Agent* WorldAgentFactoryI::createAgent() {
// open up an inputstream
// cerr << this->inputname << endl;
ifstream input(this->inputname.c_str());
// create world agent and get his database
Agent *world = new Agent();
Hive::Database *db = world->getDatabase();
// add the time counter to the world
DoubleData *localworldtime = new DoubleData("localworldtime",0.0);
db->addData(localworldtime->getName(),localworldtime);
DoubleData *eqTime = new DoubleData("eqTime", 0);
db->addData(eqTime->getName(), eqTime);
DoubleData *dt = new DoubleData("dt", 0);
db->addData(dt);
IntegerData *numberofcells = new IntegerData("numberofcells", this->numbercells);
db->addData(numberofcells->getName(), numberofcells);
// data structure for knowing which cell is stored at which index in the various vectors
// that the world agent has
// maps agent_id (key) on to vector index (value)
MapIntIntData *local_index_map = new MapIntIntData("local_index_map");
for (int i=0; i<this->numbercells; i++) {
//assume agent_ids start at 1 (because the world is agent zero)
local_index_map->insert(i+1,i);
//cout<<"adding to local index map: ["<<i+1<<"]: => "<<i<<endl;
}
db->addData(local_index_map->getName(),local_index_map);
// maps vector_index (key) onto agent_id
// this is needed for outputing the positions of the cells
MapIntIntData *index_agentid_map = new MapIntIntData("indexagentidmap");
for (int i=0; i<this->numbercells; i++) {
// again, agent_ids = i+1
index_agentid_map->insert(i,i+1);
}
db->addData(index_agentid_map->getName(), index_agentid_map);
// add data structure to the world in which it can store the cell positions
TVectorData<TVectorData<double>* > *cell_positions = new TVectorData<TVectorData<double>* > ("cellpositions","tvectordata_double_matrix");
cell_positions->reserveSize(this->numbercells);
// add data_structure for direction and up vector of the individual cells
TVectorData<TVectorData<double>* > *cell_dir_vecs = new TVectorData<TVectorData<double>* > ("celldirvecs", "tvectordata_doublematrix");
cell_dir_vecs->reserveSize(this->numbercells);
TVectorData<TVectorData<double>* > *cell_up_vecs = new TVectorData<TVectorData<double>* > ("cellupvecs", "tvectordata_doublematrix");
cell_up_vecs->reserveSize(this->numbercells);
for (int i=0; i<this->numbercells;i++) {
(*cell_positions)[i] = new TVectorData<double> ("position", "tvectordata_double");
(*cell_positions)[i]->reserveSize(3);
(*cell_dir_vecs)[i] = new TVectorData<double> ("direction", "tvectordata_double");
(*cell_dir_vecs)[i]->reserveSize(3);
/// this needs to be a unit-vector.
cell_dir_vecs->at(i)->at(0) = 1.; cell_dir_vecs->at(i)->at(1) = 0.; cell_dir_vecs->at(i)->at(2) = 0;
(*cell_up_vecs)[i] = new TVectorData<double> ("up", "tvectordata_double");
(*cell_up_vecs)[i]->reserveSize(3);
cell_up_vecs->at(i)->at(0) = 0; cell_up_vecs->at(i)->at(1) = 1; cell_up_vecs->at(i)->at(2) = 0;
}
db->addData(cell_positions->getName(), cell_positions);
db->addData(cell_dir_vecs->getName(), cell_dir_vecs);
db->addData(cell_up_vecs->getName(), cell_up_vecs);
// data structure storing how much a cell wishes to consume
// we will also use it to store the actual concentration that gets consumed by the cells
TVectorData<double> *desired_cell_consumption = new TVectorData<double>("desired_cell_consumption", "tvectordata_double");
desired_cell_consumption->reserveSize(this->numbercells);
db->addData(desired_cell_consumption->getName(), desired_cell_consumption);
// time step for movement of the cells
DoubleData *movement_dt = new DoubleData("movement_dt",1.);
db->addData(movement_dt->getName(), movement_dt);
/// speed of cells (is that the same for all the cells?)
// DoubleData *cellspeed = new DoubleData("cellspeed",0.1);
// db->addData(cellspeed->getName(), cellspeed);
TVectorData<double> *cellspeeds = new TVectorData<double>("cellspeeds", "tvector_double");
cellspeeds->reserveSize(this->numbercells);
for (int i=0; i<this->numbercells; i++)
cellspeeds->at(i) = 20.0;
db->addData(cellspeeds->getName(), cellspeeds);
TVectorData<int> *cell_wants_to_move = new TVectorData<int>("cell_wants_to_move", "tvector_bool");
cell_wants_to_move->reserveSize(this->numbercells);
for (int i=0; i<this->numbercells; i++)
cell_wants_to_move->at(i) = (int)true;
db->addData(cell_wants_to_move->getName(), cell_wants_to_move);
DoubleData *output_interval = new DoubleData("output_interval",this->output_interval);
db->addData(output_interval->getName(), output_interval);
BoolData *isGridEnv = new BoolData("is_grid_environment",false);
db->addData(isGridEnv);
if(!this->isBlindAgent) {
cerr << "# cells are of type: ECOLI" << endl;
// add data structures to the world that are unique to the E.coli model
// add data structure to the world in which it can store the swimming states of all the cells
TVectorData<int> *swimming_states = new TVectorData<int>("swimmingstates", "tvectordata_int");
swimming_states->reserveSize(this->numbercells);
db->addData(swimming_states->getName(), swimming_states);
// add data structure to the world in whihc it stores the old swimming states of all the cells
TVectorData<int> *last_swimming_states = new TVectorData<int>("lastswimmingstates", "tvectordata_int");
last_swimming_states->reserveSize(this->numbercells);
db->addData(last_swimming_states->getName(), last_swimming_states);
// rotational diffusion constant of the cells
DoubleData *rotdiffconst = new DoubleData("rotational_diffusion_constant",0.062);
db->addData(rotdiffconst->getName(), rotdiffconst);
} else {
cerr << "# cells are of type: BLIND" << endl;
// add data object needed by the blind searcher, which is the
// next angle to use during turns. Default to zero and must be
// overridden by the agent
TVectorData<double> *nextTurnAngles = new TVectorData<double>("cellnextturnangle", "tvector_double");
nextTurnAngles->reserveSize(this->numbercells);
for (int i=0; i<this->numbercells; i++)
nextTurnAngles->at(i) = 0;
db->addData(nextTurnAngles->getName(), nextTurnAngles);
}
// do the parsing of the system file. we can extend this later on if more information is needed.
if(!input.is_open()) {
cerr<<"did not open world file. quitting.";
exit(1);
}
input.seekg(0,ios_base::beg);
string line = "";
istringstream iss;
string environ_type;
string cellpos_init_type;
CellPositionInitialiser cpi;
while (getline(input,line)) {
if (line == "TYPE") {
while (getline(input,line) && line != "END") {
if (line.substr(0,1)!="#" && line != "") {
iss.clear();
iss.str(line);
iss >> environ_type;
if (environ_type == "linear") {
cerr << "# creating linear environment" << endl;
OneDLinearMathFunctionData *environ1 = new OneDLinearMathFunctionData("environment");
double s, yi;
iss >> s; iss >> yi;
environ1->setSlope(s);
environ1->setYIntercept(yi);
db->addData(environ1->getName(), environ1);
} else if (environ_type == "exponential") {
cerr << "# creating exponential environment" << endl;
OneDExponentialMathFunctionData *environ2 = new OneDExponentialMathFunctionData("environment");
double o, p;
iss >> o, iss >> p;
environ2->setOffset(o);
environ2->setParameter(p);
db->addData(environ2->getName(), environ2);
} else if (environ_type == "pointsource") {
Agent* WorldAgentFactoryI::createAgent() {
// open up an inputstream
ifstream input(this->inputname.c_str());
// create world agent and get his database
Agent *world = new Agent();
Hive::Database *db = world->getDatabase();
// add the time counter to the world
DoubleData *localworldtime = new DoubleData("localworldtime",0.0);
db->addData(localworldtime->getName(),localworldtime);
DoubleData *eqTime = new DoubleData("eqTime", 0);
db->addData(eqTime->getName(), eqTime);
DoubleData *dt = new DoubleData("dt", 1.0);
db->addData(dt);
IntegerData *numberofcells = new IntegerData("numberofcells", this->numbercells);
db->addData(numberofcells->getName(), numberofcells);
// data structure for knowing which cell is stored at which index in the various vectors
// that the world agent has
// maps agent_id (key) on to vector index (value)
MapIntIntData *local_index_map = new MapIntIntData("local_index_map");
for (int i=0; i<this->numbercells; i++) {
//assume agent_ids start at 1 (because the world is agent zero)
local_index_map->insert(i+1,i);
//cout<<"adding to local index map: ["<<i+1<<"]: => "<<i<<endl;
}
db->addData(local_index_map->getName(),local_index_map);
// maps vector_index (key) onto agent_id
// this is needed for outputing the positions of the cells
MapIntIntData *index_agentid_map = new MapIntIntData("indexagentidmap");
for (int i=0; i<this->numbercells; i++) {
// again, agent_ids = i+1
index_agentid_map->insert(i,i+1);
}
db->addData(index_agentid_map->getName(), index_agentid_map);
// ----------------- DATA STRUCTURES FOR CELL MOVEMENT ------------------------------
// add data structure to the world in which it can store the cell positions
TVectorData<TVectorData<double>* > *cell_positions = new TVectorData<TVectorData<double>* > ("cellpositions","tvectordata_double_matrix");
cell_positions->reserveSize(this->numbercells);
// add data_structure for direction and up vector of the individual cells
TVectorData<TVectorData<double>* > *cell_dir_vecs = new TVectorData<TVectorData<double>* > ("celldirvecs", "tvectordata_doublematrix");
cell_dir_vecs->reserveSize(this->numbercells);
TVectorData<TVectorData<double>* > *cell_up_vecs = new TVectorData<TVectorData<double>* > ("cellupvecs", "tvectordata_doublematrix");
cell_up_vecs->reserveSize(this->numbercells);
for (int i=0; i<this->numbercells;i++) {
(*cell_positions)[i] = new TVectorData<double> ("position", "tvectordata_double");
(*cell_positions)[i]->reserveSize(3);
(*cell_dir_vecs)[i] = new TVectorData<double> ("direction", "tvectordata_double");
(*cell_dir_vecs)[i]->reserveSize(3);
/// this needs to be a unit-vector.
cell_dir_vecs->at(i)->at(0) = 1.; cell_dir_vecs->at(i)->at(1) = 0.; cell_dir_vecs->at(i)->at(2) = 0;
(*cell_up_vecs)[i] = new TVectorData<double> ("up", "tvectordata_double");
(*cell_up_vecs)[i]->reserveSize(3);
cell_up_vecs->at(i)->at(0) = 0; cell_up_vecs->at(i)->at(1) = 1; cell_up_vecs->at(i)->at(2) = 0;
}
db->addData(cell_positions->getName(), cell_positions);
db->addData(cell_dir_vecs->getName(), cell_dir_vecs);
db->addData(cell_up_vecs->getName(), cell_up_vecs);
// cellspeeds
TVectorData<double> *cellspeeds = new TVectorData<double>("cellspeeds", "tvector_double");
cellspeeds->reserveSize(this->numbercells);
for (int i=0; i<this->numbercells; i++)
cellspeeds->at(i) = 20.0;
db->addData(cellspeeds->getName(), cellspeeds);
// DATA STRUCTURE FOR METABOLISM
// data structure for storing how much a cell wishes to consume
// we will also use it to store the actual concentration that gets consumed by the cells
TVectorData<double> *desired_cell_consumption = new TVectorData<double>("desired_cell_consumption", "tvectordata_double");
desired_cell_consumption->reserveSize(this->numbercells);
db->addData(desired_cell_consumption->getName(), desired_cell_consumption);
// DATA FOR OUTPUT
DoubleData *output_interval = new DoubleData("output_interval",this->output_interval);
db->addData(output_interval->getName(), output_interval);
// SPECIFIC DATA FOR EITHER ECOLIs OR BLIND AGENTS
// add data structures to the world that are unique to the E.coli model
if(!this->isBlindAgent) {
cerr << "# cells are of type: ECOLI" << endl;
// add data structure to the world in which it can store the swimming states of all the cells
TVectorData<int> *swimming_states = new TVectorData<int>("swimmingstates", "tvectordata_int");
swimming_states->reserveSize(this->numbercells);
db->addData(swimming_states->getName(), swimming_states);
// add data structure to the world in whihc it stores the old swimming states of all the cells
TVectorData<int> *last_swimming_states = new TVectorData<int>("lastswimmingstates", "tvectordata_int");
last_swimming_states->reserveSize(this->numbercells);
db->addData(last_swimming_states->getName(), last_swimming_states);
// rotational diffusion constant of the cells
DoubleData *rotdiffconst = new DoubleData("rotational_diffusion_constant",0.062);
db->addData(rotdiffconst->getName(), rotdiffconst);
} else { // add data object needed by the blind searcher, which is the
cerr << "# cells are of type: BLIND" << endl;
// next angle to use during turns. Default to zero and must be overwritten by the agent
TVectorData<double> *nextTurnAngles = new TVectorData<double>("cellnextturnangle", "tvector_double");
nextTurnAngles->reserveSize(this->numbercells);
for (int i=0; i<this->numbercells; i++)
nextTurnAngles->at(i) = 0;
db->addData(nextTurnAngles->getName(), nextTurnAngles);
}
// <------ DATA FOR ENVIRONMENT --------------
// we read the environment from a file.
BoolData *isGridEnv = new BoolData("is_grid_environment",false);
db->addData(isGridEnv);
// do the parsing of the system file. we can extend this later on if more information is needed.
// not optimal, arose from our need to quickly change environements without having to change the code
if(!input.is_open()) {
cerr<<"did not open world file. quitting.";
exit(1);
}
input.seekg(0,ios_base::beg);
string line = "";
istringstream iss;
string environ_type;
string cellpos_init_type;
CellPositionInitialiser cpi;
/// we need a vector of environments as we want to have multiple pointsources
TVectorData<MathFunctionData* > *environments = new TVectorData<MathFunctionData*> ("environments", "tvector_mathfunctiondata");
db->addData(environments);
/// we need a vector of birth-times for the environments
TVectorData<double> *birthtimes = new TVectorData<double> ("birthtimes_of_environments", "tvector_double");
db->addData(birthtimes);
/// we need the parameters for the simulator that randomly drops new pointsources into the environment.
while (getline(input,line)) {
if (line == "RANDOM DROP SIMULATOR") { // reading parameters for the environment simulator
// first we need to add the position of the ...
this->hasEnvironmentSimulator = true;
TVectorData<double> *lastposition = new TVectorData<double> ("last_pointsource_position","tvector_double");
lastposition->reserveSize(3);
lastposition->at(0) = 0; lastposition->at(1) = 0; lastposition->at(2) = 0;
db->addData(lastposition);
// add time of next drop event to environment.
DoubleData *tone = new DoubleData("environment_time_of_next_drop", 0);
db->addData(tone);
while (getline(input, line) && line != "END") {
if (line.substr(0,1)!="#" && line != "") {
iss.clear();
iss.str(line);
/// parameters are read as follows from the file:
/// timpe_parameter, space_parameter, mean_of_pointsource_initial_dist, sigma_of_....
/// diff
double tp, sp, mi, sigma, diff;
iss >> tp; iss >> sp; iss >> mi; iss >> sigma; iss >> diff;
DoubleData *d1 = new DoubleData("environment_time_parameter",tp);
db->addData(d1);
DoubleData *d2 = new DoubleData("environment_space_parameter", sp);
db->addData(d2);
DoubleData *d3 = new DoubleData("mean_of_pointsource_initial_distribution", mi);
db->addData(d3);
DoubleData *d4 = new DoubleData("sigma_of_pointsource_initial_distribution", sigma);
db->addData(d4);
DoubleData *d5 = new DoubleData("diffusion_coeff_ligand", diff);
db->addData(d5);
}
}
}else if (line == "TYPE") {
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;
}
