tumopp::Tissue Class Reference

Population of Cell. More...

#include <tissue.hpp>

Classes
struct	equal_ptr_cell
	Equal function object for shared_pointer<Cell> More...
struct	hash_ptr_cell
	Hashing function object for shared_pointer<Cell> More...

Public Member Functions
	Tissue (size_t initial_size=1u, unsigned dimensions=3u, const std::string &coordinate="moore", const std::string &local_density_effect="const", const std::string &displacement_path="random", const EventRates &init_event_rates=EventRates{}, uint32_t seed=std::random_device{}(), bool verbose=false, bool enable_benchmark=false)
	Constructor.
bool	grow (size_t max_size, double max_time=100.0, double snapshot_interval=0.0, size_t recording_early_growth=0u, size_t mutation_timing=0u)
	main function
void	plateau (double time)
	Simulate turnover with the increased death_rate.
void	treatment (double death_prob, size_t num_resistant_cells=3u)
	Simulate medical treatment with the increased death_prob.
std::ostream &	write_history (std::ostream &) const
	Write extant_cells_ and their ancestors.
std::ostream &	write_snapshots (std::ostream &) const
	Write snapshots_.
std::ostream &	write_drivers (std::ostream &) const
	Write drivers_.
std::ostream &	write_benchmark (std::ostream &) const
	Write benchmark_.

Friends
std::ostream &	operator<< (std::ostream &ost, const Tissue &tissue)
	Stream operator for debug print.

Getter functions
std::function< bool(const std::shared_ptr< Cell > &)>	insert
	initialized in init_insert_function()
std::unordered_set< std::shared_ptr< Cell >, hash_ptr_cell, equal_ptr_cell >	extant_cells_ {}
	cells
unsigned	id_tail_ {0}
	incremented when a new cell is born
std::multimap< double, std::shared_ptr< Cell > >	queue_ {}
	event queue
double	time_ {0.0}
	continuous time
std::unique_ptr< Coord >	coord_func_ {nullptr}
	initialized in init_coord() or init_coord_test()
std::stringstream	cemetery_ {}
	record dead cells
std::stringstream	snapshots_ {}
	record snapshots
std::stringstream	drivers_ {}
	record driver mutations
std::unordered_set< unsigned >	recorded_ {}
	id of recorded cells
std::unique_ptr< Benchmark >	benchmark_ {nullptr}
	record resource usage
std::unique_ptr< urbg_t >	engine_ {nullptr}
	random number generator
bool	verbose_ {false}
	print debug info
size_t	size () const noexcept
	Get the number of extant cells.
void	init_coord (unsigned dimensions, const std::string &coordinate)
	Set coord_func_.
void	init_insert_function (const std::string &local_density_effect, const std::string &displacement_path)
	Set insert function.
void	migrate (const std::shared_ptr< Cell > &)
	Swap with a random neighbor.
void	push (std::shared_ptr< Cell > moving, const coord_t &direction)
	Emplace daughter cell and push other cells to the direction.
void	push_minimum_drag (std::shared_ptr< Cell > moving)
	Push through the minimum drag path.
void	stroll (std::shared_ptr< Cell > moving, const coord_t &direction)
	Try insert_adjacent() on every step in push()
bool	insert_adjacent (const std::shared_ptr< Cell > &x)
	Insert x if any adjacent node is empty.
bool	swap_existing (std::shared_ptr< Cell > *x)
	Put new cell and return existing.
size_t	steps_to_empty (const coord_t &current, const coord_t &direction) const
	Count steps to the nearest empty.
const coord_t &	to_nearest_empty (const coord_t &current) const
	Direction to the nearest empty.
coord_t	roulette_direction (const coord_t &current) const
	Direction is selected with a probability proportional with 1/l.
uint_fast8_t	num_empty_neighbors (const coord_t &) const
	Count adjacent empty sites.
double	positional_value (const coord_t &) const
	TODO: Calculate positional value.
void	queue_push (const std::shared_ptr< Cell > &, bool surrounded=false)
	Push a cell to event queue_.
void	entomb (const std::shared_ptr< Cell > &)
	Put a cell to cemetery_.
void	snapshots_append ()
	Write all cells to snapshots_ with time_.

Detailed Description

Population of Cell.

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The documentation for this class was generated from the following files:

• src/tissue.hpp
• src/tissue.cpp