m->getSpeciesType(i);
printNotes(sp);
}
/* Constraint */
for(i=0; i < m->getNumConstraints(); i++)
{
Constraint* sp = m->getConstraint(i);
printNotes(sp);
}
delete document;
return errors;
}
/**
* Load a gene network from an SBML file. Overrides Structure.load(). Format must
* be equal GeneNetwork.SBML. Note, the SBML file must be in the exact same format
* as the SBML files produced by writeSBML(). In particular, we assume that reactions are listed
* *ordered* as we do in writeSBML().
* @param filename URL to the file describing the network to load
* @param format File format (GML, DOT, etc.)
* @throws IOException
*/
void GeneNetwork::load_sbml(const char *filename) {
SBMLDocument* document;
SBMLReader reader;
document = reader.readSBML(filename);
unsigned int errors = document->getNumErrors();
if (errors > 0) {
std::cerr << "Failed to open file " << filename << std::endl;
exit(1);
}
Model *m = document->getModel();
// -----------------------------------------
// Set the network size and create the genes
// do not count the species _void_
int size = m->getNumSpecies() - 1;
ListOfSpecies *species = m->getListOfSpecies();
for (int g=0; g < size; g++) {
if (species->get(g)->getId() != "_void_") {
//HillGene hg = new HillGene(this);
//hg.setLabel(species.get(g).getId());
HillGene *n = new HillGene(species->get(g)->getId());
//n.setLabel(species->get(g)->getId());
nodes_.push_back(*n);
delete n;
}
}
x_ = Vec_DP(nodes_.size());
x_ = 0;
y_ = Vec_DP(nodes_.size());
y_ = 0;
//vector<string> parameterNames; // the names of the parameters
//vector<double> parameterValues; // the values of the parameters
std::map<std::string, double> params;
std::vector<std::string> inputNodes; // the indexes of the inputs
HillGene src, tgt;
Parameter *param;
// 2 loops for one gene: both synthesis and degradation reactions
// (we assume that reactions are listed *ordered* as we do in writeSBML())
//int counter = 0;
for (unsigned int i=0; i < m->getNumReactions(); i++) {
Reaction *re = m->getReaction(i);
std::string id = re->getId();
std::stringstream ss;
ss << i;
//::logging::log::emit<Debug>() << id.c_str() <<
// ::logging::log::endl;
tgt = nodes_.at(getIndexOfNode(getGeneReactantId(id)));
//tgt->setLabel(getGeneReactantId(*re));
//SpeciesReference *rt = re->getReactant(0);
//Node *tgt = new HillGene();
//tgt->setLabel(rt->getSpecies());
//ListOfSpeciesReferences *modifiers = re->getListOfModifiers();
for (unsigned int j=0; j < re->getNumModifiers(); j++) {
ModifierSpeciesReference *md = re->getModifier(j);
src = nodes_.at(getIndexOfNode(md->getSpecies()));
inputNodes.push_back(src.getLabel());
// set output genes
std::vector<std::string> outputs = src.getOutputGenes();
outputs.push_back(tgt.getLabel());
src.setOutputGenes(outputs);
// The edge type is unknown for now, it is initialized later
Edge *e = new Edge(&src, &tgt, "+-");
edges_.push_back(*e);
//delete src;
delete e;
}
KineticLaw *kl = re->getKineticLaw();
for(unsigned int j=0; j < kl->getNumParameters(); j++) {
param = kl->getParameter(j);
params[param->getId()] = param->getValue();
//char buf[256];
//sprintf(buf, "%s\t%f", param->getId().c_str(), param->getValue());
//::logging::log::emit<Info>() << buf << ::logging::log::endl;
}
//::logging::log::emit<Info>() << ::logging::log::dec << params.size() <<
// ::logging::log::endl;
// in the second iteration for this gene
if (i%2 == 1) {
// set parameters in gene
//tgt.initialization(params, inputNodes);
nodes_.at(getIndexOfNode(getGeneReactantId(id))).initialization(params, inputNodes);;
//char buf[256];
//sprintf(buf, "%f", params["k_1"]);
//::logging::log::emit<Info>() << buf << ::logging::log::endl;
inputNodes.clear(); // don't clear because the reference was copied to the gene
//parameterNames.clear(); // reset (they were not copied)
//parameterValues.clear();
params.clear();
}
//counter++;
}
//setEdgeTypesAccordingToDynamicalModel();
//signed_ = true;
//delete document;
//delete n;
//delete e;
}
