Allowing for derived Cell objects, defined by cell types

BioFVM/BioFVM_basic_agent.h

@@ -111,7 +111,7 @@ class Basic_Agent
 	void update_position( double dt );
 
 	Basic_Agent(); 
-
+	virtual ~Basic_Agent(){};
 	// simulate secretion and uptake at the nearest voxel at the indicated microenvironment.
 	// if no microenvironment indicated, use the currently selected microenvironment. 
 	void simulate_secretion_and_uptake( Microenvironment* M, double dt ); 

core/PhysiCell_cell.cpp

@@ -101,6 +101,9 @@ std::unordered_map<int,int> cell_definition_indices_by_type;
 // in case you want the legacy method 
 std::vector<double> (*cell_division_orientation)(void) = UniformOnUnitSphere; // LegacyRandomOnUnitSphere; 
 
+Cell* standard_instantiate_cell()
+{ return new Cell; }
+
 Cell_Parameters::Cell_Parameters()
 {
 	o2_hypoxic_threshold = 15.0; // HIF-1alpha at half-max around 1.5-2%, and tumors often are below 2%
@@ -148,6 +151,7 @@ Cell_Definition::Cell_Definition()
 		// the default Custom_Cell_Data constructor should take care of this
 
 	// set up the default functions 
+	functions.instantiate_cell = NULL;
 	functions.volume_update_function = NULL; // standard_volume_update_function;
 	functions.update_migration_bias = NULL; 
 
@@ -552,7 +556,7 @@ Cell* Cell::divide( )
 	}
 
 
-	Cell* child = create_cell();
+	Cell* child = create_cell(functions.instantiate_cell);
 	child->copy_data( this );	
 	child->copy_function_pointers(this);
 	child->parameters = parameters;
@@ -1048,10 +1052,16 @@ void Cell::add_potentials(Cell* other_agent)
 	return;
 }
 
-Cell* create_cell( void )
+Cell* create_cell( Cell* (*custom_instantiate)())
 {
 	Cell* pNew; 
-	pNew = new Cell;		
+
+	if (custom_instantiate) {
+		pNew = custom_instantiate();
+	} else {
+		pNew = standard_instantiate_cell();
+	}
+
 	(*all_cells).push_back( pNew ); 
 	pNew->index=(*all_cells).size()-1;
 
@@ -1074,7 +1084,7 @@ Cell* create_cell( void )
 // In that "create_cell()" uses "create_cell( cell_defaults )" 
 Cell* create_cell( Cell_Definition& cd )
 {
-	Cell* pNew = create_cell(); 
+	Cell* pNew = create_cell(cd.functions.instantiate_cell); 
 
 	// use the cell defaults; 
 	pNew->type = cd.type; 

core/PhysiCell_cell.h

@@ -200,7 +200,7 @@ class Cell : public Basic_Agent
 	void step(double dt);
 	Cell();
 
-	~Cell(); 
+	virtual ~Cell(); 
 
 	bool assign_position(std::vector<double> new_position);
 	bool assign_position(double, double, double);
@@ -251,7 +251,7 @@ class Cell : public Basic_Agent
 	void convert_to_cell_definition( Cell_Definition& cd ); 
 };
 
-Cell* create_cell( void );  
+Cell* create_cell( Cell* (*custom_instantiate)() = NULL );  
 Cell* create_cell( Cell_Definition& cd );  
 
 void delete_cell( int ); 

core/PhysiCell_phenotype.cpp

@@ -1141,6 +1141,8 @@ void Molecular::advance( Basic_Agent* pCell, Phenotype& phenotype , double dt )
 
 Cell_Functions::Cell_Functions()
 {
+	instantiate_cell = NULL;
+
 	volume_update_function = NULL; 
 	update_migration_bias = NULL; 
 

core/PhysiCell_phenotype.h

@@ -474,6 +474,8 @@ class Cell_Functions
 {
  private:
  public:
+	Cell* (*instantiate_cell)(); 
+
 	Cycle_Model cycle_model; 
 
 	void (*volume_update_function)( Cell* pCell, Phenotype& phenotype , double dt ); // used in cell