Agent* BlindAgentFactory::createAgent()
{
//Create the agent and the Database
Agent *bond = new Agent();
Hive::Database *db = bond->getDatabase();
// //////////////////////////////////////////////////////////////////
// Create the base Data objects that are needed by the blind agent
/////////////////////////////////////////////////////////////////////
// type name
StringData *mytypename = new StringData("mytypename", "hans");
db->addData(mytypename->getName(), mytypename);
// Internal clock
DoubleData *celltime = new DoubleData("celltime", 0.0);
db->addData(celltime->getName(), celltime);
// record the last dt
DoubleData *dt = new DoubleData("dt", 0);
db->addData(dt);
DoubleData *noutt = new DoubleData("nextOutputTime", 0.0);
db->addData(noutt->getName(), noutt);
// Equilibration Time used by chemotaxis model
DoubleData *eqtime = new DoubleData("eqtime", cpi->getEqTime());
db->addData(eqtime->getName(), eqtime);
// Output frequency of data from the cell may or may not be used
DoubleData *outputinterval_Data = new DoubleData("outputinterval",this->output_interval);
db->addData(outputinterval_Data->getName(), outputinterval_Data);
// at the present the world as well as the metabolism simulatots can only handle one ligand profile
TVectorData<double> *ligands = new TVectorData<double> ("ligands","tvector_double");
ligands->reserveSize(1);
ligands->at(0) = 0;
db->addData(ligands->getName(),ligands);
// this stores how much nutrient a cell would like to get from the world
TVectorData<double> *appetite = new TVectorData<double> ("appetite", "tvector_double");
appetite->reserveSize(1);
appetite->at(0) = 0;
db->addData(appetite->getName(), appetite);
// parameter that sets the base effeciency at which nutrient is removed and added to energy
DoubleData *effeciency = new DoubleData("base_effeciency_of_conversion", 1);
db->addData(effeciency);
DoubleData *r1 = new DoubleData("r1", 1);
db->addData(r1);
// Marker of the generation of the cell
IntegerData *generationData = new IntegerData("generation",0);
db->addData(generationData);
/// flag that will be set by the death simulator, if the cell has to die
BoolData *death_flag = new BoolData("death_flag", false);
db->addData(death_flag->getName(), death_flag);
/// flag that will be set by the birth simulator, if the cell gives rise to offspring
BoolData *birth_flag = new BoolData("birth_flag", false);
db->addData(birth_flag->getName(), birth_flag);
// UPDATED METABOLISM / BIRTH / DEATH SIMULATOR
// starting or default values, same for all cells
double starting_essence = 0.5;
double default_kcat = 5;
double default_Km = 0.1;
double default_essence_cost_for_movement = 0.025;
double default_mass_threshold_for_birth = 1;
double default_essence_threshold_for_death = 0.000001;
double default_background_death_rate_per_unit_time = 0; // not sure whether it is a good idea to have this in the cell.
double default_yield = 1;
bool default_is_levy = false;
double default_parameter_for_steplength_dist = 1;
double default_rho = 0.3;
double default_velocity = 2;
double default_current_angle = 2.0;
double default_distance_desired_to_travel = 0.0;
double default_traveled_distance = 0.0;
// create the data items storing these parameters
DoubleData *essence = new DoubleData("essence",starting_essence);
// kcat and Km are the rescaled variables
DoubleData *kcat = new DoubleData("kcat",default_kcat);
DoubleData *Km = new DoubleData("Km",default_Km);
// this is the parameter alpha
DoubleData *essence_cost_for_movement = new DoubleData("essence_cost_for_movement",default_essence_cost_for_movement);
DoubleData *background_death_rate_per_unit_time = new DoubleData("background_death_rate_per_unit_time",default_background_death_rate_per_unit_time);
// the user will not be able to set the birth threshold it is always equal to one
DoubleData *essence_threshold_for_birth = new DoubleData("essence_threshold_for_birth",default_mass_threshold_for_birth);
DoubleData *essence_threshold_for_death = new DoubleData("essence_threshold_for_death",default_essence_threshold_for_death);
DoubleData *velocity = new DoubleData("velocity",default_velocity);
DoubleData *yield = new DoubleData("yield", default_yield);
BoolData *is_levy = new BoolData("is_levy", default_is_levy);
DoubleData *rho = new DoubleData("rho", default_rho);
DoubleData *parameter_for_steplength_dist =new DoubleData("parameter_for_steplength_dist", default_parameter_for_steplength_dist);
// variables needed for the movement simulator to operate correctly
DoubleData *current_angle = new DoubleData("current_angle", default_current_angle);
DoubleData *distance_desired_to_travel = new DoubleData("distance_desired_to_travel", default_distance_desired_to_travel);
DoubleData *traveled_distance = new DoubleData("traveled_distance", default_traveled_distance);
// add the data items to the database
db->addData(essence);
db->addData(kcat);
db->addData(Km);
db->addData(essence_cost_for_movement);
db->addData(background_death_rate_per_unit_time);
db->addData(essence_threshold_for_birth);
db->addData(essence_threshold_for_death);
db->addData(velocity);
db->addData(yield);
db->addData(current_angle);
db->addData(distance_desired_to_travel);
db->addData(traveled_distance);
db->addData(is_levy);
db->addData(rho);
db->addData(parameter_for_steplength_dist);
this->cpi->setNextCellParameters(bond);
// ///////////////////////////////////////////////////////////////////
// add simulators to agent
//////////////////////////////////////////////////////////////////////
this->addSimulatorToAgent(bond);
//////////////////////////////////////////////////////////////////////
// add actions to agents action set
//////////////////////////////////////////////////////////////////////
this->addActionsToAgentsActionSet(bond);
//////////////////////////////////////////////////////////////////////
// add message generators to action set
//////////////////////////////////////////////////////////////////////
this->addMessageGeneratorsToAgent(bond);
return bond;
}
