node_t Class Reference

Encodes a genealogical node. More...

#include <node.h>

Inheritance diagram for node_t:

Collaboration diagram for node_t:

Public Member Functions
size_t	bytesize (void) const
	size of binary serialization
	node_t (name_t u=0, slate_t t=R_NaReal)
	basic constructor for node class
	node_t (const node_t &p)=delete
	copy constructor
	node_t (node_t &&p)=delete
	move constructor
node_t &	operator= (const node_t &p)=delete
	copy assignment operator
node_t &	operator= (node_t &&p)=delete
	move assignment operator
	~node_t (void)
	destructor
ball_t *	green_ball (void) const
	pointer to my green ball
ball_t *&	green_ball (void)
	set green ball
name_t	deme (void) const
	view deme
name_t &	deme (void)
	set deme
name_t	lineage (void) const
	view lineage
name_t	lineage (const ball_t *g) const
	view lineage associated with a green ball
name_t &	lineage (void)
	set lineage
node_t *	parent (void) const
bool	holds_own (void) const
bool	is_root (void) const
bool	dead_root (void) const
int	nchildren (void) const
	number of descendants
void	lineage_incr (int *incr, int *sat, int *etype) const
std::string	describe (void) const
	human-readable info
std::string	yaml (std::string tab="") const
	machine-readable info
SEXP	structure (void) const
	R list description.
std::string	newick (const slate_t &tnow, const slate_t &tpar) const
	Newick format.
Public Member Functions inherited from pocket_t
size_t	bytesize (void) const
	size of binary serialization
void	repair_owners (const std::unordered_map< name_t, node_t * > &node_name, std::unordered_map< name_t, ball_t * > *ball_name)
	~pocket_t (void)
	destructor
bool	holds (ball_t *b) const
	does this node hold the given ball?
bool	holds (color_t c) const
	does this node hold a ball of this color?
ball_t *	last_ball (void) const
	retrieve the last ball
ball_t *	ball (const color_t c) const
	retrieve the first ball of the specified color.
ball_t *	other (const ball_t *b) const
	return a pointer to another ball
std::string	describe (void) const
	human-readable info
SEXP	structure (void) const
	R list description.
std::string	yaml (std::string tab="") const
	human/machine-readable info

Data Fields
name_t	uniq
slate_t	slate

Private Member Functions
void	clean (void)

Private Attributes
ball_t *	_green_ball
name_t	_lineage

Friends
raw_t *	operator>> (const node_t &p, raw_t *o)
	binary serialization of node_t
raw_t *	operator>> (raw_t *o, node_t &p)
	binary deserialization of node_t

Additional Inherited Members
Protected Member Functions inherited from pocket_t
void	repair_holder (node_t *p)

Detailed Description

Encodes a genealogical node.

Each node has:

• a unique name (uniq)
• a pocket containting two or more balls
• a "slate" with the time
• a lineage
• a pointer to its own green ball

Definition at line 23 of file node.h.

Constructor & Destructor Documentation

node_t() [1/3]

node_t::node_t ( name_t u = 0, slate_t t = R_NaReal )

inline

basic constructor for node class

Definition at line 66 of file node.h.

                                              {
    uniq = u;
    slate = t;
    _green_ball = 0;
    _lineage = null_lineage;
  };

Here is the caller graph for this function:

node_t() [2/3]

node_t::node_t ( const node_t & p )

delete

copy constructor

Here is the call graph for this function:

node_t() [3/3]

node_t::node_t ( node_t && p )

delete

move constructor

Here is the call graph for this function:

~node_t()

node_t::~node_t ( void )

inline

destructor

Definition at line 81 of file node.h.

                 {
    clean();
  };

Here is the call graph for this function:

Member Function Documentation

bytesize()

size_t node_t::bytesize ( void ) const

inline

size of binary serialization

Definition at line 40 of file node.h.

                               {
    return 2*sizeof(name_t) + sizeof(slate_t)
      + pocket_t::bytesize();
  };

Here is the call graph for this function:

Here is the caller graph for this function:

clean()

void node_t::clean ( void )

inlineprivate

Definition at line 30 of file node.h.

{ };

Here is the caller graph for this function:

dead_root()

bool node_t::dead_root ( void ) const

inline

Definition at line 124 of file node.h.

                              {
    return holds_own() && size()==1;
  };

Here is the call graph for this function:

Here is the caller graph for this function:

deme() [1/2]

name_t & node_t::deme ( void )

inline

set deme

Definition at line 100 of file node.h.

                      {
    return _green_ball->deme();
  };

deme() [2/2]

name_t node_t::deme ( void ) const

inline

view deme

Definition at line 96 of file node.h.

                           {
    return _green_ball->deme();
  };

Here is the caller graph for this function:

describe()

std::string node_t::describe ( void ) const

inline

human-readable info

Definition at line 177 of file node.h.

                                  {
    std::string s = "node("
      + std::to_string(uniq)
      + "," + std::to_string(deme()) + ",";
    if (lineage() != null_lineage) {
      s += std::to_string(lineage());
    }
    s += ")" + pocket_t::describe();
    s += ", t = " + std::to_string(slate) + "\n";
    return s;
  };

Here is the call graph for this function:

Here is the caller graph for this function:

green_ball() [1/2]

ball_t *& node_t::green_ball ( void )

inline

set green ball

Definition at line 92 of file node.h.

                             {
    return _green_ball;
  };

green_ball() [2/2]

ball_t * node_t::green_ball ( void ) const

inline

pointer to my green ball

Definition at line 88 of file node.h.

                                  {
    return _green_ball;
  };

Here is the caller graph for this function:

holds_own()

bool node_t::holds_own ( void ) const

inline

Definition at line 118 of file node.h.

                              {
    return (_green_ball->holder() == this);
  };

Here is the caller graph for this function:

is_root()

bool node_t::is_root ( void ) const

inline

Definition at line 121 of file node.h.

                            {
    return holds_own();
  };

Here is the call graph for this function:

Here is the caller graph for this function:

lineage() [1/3]

name_t node_t::lineage ( const ball_t * g ) const

inline

view lineage associated with a green ball

Definition at line 108 of file node.h.

                                         {
    return g->owner()->lineage();
  };

Here is the call graph for this function:

lineage() [2/3]

name_t & node_t::lineage ( void )

inline

set lineage

Definition at line 112 of file node.h.

                         {
    return _lineage;
  };

lineage() [3/3]

name_t node_t::lineage ( void ) const

inline

view lineage

Definition at line 104 of file node.h.

                              {
    return _lineage;
  };

Here is the caller graph for this function:

lineage_incr()

void node_t::lineage_incr ( int * incr, int * sat, int * etype ) const

inline

lineage count, saturation, and event-type types are:

• 0 = non-event
• -1 = root
• 1 = sample
• 2 = non-sample node

Definition at line 151 of file node.h.

                                                            {
    const name_t d = deme();
    incr[d]--;
    for (ball_t *b : *this) {
      switch (b->color) {
      case green: case black:
        incr[b->deme()]++;
        sat[b->deme()]++;
        break;
      default:
        break;
      }
    }
    if (holds_own()) {
      sat[d]--;
      etype[d] = -1;
    } else if (holds(blue)) {
      etype[d] = 1;
    } else {
      etype[d] = 2;
    }
  };

Here is the call graph for this function:

Here is the caller graph for this function:

nchildren()

int node_t::nchildren ( void ) const

inline

number of descendants

Definition at line 131 of file node.h.

                             {
    int n = 0;
    for (ball_t *b : *this) {
      switch (b->color) {
      case green: case black:
        n++;
        break;
      default:
        break;
      }
    }
    if (holds_own()) n--;
    return n;
  };

Here is the call graph for this function:

Here is the caller graph for this function:

newick()

std::string node_t::newick ( const slate_t & tnow, const slate_t & tpar ) const

inline

Newick format.

Definition at line 214 of file node.h.

                                                                    {
    std::string o1 = "", o2 = "", o3 = "";
    int n = nchildren();
    if (n > 0) {
      o1 = "("; o3 = ")";
    }
    if (holds(blue)) {
      o3 += "b_";
    } else if (holds_own()) {
      o3 += "m_";
    } else {
      o3 += "g_";
    }
    n = 0;
    for (ball_t *b : *this) {
      node_t *p = 0;
      switch (b->color) {
      case green:
        p = b->child();
        if (p != this) {
          if (n++ > 0) o2 += ",";
          o2 += p->newick(tnow,slate);
        }
        break;
      case black:
        if (n++ > 0) o2 += ",";
        o2 += b->newick(tnow-slate);
        break;
      case blue:
        break;
      }
    }
    return o1 + o2 + o3
      + std::to_string(deme())
      + "_" + std::to_string(uniq)
      + ":" + std::to_string(slate - tpar);
  };

Here is the call graph for this function:

Here is the caller graph for this function:

operator=() [1/2]

node_t & node_t::operator= ( const node_t & p )

delete

copy assignment operator

Here is the call graph for this function:

operator=() [2/2]

node_t & node_t::operator= ( node_t && p )

delete

move assignment operator

Here is the call graph for this function:

parent()

node_t * node_t::parent ( void ) const

inline

Definition at line 115 of file node.h.

                              {
    return _green_ball->holder();
  };

Here is the call graph for this function:

Here is the caller graph for this function:

structure()

SEXP node_t::structure ( void ) const

inline

R list description.

Definition at line 201 of file node.h.

                              {
    SEXP O, On;
    PROTECT(O = NEW_LIST(4));
    PROTECT(On = NEW_CHARACTER(4));
    set_list_elem(O,On,ScalarInteger(int(uniq)),"name",0);
    set_list_elem(O,On,ScalarReal(double(slate)),"time",1);
    set_list_elem(O,On,ScalarInteger(int(deme())),"deme",2);
    set_list_elem(O,On,pocket_t::structure(),"pocket",3);
    SET_NAMES(O,On);
    UNPROTECT(2);
    return O;
  };

Here is the call graph for this function:

Here is the caller graph for this function:

yaml()

std::string node_t::yaml ( std::string tab = "" ) const

inline

machine-readable info

Definition at line 189 of file node.h.

                                            {
    std::string t = tab + "  ";
    std::string o = "name: " + std::to_string(uniq) + "\n"
      + tab + "time: " + std::to_string(slate) + "\n"
      + tab + "deme: " + std::to_string(deme()) + "\n";
    if (lineage() != null_lineage) {
      o += tab + "lineage: " + std::to_string(lineage()) + "\n";
    }
    o += tab + "pocket:\n" + pocket_t::yaml(tab);
    return o;
  };

Here is the call graph for this function:

Here is the caller graph for this function:

Friends And Related Symbol Documentation

operator>> [1/2]

raw_t * operator>> ( const node_t & p, raw_t * o )

friend

binary serialization of node_t

Definition at line 45 of file node.h.

                                                       {
    name_t buf[2] = {p.uniq, p._lineage};
    memcpy(o,buf,sizeof(buf)); o += sizeof(buf);
    memcpy(o,&p.slate,sizeof(slate_t)); o += sizeof(slate_t);
    return reinterpret_cast<const pocket_t&>(p) >> o;
  };

operator>> [2/2]

raw_t * operator>> ( raw_t * o, node_t & p )

friend

binary deserialization of node_t

Definition at line 52 of file node.h.

                                                 {
    p.clean();
    name_t buf[2];
    memcpy(buf,o,sizeof(buf)); o += sizeof(buf);
    memcpy(&p.slate,o,sizeof(slate_t)); o += sizeof(slate_t);
    p.uniq = buf[0]; p._lineage = buf[1];
    o = (o >> reinterpret_cast<pocket_t&>(p));
    p.repair_holder(&p);
    return o;
  };

Field Documentation

_green_ball

ball_t* node_t::_green_ball

private

Definition at line 27 of file node.h.

_lineage

name_t node_t::_lineage

private

Definition at line 28 of file node.h.

slate

slate_t node_t::slate

Definition at line 35 of file node.h.

uniq

name_t node_t::uniq

Definition at line 34 of file node.h.

---

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

• src/node.h