/* convert from L1 to L3 */
void
Model::convertL3ToL2 (bool strict)
{
dealWithModelUnits();
dealWithStoichiometry();
dealWithEvents(strict);
for (unsigned int i = 0; i < getNumReactions(); i++)
{
Reaction *r = getReaction(i);
if (r->isSetKineticLaw())
{
KineticLaw *kl = r->getKineticLaw();
for (unsigned int j = 0; j < kl->getNumLocalParameters(); j++)
{
Parameter *lp = new Parameter(getLevel(), getVersion());
(*lp) = *(kl->getLocalParameter(j));
kl->addParameter(lp);
}
}
}
}
void
Model::removeDuplicateTopLevelAnnotations()
{
unsigned int i, n;
this->removeDuplicateAnnotations();
if (getNumFunctionDefinitions() > 0)
{
getListOfFunctionDefinitions()->removeDuplicateAnnotations();
for (i = 0; i < getNumFunctionDefinitions(); i++)
{
getFunctionDefinition(i)->removeDuplicateAnnotations();
}
}
if (getNumUnitDefinitions() > 0)
{
getListOfUnitDefinitions()->removeDuplicateAnnotations();
for (i = 0; i < getNumUnitDefinitions(); i++)
{
getUnitDefinition(i)->removeDuplicateAnnotations();
getUnitDefinition(i)->getListOfUnits()->removeDuplicateAnnotations();
for (n = 0; n < getUnitDefinition(i)->getNumUnits(); n++)
{
getUnitDefinition(i)->getUnit(n)->removeDuplicateAnnotations();
}
}
}
if (getNumCompartmentTypes() > 0)
{
getListOfCompartmentTypes()->removeDuplicateAnnotations();
for (i = 0; i < getNumCompartmentTypes(); i++)
{
getCompartmentType(i)->removeDuplicateAnnotations();
}
}
if (getNumSpeciesTypes() > 0)
{
getListOfSpeciesTypes()->removeDuplicateAnnotations();
for (i = 0; i < getNumSpeciesTypes(); i++)
{
getSpeciesType(i)->removeDuplicateAnnotations();
}
}
if (getNumCompartments() > 0)
{
getListOfCompartments()->removeDuplicateAnnotations();
for (i = 0; i < getNumCompartments(); i++)
{
getCompartment(i)->removeDuplicateAnnotations();
}
}
if (getNumSpecies() > 0)
{
getListOfSpecies()->removeDuplicateAnnotations();
for (i = 0; i < getNumSpecies(); i++)
{
getSpecies(i)->removeDuplicateAnnotations();
}
}
if (getNumParameters() > 0)
{
getListOfParameters()->removeDuplicateAnnotations();
for (i = 0; i < getNumParameters(); i++)
{
getParameter(i)->removeDuplicateAnnotations();
}
}
if (getNumInitialAssignments() > 0)
{
getListOfInitialAssignments()->removeDuplicateAnnotations();
for (i = 0; i < getNumInitialAssignments(); i++)
{
getInitialAssignment(i)->removeDuplicateAnnotations();
}
}
if (getNumConstraints() > 0)
{
getListOfConstraints()->removeDuplicateAnnotations();
for (i = 0; i < getNumConstraints(); i++)
{
getConstraint(i)->removeDuplicateAnnotations();
}
}
if (getNumRules() > 0)
{
getListOfRules()->removeDuplicateAnnotations();
for (i = 0; i < getNumRules(); i++)
{
getRule(i)->removeDuplicateAnnotations();
}
}
if (getNumReactions() > 0)
{
getListOfReactions()->removeDuplicateAnnotations();
for (i = 0; i < getNumReactions(); i++)
{
Reaction * r = getReaction(i);
r->removeDuplicateAnnotations();
if (r->getNumReactants() > 0)
{
r->getListOfReactants()->removeDuplicateAnnotations();
for (n = 0; n < r->getNumReactants(); n++)
{
r->getReactant(n)->removeDuplicateAnnotations();
}
}
if (r->getNumProducts() > 0)
{
r->getListOfProducts()->removeDuplicateAnnotations();
for (n = 0; n < r->getNumProducts(); n++)
{
r->getProduct(n)->removeDuplicateAnnotations();
}
}
if (r->getNumModifiers() > 0)
{
r->getListOfModifiers()->removeDuplicateAnnotations();
for (n = 0; n < r->getNumModifiers(); n++)
{
r->getModifier(n)->removeDuplicateAnnotations();
}
}
if (r->isSetKineticLaw())
{
r->getKineticLaw()->removeDuplicateAnnotations();
if (r->getKineticLaw()->getNumParameters() > 0)
{
r->getKineticLaw()->getListOfParameters()
->removeDuplicateAnnotations();
for (n = 0; n < r->getKineticLaw()->getNumParameters(); n++)
{
r->getKineticLaw()->getParameter(n)->removeDuplicateAnnotations();
}
}
}
}
}
if (getNumEvents() > 0)
{
getListOfEvents()->removeDuplicateAnnotations();
for (i = 0; i < getNumEvents(); i++)
{
getEvent(i)->removeDuplicateAnnotations();
if (getEvent(i)->getNumEventAssignments() > 0)
{
getEvent(i)->getListOfEventAssignments()->removeDuplicateAnnotations();
for (n = 0; n < getEvent(i)->getNumEventAssignments(); n++)
{
getEvent(i)->getEventAssignment(n)->removeDuplicateAnnotations();
}
}
}
}
}
void
Model::convertStoichiometryMath()
{
unsigned int n, j;
Reaction * r;
SpeciesReference *sr;
unsigned int idCount = 0;
char newid[15];
std::string id;
for (n = 0; n < getNumReactions(); n++)
{
r = getReaction(n);
for (j = 0; j < r->getNumReactants(); j++)
{
sr = r->getReactant(j);
if (sr->isSetStoichiometryMath())
{
if (!sr->isSetId())
{
sprintf(newid, "generatedId_%u", idCount);
id.assign(newid);
sr->setId(id);
idCount++;
}
else
{
id = sr->getId();
}
sr->setConstant(false);
AssignmentRule * ar = createAssignmentRule();
ar->setVariable(id);
if (sr->getStoichiometryMath()->isSetMath())
{
ar->setMath(sr->getStoichiometryMath()->getMath());
}
}
}
for (j = 0; j < r->getNumProducts(); j++)
{
sr = r->getProduct(j);
if (sr->isSetStoichiometryMath())
{
if (!sr->isSetId())
{
sprintf(newid, "generatedId_%u", idCount);
id.assign(newid);
sr->setId(id);
idCount++;
}
else
{
id = sr->getId();
}
sr->setConstant(false);
AssignmentRule * ar = createAssignmentRule();
ar->setVariable(id);
if (sr->getStoichiometryMath()->isSetMath())
{
ar->setMath(sr->getStoichiometryMath()->getMath());
}
}
}
}
}
void
Model::removeSBOTermsNotInL2V2(bool strict)
{
unsigned int n, i;
if (strict == true)
{
for (n = 0; n < getNumUnitDefinitions(); n++)
{
getUnitDefinition(n)->unsetSBOTerm();
for (i = 0; i < getUnitDefinition(n)->getNumUnits(); i++)
{
getUnitDefinition(n)->getUnit(i)->unsetSBOTerm();
}
}
for (n = 0; n < getNumCompartments(); n++)
{
getCompartment(n)->unsetSBOTerm();
}
for (n = 0; n < getNumSpecies(); n++)
{
getSpecies(n)->unsetSBOTerm();
}
for (n = 0; n < getNumCompartmentTypes(); n++)
{
getCompartmentType(n)->unsetSBOTerm();
}
for (n = 0; n < getNumSpeciesTypes(); n++)
{
getSpeciesType(n)->unsetSBOTerm();
}
for (n = 0; n < getNumReactions(); n++)
{
for (i = 0; i < getReaction(n)->getNumReactants(); i++)
{
if (getReaction(n)->getReactant(i)->isSetStoichiometryMath())
{
getReaction(n)->getReactant(i)->getStoichiometryMath()->unsetSBOTerm();
}
}
for (i = 0; i < getReaction(n)->getNumProducts(); i++)
{
if (getReaction(n)->getProduct(i)->isSetStoichiometryMath())
{
getReaction(n)->getProduct(i)->getStoichiometryMath()->unsetSBOTerm();
}
}
}
for (n = 0; n < getNumEvents(); n++)
{
if (getEvent(n)->isSetTrigger())
{
getEvent(n)->getTrigger()->unsetSBOTerm();
}
if (getEvent(n)->isSetDelay())
{
getEvent(n)->getDelay()->unsetSBOTerm();
}
}
}
}
void
Model::removeSBOTerms(bool strict)
{
unsigned int n, i;
if (strict == true)
{
unsetSBOTerm();
for (n = 0; n < getNumUnitDefinitions(); n++)
{
getUnitDefinition(n)->unsetSBOTerm();
for (i = 0; i < getUnitDefinition(n)->getNumUnits(); i++)
{
getUnitDefinition(n)->getUnit(i)->unsetSBOTerm();
}
}
for (n = 0; n < getNumCompartments(); n++)
{
getCompartment(n)->unsetSBOTerm();
}
for (n = 0; n < getNumSpecies(); n++)
{
getSpecies(n)->unsetSBOTerm();
}
for (n = 0; n < getNumParameters(); n++)
{
getParameter(n)->unsetSBOTerm();
}
for (n = 0; n < getNumRules(); n++)
{
getRule(n)->unsetSBOTerm();
}
for (n = 0; n < getNumReactions(); n++)
{
getReaction(n)->unsetSBOTerm();
for (i = 0; i < getReaction(n)->getNumReactants(); i++)
{
getReaction(n)->getReactant(i)->unsetSBOTerm();
if (getReaction(n)->getReactant(i)->isSetStoichiometryMath())
{
getReaction(n)->getReactant(i)->getStoichiometryMath()->unsetSBOTerm();
}
}
for (i = 0; i < getReaction(n)->getNumProducts(); i++)
{
getReaction(n)->getProduct(i)->unsetSBOTerm();
if (getReaction(n)->getProduct(i)->isSetStoichiometryMath())
{
getReaction(n)->getProduct(i)->getStoichiometryMath()->unsetSBOTerm();
}
}
for (i = 0; i < getReaction(n)->getNumModifiers(); i++)
{
getReaction(n)->getModifier(i)->unsetSBOTerm();
}
if (getReaction(n)->isSetKineticLaw())
{
getReaction(n)->getKineticLaw()->unsetSBOTerm();
}
}
for (n = 0; n < getNumFunctionDefinitions(); n++)
{
getFunctionDefinition(n)->unsetSBOTerm();
}
for (n = 0; n < getNumEvents(); n++)
{
getEvent(n)->unsetSBOTerm();
for (i = 0; i < getEvent(n)->getNumEventAssignments(); i++)
{
getEvent(n)->getEventAssignment(i)->unsetSBOTerm();
}
if (getEvent(n)->isSetTrigger())
{
getEvent(n)->getTrigger()->unsetSBOTerm();
}
if (getEvent(n)->isSetDelay())
{
getEvent(n)->getDelay()->unsetSBOTerm();
}
}
}
}
void
Model::dealWithStoichiometry()
{
unsigned int idCount = 0;
for (unsigned int i = 0; i < getNumReactions(); i++)
{
Reaction *r = getReaction(i);
unsigned int j;
for (j = 0; j < r->getNumReactants(); j++)
{
SpeciesReference *sr = r->getReactant(j);
if (sr->isSetStoichiometry() == false)
{
if (sr->isSetId() == false)
{
createNoValueStoichMath(*this, *sr, idCount);
idCount++;
}
else
{
// id is set it could be used by initialAssignment
// used by rule
// not used
if (getInitialAssignment(sr->getId()) != NULL)
{
useStoichMath(*this, *sr, false);
}
else if (getRule(sr->getId()) != NULL)
{
//assignmentRule
if (getRule(sr->getId())->getTypeCode() == SBML_ASSIGNMENT_RULE)
{
useStoichMath(*this, *sr, true);
}
else if (getRule(sr->getId())->getTypeCode() == SBML_RATE_RULE)
{
createParameterAsRateRule(*this, *sr, *(getRule(sr->getId())), idCount);
idCount++;
}
}
else
{
createNoValueStoichMath(*this, *sr, idCount);
idCount++;
}
}
}
else
{
// stoichiometry is set
if (sr->isSetId())
{
// id is set it could be used by initialAssignment
// used by rule
// not used
if (getInitialAssignment(sr->getId()) != NULL)
{
useStoichMath(*this, *sr, false);
}
else if (getRule(sr->getId()) != NULL)
{
//assignmentRule
if (getRule(sr->getId())->getTypeCode() == SBML_ASSIGNMENT_RULE)
{
useStoichMath(*this, *sr, true);
}
else if (getRule(sr->getId())->getTypeCode() == SBML_RATE_RULE)
{
createParameterAsRateRule(*this, *sr, *(getRule(sr->getId())), idCount);
idCount++;
}
}
}
// no id set - do not need to do anything
}
}
for (j = 0; j < r->getNumProducts(); j++)
{
SpeciesReference *sr = r->getProduct(j);
if (sr->isSetStoichiometry() == false)
{
if (sr->isSetId() == false)
{
createNoValueStoichMath(*this, *sr, idCount);
idCount++;
}
else
{
// id is set it could be used by initialAssignment
// used by rule
// not used
if (getInitialAssignment(sr->getId()) != NULL)
{
useStoichMath(*this, *sr, false);
}
else if (getRule(sr->getId()) != NULL)
{
//assignmentRule
if (getRule(sr->getId())->getTypeCode() == SBML_ASSIGNMENT_RULE)
{
useStoichMath(*this, *sr, true);
}
else if (getRule(sr->getId())->getTypeCode() == SBML_RATE_RULE)
{
createParameterAsRateRule(*this, *sr, *(getRule(sr->getId())), idCount);
idCount++;
}
}
else
{
createNoValueStoichMath(*this, *sr, idCount);
idCount++;
}
}
}
else
{
// stoichiometry is set
if (sr->isSetId())
{
// id is set it could be used by initialAssignment
// used by rule
// not used
if (getInitialAssignment(sr->getId()) != NULL)
{
useStoichMath(*this, *sr, false);
}
else if (getRule(sr->getId()) != NULL)
{
//assignmentRule
if (getRule(sr->getId())->getTypeCode() == SBML_ASSIGNMENT_RULE)
{
useStoichMath(*this, *sr, true);
}
else if (getRule(sr->getId())->getTypeCode() == SBML_RATE_RULE)
{
createParameterAsRateRule(*this, *sr, *(getRule(sr->getId())), idCount);
idCount++;
}
}
}
// no id set - do not need to do anything
}
}
}
}
void
Model::assignRequiredValues()
{
// when converting to L3 some attributes which have default values in L1/L2
// but are required in L3 are not present or set
unsigned int i, n;
if (getNumUnitDefinitions() > 0)
{
for (i = 0; i < getNumUnitDefinitions(); i++)
{
for (n = 0; n < getUnitDefinition(i)->getNumUnits(); n++)
{
Unit *u = getUnitDefinition(i)->getUnit(n);
if (!u->isSetExponent())
u->setExponent(1.0);
if (!u->isSetScale())
u->setScale(0);
if (!u->isSetMultiplier())
u->setMultiplier(1.0);
}
}
}
if (getNumCompartments() > 0)
{
for (i = 0; i < getNumCompartments(); i++)
{
Compartment *c = getCompartment(i);
c->setConstant(c->getConstant());
}
}
if (getNumSpecies() > 0)
{
for (i = 0; i < getNumSpecies(); i++)
{
Species * s = getSpecies(i);
s->setBoundaryCondition(s->getBoundaryCondition());
s->setHasOnlySubstanceUnits(s->getHasOnlySubstanceUnits());
s->setConstant(s->getConstant());
}
}
if (getNumParameters() > 0)
{
for (i = 0; i < getNumParameters(); i++)
{
Parameter * p = getParameter(i);
p->setConstant(p->getConstant());
}
}
if (getNumReactions() > 0)
{
for (i = 0; i < getNumReactions(); i++)
{
Reaction * r = getReaction(i);
r->setFast(r->getFast());
r->setReversible(r->getReversible());
if (r->getNumReactants() > 0)
{
for (n = 0; n < r->getNumReactants(); n++)
{
SpeciesReference *sr = r->getReactant(n);
if (sr->isSetStoichiometryMath())
{
sr->setConstant(false);
}
else
{
sr->setConstant(true);
}
}
}
if (r->getNumProducts() > 0)
{
for (n = 0; n < r->getNumProducts(); n++)
{
SpeciesReference *sr = r->getProduct(n);
if (sr->isSetStoichiometryMath())
{
sr->setConstant(false);
}
else
{
sr->setConstant(true);
}
}
}
}
}
if (getNumEvents() > 0)
{
for (i = 0; i < getNumEvents(); i++)
{
Event * e = getEvent(i);
e->setUseValuesFromTriggerTime(e->getUseValuesFromTriggerTime());
if (e->isSetTrigger())
{
Trigger *t = e->getTrigger();
t->setPersistent(true);
t->setInitialValue(true);
}
}
}
}
static int callBackWithLogKeeping(int iter, int popSz, GApopulation pop, double * fitnessArray, int *** parentsArray)
{
unsigned long long * seeds;
double f;
int i,j,k,*parents, num = 10*popSz, max = 0, stop = 0;
int * temp = 0, * ids = 0;
GAindividual * p;
//save
int each_fitness = PRINT_EACH_FITNESS,
each_script = PRINT_EACH_SCRIPT,
each_size = PRINT_EACH_SIZE,
each_best_lineage = PRINT_EACH_BEST_LINEAGE,
each_all_fitness = PRINT_EACH_ALL_FITNESS,
each_all_lineage = PRINT_EACH_ALL_LINEAGE;
if (USER_CALLBACK_FNC)
stop = USER_CALLBACK_FNC(iter,popSz,pop,fitnessArray, parentsArray);
if (!stop)
stop = (iter == _MAX_ITER);
if (stop)
{
//cheat
PRINT_EACH_FITNESS = PRINT_FINAL_FITNESS;
PRINT_EACH_SCRIPT = PRINT_FINAL_SCRIPT;
PRINT_EACH_SIZE = PRINT_FINAL_SIZE;
PRINT_EACH_BEST_LINEAGE = PRINT_FINAL_BEST_LINEAGE;
PRINT_EACH_ALL_FITNESS = PRINT_FINAL_ALL_FITNESS;
PRINT_EACH_ALL_LINEAGE = PRINT_FINAL_ALL_LINEAGE;
//printf("\n========final results=======\n");
fprintf(LOGFILE,"\n========final results=======\n");
if (LOGFILE && PRINT_SEEDS)
{
seeds = getMTseeds();
fprintf(LOGFILE,"random number generator seeds: %llf,%llf,%llf,%llf\n",seeds[0],seeds[1],seeds[2],seeds[3]);
}
}
if (iter == 0) //header
{
printf("gen");
fprintf(LOGFILE,"gen");
if (PRINT_EACH_FITNESS && !PRINT_EACH_ALL_FITNESS)
{
printf("\tfitness ");
fprintf(LOGFILE,"\tfitness ");
}
if (PRINT_EACH_ALL_FITNESS)
{
for (i=0; i < popSz; ++i)
{
//printf("\tfitness_%i",i);
fprintf(LOGFILE,"\tfitness_%i",i);
}
}
if (PRINT_EACH_SIZE)
{
printf("\tspecies\treactions");
fprintf(LOGFILE,"\tspecies\treactions");
}
if (TRACK_NETWORK_PARENTS && (PRINT_EACH_BEST_LINEAGE || PRINT_EACH_ALL_LINEAGE))
{
//printf("\tparents");
fprintf(LOGFILE,"\tparents");
}
printf("\n");
fprintf(LOGFILE,"\n");
printf("---");
fprintf(LOGFILE,"---");
if (PRINT_EACH_FITNESS && !PRINT_EACH_ALL_FITNESS)
{
printf("\t------- ");
fprintf(LOGFILE,"\t------- ");
}
if (PRINT_EACH_ALL_FITNESS)
{
for (i=0; i < popSz; ++i)
{
//printf("\t----------",i);
fprintf(LOGFILE,"\t -------- ",i);
}
}
if (PRINT_EACH_SIZE)
{
printf("\t-------\t---------");
fprintf(LOGFILE,"\t-------\t---------");
}
if (TRACK_NETWORK_PARENTS && (PRINT_EACH_BEST_LINEAGE || PRINT_EACH_ALL_LINEAGE))
{
//printf("\t-------");
fprintf(LOGFILE,"\t-------");
}
printf("\n");
fprintf(LOGFILE,"\n");
}
if (TRACK_NETWORK_PARENTS && (PRINT_EACH_BEST_LINEAGE || PRINT_EACH_ALL_LINEAGE))
{
ids = (int*)malloc(num * sizeof(int));
for (i=0; i < num; ++i)
ids[i] = 0;
for (i=0; i < popSz; ++i)
{
p = pop[i];
if (!p) continue;
parents = GAgetOriginalParents(i,iter,parentsArray);
if (parents)
{
for (j=0; parents[j] > 0; ++j)
{
if (parents[j] >= max)
max = parents[j];
if (parents[j] >= num)
{
temp = ids;
ids = (int*)malloc( num * 2 * sizeof(int) );
for (k=0; k < num; ++k)
ids[k] = temp[k];
num *= 2;
for (; k < num; ++k)
ids[k] = 0;
free(temp);
}
ids[ parents[j] ] += 1;
}
}
else
{
}
if (PRINT_EACH_BEST_LINEAGE && !PRINT_EACH_ALL_LINEAGE)
break;
}
}
printf("%i",iter);
fprintf(LOGFILE,"%i",iter);
if (PRINT_EACH_FITNESS && !PRINT_EACH_ALL_FITNESS)
{
f = fitnessArray[0];
printf("\t%lf",f);
fprintf(LOGFILE,"\t%lf",f);
}
if (PRINT_EACH_ALL_FITNESS)
{
for (i=0; i < popSz; ++i)
{
f = fitnessArray[i];
//printf("\t%lf",f);
fprintf(LOGFILE,"\t%lf",f);
}
}
if (PRINT_EACH_SIZE)
{
printf("\t%i\t%i",getNumSpecies(pop[0]),getNumReactions(pop[0]));
fprintf(LOGFILE,"\t%i\t%i",getNumSpecies(pop[0]),getNumReactions(pop[0]));
}
if (TRACK_NETWORK_PARENTS && (PRINT_EACH_BEST_LINEAGE || PRINT_EACH_ALL_LINEAGE))
{
for (i=0; i < max; ++i)
{
//printf("\t%i",ids[i]);
fprintf(LOGFILE,"\t%i",ids[i]);
}
}
if (PRINT_EACH_SCRIPT)
{
//printf("\n========script=======\n");
fprintf(LOGFILE,"\n========script=======\n");
//printNetwork(stdout,pop[0]);
printNetwork(LOGFILE,pop[0]);
//printf("\n=====================\n");
fprintf(LOGFILE,"\n=====================\n");
}
printf("\n");
fprintf(LOGFILE,"\n");
if (ids && (num > 0))
free(ids);
if (iter == _MAX_ITER)
{
//restore
PRINT_EACH_FITNESS = each_fitness;
PRINT_EACH_SCRIPT = each_script;
PRINT_EACH_SIZE = each_size;
PRINT_EACH_BEST_LINEAGE = each_best_lineage;
PRINT_EACH_ALL_FITNESS = each_all_fitness;
PRINT_EACH_ALL_LINEAGE = each_all_lineage;
}
return stop;
}
