void Term::get_all_arguments(int fun_id, int arg_num, set<Term*> & args)
{
switch(this->get_term_type())
{
case CONSTANT_TERM:
case VARIABLE_TERM:
return;
case FUNCTION_TERM:
{
FunctionTerm* ft = (FunctionTerm*)this;
if(ft->get_id() == fun_id){
assert((int) ft->get_args().size() > arg_num);
args.insert(ft->get_args()[arg_num]);
}
for(unsigned int i=0; i < ft->get_args().size(); i++)
{
ft->get_args()[i]->get_all_arguments(fun_id, arg_num, args);
}
return;
}
case ARITHMETIC_TERM:
{
ArithmeticTerm* at = (ArithmeticTerm*) this;
const map<Term*, long int>& elems = at->get_elems();
map<Term*, long int>::const_iterator it = elems.begin();
for(; it!=elems.end(); it++)
{
it->first->get_all_arguments(fun_id, arg_num, args);
}
return;
}
default:
assert(false);
}
}
LIBSBML_CPP_NAMESPACE_USE
int main(int argc,char** argv)
{
if (argc != 2)
{
std::cout << "Usage: example1\n";
return 1;
}
//
// Creates an SBMLNamespaces object with the given SBML level, version
// package name, package version.
//
// (NOTE) By defualt, the name of package (i.e. "qual") will be used
// if the arugment for the prefix is missing or empty. Thus the argument
// for the prefix can be added as follows:
//
// SBMLNamespaces sbmlns(3,1,"qual",1,"QUAL");
//
SBMLNamespaces sbmlns(3,1,"qual",1);
//
// (NOTES) The above code creating an SBMLNamespaces object can be replaced
// with one of the following other styles.
//
// (1) Creates an SBMLNamespace object with a SBML core namespace and then
// adds a qual package namespace to the object.
//
// SBMLNamespaces sbmlns(3,1);
// sbmlns.addPkgNamespace("qual",1);
//
// OR
//
// SBMLNamespaces sbmlns(3,1);
// sbmlns.addNamespace(QualExtension::XmlnsL3V1V1,"qual");
//
// (2) Creates a QualPkgNamespaces object (SBMLNamespace derived class for
// qual package. The class is basically used for createing an SBase
// derived objects defined in the qual package) with the given SBML
// level, version, and package version
//
// QualPkgNamespaces sbmlns(3,1,1);
//
// create the document
SBMLDocument *document = new SBMLDocument(&sbmlns);
// mark qual as required
document->setPackageRequired("qual", true);
// create the Model
Model* model=document->createModel();
// create the Compartment
Compartment* compartment = model->createCompartment();
compartment->setId("c");
compartment->setConstant(true);
//
// Get a QualModelPlugin object plugged in the model object.
//
// The type of the returned value of SBase::getPlugin() function is
// SBasePlugin*, and thus the value needs to be casted for the
// corresponding derived class.
//
QualModelPlugin* mplugin
= static_cast<QualModelPlugin*>(model->getPlugin("qual"));
// create the QualitativeSpecies
QualitativeSpecies* qs = mplugin->createQualitativeSpecies();
qs->setId("s1");
qs->setCompartment("c");
qs->setConstant(false);
qs->setInitialLevel(1);
qs->setMaxLevel(4);
qs->setName("sss");
// create the Transition
Transition* t = mplugin->createTransition();
t->setId("d");
t->setSBOTerm(1);
Input* i = t->createInput();
i->setId("RD");
i->setQualitativeSpecies("s1");
i->setTransitionEffect(INPUT_TRANSITION_EFFECT_NONE);
i->setSign(INPUT_SIGN_NEGATIVE);
i->setThresholdLevel(2);
i->setName("aa");
Output* o = t->createOutput();
o->setId("wd");
o->setQualitativeSpecies("s1");
o->setTransitionEffect(OUTPUT_TRANSITION_EFFECT_PRODUCTION);
o->setOutputLevel(2);
o->setName("aa");
DefaultTerm* dt = t->createDefaultTerm();
dt->setResultLevel(2) ;
FunctionTerm* ft = t->createFunctionTerm();
ASTNode* math = SBML_parseL3Formula("geq(s1, 2)");
ft->setResultLevel(1);
ft->setMath(math);
writeSBML(document,"qual_example1.xml");
delete document;
return 0;
}
END_TEST
START_TEST (test_QualExtension_create_add_and_write_L3V1V1)
{
const char* s1 =
"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
"<sbml xmlns=\"http://www.sbml.org/sbml/level3/version1/core\" xmlns:qual=\"http://www.sbml.org/sbml/level3/version1/qual/version1\" level=\"3\" version=\"1\" qual:required=\"true\">\n"
" <model>\n"
" <listOfCompartments>\n"
" <compartment id=\"c\" constant=\"true\"/>\n"
" </listOfCompartments>\n"
" <qual:listOfQualitativeSpecies>\n"
" <qual:qualitativeSpecies metaid=\"ddd\" qual:id=\"s1\" qual:compartment=\"c\" qual:constant=\"false\" qual:name=\"sss\" qual:initialLevel=\"1\" qual:maxLevel=\"4\"/>\n"
" </qual:listOfQualitativeSpecies>\n"
" <qual:listOfTransitions>\n"
" <qual:transition sboTerm=\"SBO:0000001\" qual:id=\"d\">\n"
" <qual:listOfInputs>\n"
" <qual:input qual:id=\"RD\" qual:qualitativeSpecies=\"s1\" qual:transitionEffect=\"none\" qual:name=\"aa\" qual:sign=\"negative\" qual:thresholdLevel=\"2\"/>\n"
" </qual:listOfInputs>\n"
" <qual:listOfOutputs>\n"
" <qual:output qual:id=\"wd\" qual:qualitativeSpecies=\"s1\" qual:transitionEffect=\"production\" qual:name=\"aa\" qual:outputLevel=\"2\"/>\n"
" </qual:listOfOutputs>\n"
" <qual:listOfFunctionTerms>\n"
" <qual:defaultTerm qual:resultLevel=\"1\"/>\n"
" <qual:functionTerm qual:resultLevel=\"2\">\n"
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
" <apply>\n"
" <geq/>\n"
" <ci> s1 </ci>\n"
" <cn type=\"integer\"> 2 </cn>\n"
" </apply>\n"
" </math>\n"
" </qual:functionTerm>\n"
" </qual:listOfFunctionTerms>\n"
" </qual:transition>\n"
" </qual:listOfTransitions>\n"
" </model>\n"
"</sbml>\n"
;
QualPkgNamespaces *sbmlns = new QualPkgNamespaces(3,1,1);
// create the document
SBMLDocument *document = new SBMLDocument(sbmlns);
//// mark qual as required
document->setPackageRequired("qual", true);
// create the Model
Model* model= new Model(sbmlns);
// create the Compartment
Compartment* compartment = new Compartment(sbmlns);
compartment->setId("c");
compartment->setConstant(true);
fail_unless(model->addCompartment(compartment) == LIBSBML_OPERATION_SUCCESS);
//// create the QualitativeSpecies
QualModelPlugin* mplugin = static_cast<QualModelPlugin*>(model->getPlugin("qual"));
fail_unless(mplugin != NULL);
QualitativeSpecies* qs = new QualitativeSpecies(sbmlns);
fail_unless(qs->setId("s1") == LIBSBML_OPERATION_SUCCESS);
fail_unless(qs->setCompartment("c") == LIBSBML_OPERATION_SUCCESS);
fail_unless(qs->setConstant(false) == LIBSBML_OPERATION_SUCCESS);
fail_unless(qs->setInitialLevel(1) == LIBSBML_OPERATION_SUCCESS);
fail_unless(qs->setMaxLevel(4) == LIBSBML_OPERATION_SUCCESS);
fail_unless(qs->setName("sss") == LIBSBML_OPERATION_SUCCESS);
fail_unless(qs->setMetaId("ddd") == LIBSBML_OPERATION_SUCCESS);
fail_unless(mplugin->addQualitativeSpecies(qs) == LIBSBML_OPERATION_SUCCESS);
Transition* t = new Transition(sbmlns);
fail_unless(t->setId("d") == LIBSBML_OPERATION_SUCCESS);
fail_unless(t->setSBOTerm(1) == LIBSBML_OPERATION_SUCCESS);
Input* i = new Input(sbmlns);
fail_unless(i->setId("RD") == LIBSBML_OPERATION_SUCCESS);
fail_unless(i->setQualitativeSpecies("s1") == LIBSBML_OPERATION_SUCCESS);
fail_unless(i->setTransitionEffect
(InputTransitionEffect_fromString("none")) == LIBSBML_OPERATION_SUCCESS);
fail_unless(i->setSign(InputSign_fromString("negative"))
== LIBSBML_OPERATION_SUCCESS);
fail_unless(i->setThresholdLevel(2) == LIBSBML_OPERATION_SUCCESS);
fail_unless(i->setName("aa") == LIBSBML_OPERATION_SUCCESS);
fail_unless(t->addInput(i) == LIBSBML_OPERATION_SUCCESS);
Output* o = new Output(sbmlns);
fail_unless(o->setId("wd") == LIBSBML_OPERATION_SUCCESS);
fail_unless(o->setQualitativeSpecies("s1") == LIBSBML_OPERATION_SUCCESS);
fail_unless(o->setTransitionEffect
(OutputTransitionEffect_fromString("production")) == LIBSBML_OPERATION_SUCCESS);
fail_unless(o->setOutputLevel(2) == LIBSBML_OPERATION_SUCCESS);
fail_unless(o->setName("aa") == LIBSBML_OPERATION_SUCCESS);
fail_unless(t->addOutput(o) == LIBSBML_OPERATION_SUCCESS);
FunctionTerm* ft = new FunctionTerm(sbmlns);
ASTNode* math = SBML_parseL3Formula("geq(s1, 2)");
fail_unless(ft->setResultLevel(2) == LIBSBML_OPERATION_SUCCESS);
fail_unless(ft->setMath(math) == LIBSBML_OPERATION_SUCCESS);
fail_unless(t->addFunctionTerm(ft) == LIBSBML_OPERATION_SUCCESS);
DefaultTerm* dt = new DefaultTerm(sbmlns);
fail_unless(dt->setResultLevel(1) == LIBSBML_OPERATION_SUCCESS);
fail_unless(t->setDefaultTerm(dt) == LIBSBML_OPERATION_SUCCESS);
fail_unless(mplugin->addTransition(t) == LIBSBML_OPERATION_SUCCESS);
fail_unless(document->setModel(model) == LIBSBML_OPERATION_SUCCESS);
char *s2 = writeSBMLToString(document);
fail_unless(strcmp(s1,s2) == 0);
free(s2);
delete document;
}
/*
* Substitutes variables if there are any
* active subtituitons & byuilds the fun_arg_universal
* and reverse_fun_arg universal maps. This is
* recursive since we need to cdr down
* nested function terms.
*/
Term* UniversalInstantiator::process_term(Term* t, map<int,int> & var_subs,
int fun_id, int arg_num, QuantifiedLeaf* ql)
{
if(t->get_term_type() == CONSTANT_TERM) return t;
if(t->get_term_type() == VARIABLE_TERM){
VariableTerm* vt = (VariableTerm*)t;
int var_id = vt->get_var_id();
if(var_subs.count(var_id)>0){
Term* new_vt = VariableTerm::make(var_subs[var_id]);
return new_vt;
}
else if(fun_id != -1 && ql!= NULL &&
ql->get_quantified_vars().count(var_id) >0)
{
assert(arg_num != -1);
qvar qv;
//qv.orig_id = ql->get_orig_id();
qv.id = (long int) ql;
qv.var_id = var_id;
map<int, int> *fun_map = NULL;
if(fun_arg_universal.count(qv)>0) {
fun_map = fun_arg_universal[qv];
}
else
{
fun_map = new map<int, int>();
fun_arg_universal[qv] = fun_map;
}
if(fun_map->count(fun_id) == 0){
(*fun_map)[fun_id] = arg_num;
pair<int, int> key(fun_id, arg_num);
set<qvar>* val = reverse_fun_arg_universal[key];
if(val == NULL){
val = new set<qvar>();
reverse_fun_arg_universal[key] = val;
}
val->insert(qv);
}
else {
if((*fun_map)[fun_id] != arg_num)
return NULL;
}
}
return t;
}
if(t->get_term_type() == FUNCTION_TERM)
{
FunctionTerm* ft = (FunctionTerm*)t;
vector<Term*> new_args;
for(unsigned int i=0; i < ft->get_args().size(); i++)
{
Term* cur_arg = process_term(ft->get_args()[i], var_subs,
ft->get_id(), i, ql);
if(cur_arg == NULL){
return NULL;
}
new_args.push_back(cur_arg);
}
Term* new_ft = FunctionTerm::make(ft->get_id(), new_args,
ft->is_invertible());
return new_ft;
}
else {
assert(t->get_term_type() == ARITHMETIC_TERM);
ArithmeticTerm* at = (ArithmeticTerm*) t;
bool changed = false;
map<Term*, long int> new_elems;
map<Term*, long int>::const_iterator it = at->get_elems().begin();
for(; it!= at->get_elems().end(); it++){
Term* new_t = process_term(it->first, var_subs, -1, -1, ql);
if(new_t == NULL) return NULL;
new_elems[new_t] = it->second;
}
if(!changed) return at;
Term* new_at = ArithmeticTerm::make(new_elems, at->get_constant());
return new_at;
}
}