Transition* TransitionBase::getTransitionLocally(string transitionId) {
vector<Transition*>::iterator i;
Transition* transition;
i = transitionSet->begin();
while (i != transitionSet->end()) {
transition = *i;
if (transition->getId() == transitionId) {
return transition;
}
++i;
}
return NULL;
}
void
ResultBecomesNegative::logNegativeResult (const Transition& tr,
const SBase& object)
{
msg =
"The Transition with id '";
msg += tr.getId();
msg += "' includes a resultLevel";
msg += " that may cause the QualitativeSpecies '";
msg += object.getId();
msg += "' to become negative.";
logFailure(object);
}
void
ResultExceedsMaximum::logExceedsMaximum (const Transition& tr,
const SBase& object)
{
msg =
"The <transition> with id '";
msg += tr.getId();
msg += "' includes a resultLevel";
msg += " that may cause the <qualitativeSpecies> '";
msg += object.getId();
msg += "' to exceed its maximumLevel.";
logFailure(object);
}
void
QSAssignedOnce::logMultipleAssignment (const Transition& tr,
const SBase& object,
std::string name)
{
msg =
"The Transition with id '";
msg += tr.getId();
msg += "' includes an Output";
msg += " that uses an assignment to the QualitativeSpecies '";
msg += name;
msg += "' that has already been assigned.";
logFailure(object);
}
string DescriptorGenerator::generateCode() {
string ret = "<descriptor id=\"" + this->getId() + "\" ";
LayoutRegion* region = this->getRegion();
if (region != NULL) {
ret += "region=\"" + region->getId() + "\" ";
}
string player = this->getPlayerName();
if (player != "") {
ret += "player=\"" + player + "\" ";
}
double explicitDuration = this->getExplicitDuration();
if (!isNaN(explicitDuration)) {
ret +="explicitDur=\"" + itos(explicitDuration/1000.0) + "s\" ";
}
if (this->isFreeze()) {
ret+= "freeze=\"true\" ";
}
long repetitions = this->getRepetitions();
if (repetitions > 0) {
ret +="explicitDur=\"" + itos(repetitions) + "\" ";
}
KeyNavigation* keys = this->getKeyNavigation() ;
if (keys != NULL) {
ret += generateKeyNavigation(keys);
}
FocusDecoration* focus = this->getFocusDecoration(); {
if (focus != NULL)
ret += generateFocusDecoration(focus);
}
vector<Transition*>* inputTransitions = this->getInputTransitions();
vector<Transition*>::iterator transIt;
transIt = inputTransitions->begin();
if (transIt != (inputTransitions->end())) {
ret +="transIn=\"";
while (true) {
Transition* transition = *transIt;
ret += transition->getId();
transIt++;
if (transIt != inputTransitions->end()) {
ret +=",";
} else {
ret +="\" ";
break;
}
}
}
vector<Transition*>* outputTransitions = this->getOutputTransitions();
transIt = outputTransitions->begin();
if (transIt != (outputTransitions->end())) {
ret +="transOut=\"";
while (true) {
Transition* transition = *transIt;
ret += transition->getId();
transIt++;
if (transIt != outputTransitions->end()) {
ret +=",";
} else {
ret +="\" ";
break;
}
}
}
vector<Parameter*>* parameters = this->getParameters();
if (parameters->size() == 0) {
ret += "/>";
} else {
ret += ">";
vector<Parameter*>::iterator it;
it = parameters->begin();
while (it != parameters->end()) {
ParameterGenerator* paramGen = static_cast<ParameterGenerator*>(*it);
ret += paramGen->generateCode("descriptorParam", "value") + "\n";
it++;
}
ret += "</descriptor>\n";
}
return ret;
}
END_TEST
START_TEST (test_QualExtension_read_L3V1V1_defaultNS)
{
string filename = string(TestDataDirectory) + "qual-example1-defaultNS.xml";
SBMLDocument *document = readSBMLFromFile(filename.c_str());
fail_unless(document->getPackageName() == "core");
Model *model = document->getModel();
fail_unless(model != NULL);
fail_unless(model->getPackageName() == "core");
// get the Qualitative species
QualModelPlugin* mplugin = static_cast<QualModelPlugin*>(model->getPlugin("qual"));
fail_unless(mplugin != NULL);
fail_unless(mplugin->getNumQualitativeSpecies() == 1);
fail_unless(mplugin->getListOfQualitativeSpecies()->getPackageName() == "qual");
fail_unless(mplugin->getNumTransitions() == 1);
fail_unless(mplugin->getListOfTransitions()->getPackageName() == "qual");
QualitativeSpecies* qs = mplugin->getQualitativeSpecies(0);
fail_unless(qs->getPackageName() == "qual");
fail_unless(qs->getId() == "s1");
fail_unless(qs->getName() == "sss");
fail_unless(qs->getMetaId() == "_ddd");
fail_unless(qs->getCompartment() == "c");
fail_unless(qs->getConstant() == false);
fail_unless(qs->getInitialLevel() == 1);
fail_unless(qs->getMaxLevel() == 4);
Transition* t = mplugin->getTransition(0);
fail_unless(t->getPackageName() == "qual");
fail_unless(t->getId() == "d");
fail_unless(t->getNumInputs() == 1);
fail_unless(t->getNumOutputs() == 1);
fail_unless(t->getNumFunctionTerms() == 1);
fail_unless(t->isSetDefaultTerm() == true);
Input *i = t->getInput(0);
fail_unless(i->getPackageName() == "qual");
fail_unless(i->getId() == "RD");
fail_unless(i->getName() == "aa" );
fail_unless(i->getQualitativeSpecies() == "s1");
fail_unless(i->getTransitionEffect() == INPUT_TRANSITION_EFFECT_NONE );
fail_unless(i->getSign() == INPUT_SIGN_NEGATIVE);
fail_unless(i->getThresholdLevel() == 2);
Output *o = t->getOutput(0);
fail_unless(o->getPackageName() == "qual");
fail_unless(o->getId() == "wd");
fail_unless(o->getName() == "asa" );
fail_unless(o->getQualitativeSpecies() == "s1");
fail_unless(o->getTransitionEffect() == OUTPUT_TRANSITION_EFFECT_PRODUCTION );
fail_unless(o->getOutputLevel() == 2);
FunctionTerm* ft1 = t->getFunctionTerm(0);
fail_unless(ft1->getPackageName() == "qual");
fail_unless(ft1->getResultLevel() == 1);
fail_unless(ft1->getMath() != NULL);
DefaultTerm* dt = t->getDefaultTerm();
fail_unless(dt->getPackageName() == "qual");
fail_unless(dt->getResultLevel() == 2);
delete document;
}
void SubAutomata::addTransition ( Transition trans, Point* p ) {
this->transitionList.push_back(trans);
this->mapTransPoint[trans.getId()] = p;
}
