void NetworkModel::remove_reaction_rule(const ReactionRule& rr)
{
reaction_rule_container_type::iterator
i(std::find(reaction_rules_.begin(), reaction_rules_.end(), rr));
if (i == reaction_rules_.end())
{
throw NotFound("reaction rule not found");
}
reaction_rule_container_type::size_type const
idx(i - reaction_rules_.begin()), last_idx(reaction_rules_.size() - 1);
reaction_rules_map_type::iterator
j(reaction_rules_map_.find(rr.reactants()));
if (j == reaction_rules_map_.end())
{
throw IllegalState("no corresponding map key found");
}
else if ((*j).second.erase(idx) == 0)
{
throw IllegalState("no corresponding map value found");
}
if (idx < last_idx)
{
reaction_rule_container_type::value_type const
last_value(reaction_rules_[last_idx]);
(*i) = last_value;
j = reaction_rules_map_.find(last_value.reactants());
if (j == reaction_rules_map_.end())
{
throw IllegalState("no corresponding map key for the last found");
}
else if ((*j).second.erase(last_idx) == 0)
{
throw IllegalState("no corresponding map value for the last found");
}
(*j).second.insert(idx);
}
reaction_rules_.pop_back();
dirty_ = true;
}
Real ODERatelawCppCallback::deriv_func(
state_container_type const &reactants_state_array,
state_container_type const &products_state_array,
Real const volume, Real const t,
ODEReactionRule const &rr)
{
if (!is_available())
{
throw IllegalState("Callback Function has not been registerd");
}
return this->func_(reactants_state_array, products_state_array, volume, t, rr);
}
Real3 MeshSurface::draw_position(boost::shared_ptr<RandomNumberGenerator>& rng) const
{
#ifdef HAVE_VTK
vtkPolyData* polydata = reader_->GetOutput();
std::vector<double> areas(polydata->GetNumberOfCells());
for (vtkIdType i(0); i < polydata->GetNumberOfCells(); i++)
{
vtkCell* cell = polydata->GetCell(i);
vtkTriangle* triangle = dynamic_cast<vtkTriangle*>(cell);
double p0[3];
double p1[3];
double p2[3];
triangle->GetPoints()->GetPoint(0, p0);
triangle->GetPoints()->GetPoint(1, p1);
triangle->GetPoints()->GetPoint(2, p2);
const double area = vtkTriangle::TriangleArea(p0, p1, p2);
// std::cout << "p0: " << p0[0] << " " << p0[1] << " " << p0[2] << std::endl;
// std::cout << "p1: " << p1[0] << " " << p1[1] << " " << p1[2] << std::endl;
// std::cout << "p2: " << p2[0] << " " << p2[1] << " " << p2[2] << std::endl;
// std::cout << "area of triangle " << i << ": " << area << std::endl;
areas[i] = area;
}
const double rnd = rng->uniform(0.0, std::accumulate(areas.begin(), areas.end(), 0.0));
double totarea = 0.0;
for (vtkIdType i(0); i < polydata->GetNumberOfCells(); i++)
{
totarea += areas[i];
if (rnd < totarea)
{
vtkCell* cell = polydata->GetCell(i);
vtkTriangle* triangle = dynamic_cast<vtkTriangle*>(cell);
double p0[3];
double p1[3];
double p2[3];
triangle->GetPoints()->GetPoint(0, p0);
triangle->GetPoints()->GetPoint(1, p1);
triangle->GetPoints()->GetPoint(2, p2);
const Real3 P0(p0[0], p0[1], p0[2]);
const Real3 P1(p1[0], p1[1], p1[2]);
const Real3 P2(p2[0], p2[1], p2[2]);
const Real p(rng->uniform(0.0, 1.0)), q(rng->uniform(0.0, 1.0 - p));
return (((P1 - P0) * p + (P2 - P0) * q + P0) + shift_) * ratio_;
}
}
throw IllegalState("Never reach here.");
#else
throw NotImplemented("not implemented yet.");
#endif
}
Real ODERatelawCythonCallback::deriv_func(
state_container_type const &reactants_state_array,
state_container_type const &products_state_array,
Real const volume, Real const t,
ODEReactionRule const &rr)
{
if (!is_available())
{
throw IllegalState("Callback Function has not been registerd");
}
ODEReactionRule rr_tempolrary(rr);
return this->indirect_func_(
this->python_func_, reactants_state_array, products_state_array,
volume, t, &rr_tempolrary);
}
void initialize()
{
boost::shared_ptr<Model> expanded(model_->expand(world_->list_species()));
if (!expanded)
{
throw IllegalState("The model failed to be expanded.");
}
expanded_.swap(expanded); // use expanded_, but not model_
const std::vector<Species> species(expanded_->list_species());
for (std::vector<Species>::const_iterator
i(species.begin()); i != species.end(); ++i)
{
if (!(*world_).has_species(*i))
{
(*world_).reserve_species(*i);
}
}
}
void NetworkModel::remove_reaction_rule(const ReactionRule& rr)
{
reaction_rule_container_type::iterator
i(std::find(reaction_rules_.begin(), reaction_rules_.end(), rr));
if (i == reaction_rules_.end())
{
throw NotFound("reaction rule not found");
}
reaction_rule_container_type::size_type const
idx(i - reaction_rules_.begin()), last_idx(reaction_rules_.size() - 1);
if (rr.reactants().size() == 1)
{
first_order_reaction_rules_map_type::iterator
j(first_order_reaction_rules_map_.find(rr.reactants()[0].serial()));
if (j == first_order_reaction_rules_map_.end())
{
throw IllegalState("no corresponding map key found");
}
first_order_reaction_rules_map_type::mapped_type::iterator
k(std::remove((*j).second.begin(), (*j).second.end(), idx));
if (k == (*j).second.end())
{
throw IllegalState("no corresponding map value found");
}
else
{
(*j).second.erase(k, (*j).second.end());
}
}
else if (rr.reactants().size() == 2)
{
second_order_reaction_rules_map_type::iterator
j(second_order_reaction_rules_map_.find(std::make_pair(
rr.reactants()[0].serial(), rr.reactants()[1].serial())));
if (j == second_order_reaction_rules_map_.end())
{
throw IllegalState("no corresponding map key found");
}
second_order_reaction_rules_map_type::mapped_type::iterator
k(std::remove((*j).second.begin(), (*j).second.end(), idx));
if (k == (*j).second.end())
{
throw IllegalState("no corresponding map value found");
}
else
{
(*j).second.erase(k, (*j).second.end());
}
}
if (idx < last_idx)
{
reaction_rule_container_type::value_type const
last_value(reaction_rules_[last_idx]);
(*i) = last_value;
if (last_value.reactants().size() == 1)
{
first_order_reaction_rules_map_type::iterator
j(first_order_reaction_rules_map_.find(
last_value.reactants()[0].serial()));
if (j == first_order_reaction_rules_map_.end())
{
throw IllegalState("no corresponding map key for the last found");
}
first_order_reaction_rules_map_type::mapped_type::iterator
k(std::remove((*j).second.begin(), (*j).second.end(), last_idx));
if (k == (*j).second.end())
{
throw IllegalState("no corresponding map value found");
}
else
{
(*j).second.erase(k, (*j).second.end());
}
(*j).second.push_back(idx);
}
else if (last_value.reactants().size() == 2)
{
second_order_reaction_rules_map_type::iterator
j(second_order_reaction_rules_map_.find(std::make_pair(
last_value.reactants()[0].serial(),
last_value.reactants()[1].serial())));
if (j == second_order_reaction_rules_map_.end())
{
throw IllegalState("no corresponding map key for the last found");
}
second_order_reaction_rules_map_type::mapped_type::iterator
k(std::remove((*j).second.begin(), (*j).second.end(), last_idx));
if (k == (*j).second.end())
{
throw IllegalState("no corresponding map value found");
}
else
{
(*j).second.erase(k, (*j).second.end());
}
(*j).second.push_back(idx);
}
}
reaction_rules_.pop_back();
}
/* Parses a key, checks whether or not it is legal.
* Returns
* 1 if the key is illegal (a nested error message is printed)
* , 0 if succesfull.
*/
static int ParseKey(
LOOK_UP_KEY *k, /* write-only key, if k->t == TEST_NOKEY
* then the end of file is reached
*/
CSF_VS vs) /* value scale */
{
typedef enum STATE { STATE_START, STATE_LOWNUM, STATE_COMMA,
STATE_HIGHNUM, STATE_HIGHTOKEN } STATE;
STATE state = STATE_START;
int t; /* token */
long startLineNr = LexGetLineNr();
while(1)
{
t = LexGetToken();
if (t >= 0 && LexGetLineNr() != startLineNr)
{
if (state == STATE_START) /* parsed empty line */
startLineNr = LexGetLineNr();
else
t = LEX_EOL;
}
switch(state)
{
case STATE_START: switch(t) {
case LEX_NUMBER:
k->t = TEST_ONE;
if (SetNumber(k, TRUE, vs))
return 1;
return 0;
case '[' :
k->t = TEST_GE_INF;
state = STATE_LOWNUM;
break;
case '<' :
k->t = TEST_GT_INF;
state = STATE_LOWNUM;
break;
case 0 :
k->t = TEST_NOKEY;
return 0;
default : return IllegalState(k,t,"$[<");
} break;
case STATE_LOWNUM:
PRECOND(k->t == TEST_GE_INF || k->t == TEST_GT_INF);
switch(t) {
case LEX_NUMBER:
if (SetNumber(k, TRUE, vs))
return 1;
state = STATE_COMMA;
break;
case ',':
k->t = TEST_INF_INF;
state = STATE_HIGHNUM;
break;
default : return IllegalState(k,t,"$,");
} break;
case STATE_COMMA:
if (t != ',')
return IllegalState(k,t,",");
state = STATE_HIGHNUM;
break;
case STATE_HIGHNUM:
POSTCOND(k->t==TEST_GE_INF||k->t==TEST_GT_INF ||k->t==TEST_INF_INF);
switch(t) {
case LEX_NUMBER:
if (SetNumber(k, FALSE, vs))
return 1;
state = STATE_HIGHTOKEN;
if (k->t != TEST_INF_INF && (k->l > k->h) )
{
k->t = TEST_ERROR; // pcrcalc/test69
return RetErrorNested(1,"low value ('%g') of range larger than high value ('%g')", k->l,k->h);
}
break;
case ']':
case '>':
/* already set, by choosing
* intermediate states of k->t
*/
return 0;
default : return IllegalState(k,t,"$]>");
}break;
case STATE_HIGHTOKEN:
POSTCOND(k->t==TEST_GE_INF||k->t==TEST_GT_INF ||k->t==TEST_INF_INF);
switch(t) {
/* inc over enums, that's why particular order */
case ']':
k->t += 3;
return 0;
case '>':
k->t += 6;
return 0;
default : return IllegalState(k,t,"]>");
} break;
} /* eoswitch state */
} /* eowhile */
}
