genealogy_t Class Reference

Encodes a genealogy. More...

#include <genealogy.h>

Inheritance diagram for genealogy_t:

Collaboration diagram for genealogy_t:

Public Member Functions
size_t	ndeme (void) const
	number of demes
size_t &	ndeme (void)
	number of demes
size_t	bytesize (void) const
	size of serialized binary form
	genealogy_t (double t0=0, name_t u=0, size_t nd=1)
	genealogy_t (raw_t *o)
	constructor from serialized binary form
	genealogy_t (SEXP o)
	constructor from RAW SEXP (containing binary serialization)
	genealogy_t (const genealogy_t &G)
	copy constructor
genealogy_t &	operator= (const genealogy_t &G)
	copy assignment operator
	genealogy_t (genealogy_t &&)=default
	move constructor
genealogy_t &	operator= (genealogy_t &&)=default
	move assignment operator
	~genealogy_t (void)
	destructor
slate_t &	time (void)
	view/set current time.
slate_t	time (void) const
	view current time.
slate_t &	timezero (void)
	view/set zero time.
slate_t	timezero (void) const
	get zero time.
void	lineage_count (double *tout, int *deme, int *ell, int *sat, int *etype) const
SEXP	lineage_count (void) const
	lineage count and saturation
void	gendat (double *tout, int *anc, int *lin, int *sat, int *type, int *deme, int *index, int *child) const
	genealogy information in list format
SEXP	gendat (void) const
	genealogy information in list format
size_t	nsample (void) const
	number of samples
SEXP	structure (void) const
	R list description.
std::string	describe (void) const
	human-readable info
virtual std::string	yaml (std::string tab="") const
	machine-readable info
std::string	newick (void) const
	put genealogy at current time into Newick format.
void	valid (void) const
	check the validity of the genealogy.
bool	check_genealogy_size (size_t grace=0) const
	check the size of the genealogy (to prevent memory exhaustion).
node_t *	make_node (name_t d)
ball_t *	birth (ball_t *a, slate_t t, name_t d)
	birth into deme d
ball_t *	birth (node_t *p, name_t d)
	birth of second or subsequent sibling into deme d
void	death (ball_t *a, slate_t t)
	death
ball_t *	graft (slate_t t, name_t d)
	graft a new lineage into deme d
void	sample (ball_t *a, slate_t t)
	insert a sample node
void	sample_death (ball_t *a, slate_t t)
	insert a sample node and simultaneously terminate the lineage
void	migrate (ball_t *a, slate_t t, name_t d=0)
	movement into deme d
void	sample_migrate (ball_t *a, slate_t t, name_t d=0)
	insert a sample node and simultaneously migrate the lineage
std::pair< node_it, node_it >	extant (void) const
genealogy_t &	prune (void)
	prune the tree (drop all black balls)
genealogy_t &	obscure (void)
	erase all deme information
void	curtail (slate_t tnew, slate_t troot)
genealogy_t &	operator+= (genealogy_t &G)
genealogy_t &	parse (const std::string &s, slate_t t0, node_t *p=0)
	Parse a Newick string and create the indicated genealogy.
Public Member Functions inherited from nodeseq_t
	~nodeseq_t (void)
	destructor
size_t	bytesize (void) const
	size of serialized binary form
nodeseq_t &	operator+= (nodeseq_t &other)
	merge two node sequences
void	sort (void)
	order nodes in order of increasing time
pocket_t *	colored (color_t col) const
	Get all balls of a color.
size_t	ntime (slate_t t) const
	Number of distinct timepoints.
size_t	length (void) const
	Number of nodes in the sequence.
node_t *	position (int n)
	traverse to nth node, retrieve pointer
void	swap (ball_t *a, ball_t *b)
	swap balls a and b, wherever they lie
void	add (node_t *p, ball_t *a)
void	drop (ball_t *a)
void	destroy_node (node_t *p)
	remove a dead root node
void	comb (void)
void	trace_lineages (void)
std::string	describe (void) const
	human-readable info
SEXP	structure (void) const
	R list description.
std::string	newick (slate_t t) const
	put genealogy at time t into Newick format.

Private Member Functions
name_t	unique (void)
	get the next unique name
void	clean (void)
	clean up
size_t	scan_color (const std::string &s, color_t *col) const
size_t	scan_label (const std::string &s, color_t *col, name_t *deme, slate_t *time) const
size_t	scan_ball (const std::string &s, const slate_t t0, node_t *p)
size_t	scan_node (const std::string &s, const slate_t t0, node_t **q)
	Scan the Newick string and create the indicated node.
size_t	scan_tree (const std::string &s, const slate_t t0, node_t **root)

Private Attributes
name_t	_unique
	The next unique name.
slate_t	_t0
	The initial time.
slate_t	_time
	The current time.
size_t	_ndeme
	The number of demes.

Static Private Attributes
static const name_t	magic = 1123581321

Friends
raw_t *	operator>> (const genealogy_t &G, raw_t *o)
	binary serialization
raw_t *	operator>> (raw_t *o, genealogy_t &G)
	binary deserialization

Detailed Description

Encodes a genealogy.

A genealogy consists of a sequence of nodes and the current time.

Definition at line 22 of file genealogy.h.

Constructor & Destructor Documentation

genealogy_t() [1/5]

genealogy_t::genealogy_t ( double t0 = 0, name_t u = 0, size_t nd = 1 )

inline

basic constructor for genealogy class t0 = initial time

Definition at line 105 of file genealogy.h.

                                                           {
    clean();
    _ndeme = nd;
    _unique = u;
    _time = _t0 = slate_t(t0);
  };

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genealogy_t() [2/5]

genealogy_t::genealogy_t ( raw_t * o )

inline

constructor from serialized binary form

Definition at line 112 of file genealogy.h.

                         {
    o >> *this;
  };

genealogy_t() [3/5]

genealogy_t::genealogy_t ( SEXP o )

inline

constructor from RAW SEXP (containing binary serialization)

Definition at line 116 of file genealogy.h.

                       {
    if (LENGTH(o)==0)
      err("in %s (%s line %d): cannot deserialize a NULL.",
          __func__,__FILE__,__LINE__);
    PROTECT(o = AS_RAW(o));
    RAW(o) >> *this;
    UNPROTECT(1);
  };

genealogy_t() [4/5]

genealogy_t::genealogy_t ( const genealogy_t & G )

inline

copy constructor

Definition at line 125 of file genealogy.h.

                                     {
    raw_t *o = new raw_t[G.bytesize()];
    G >> o;
    o >> *this;
    delete[] o;
  };

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genealogy_t() [5/5]

genealogy_t::genealogy_t ( genealogy_t && )

default

move constructor

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~genealogy_t()

genealogy_t::~genealogy_t ( void )

inline

destructor

Definition at line 145 of file genealogy.h.

                      {
    clean();
  };

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Member Function Documentation

birth() [1/2]

ball_t * genealogy_t::birth ( ball_t * a, slate_t t, name_t d )

inline

birth into deme d

Definition at line 407 of file genealogy.h.

                                                 {
    time() = t;
    node_t *p = make_node(a->deme());
    ball_t *b = new ball_t (p,p->uniq,black,d);
    p->insert(b);
    p->slate = time();
    add(p,a);
    return b;
  };

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birth() [2/2]

ball_t * genealogy_t::birth ( node_t * p, name_t d )

inline

birth of second or subsequent sibling into deme d

Definition at line 417 of file genealogy.h.

                                      {
    ball_t *b = new ball_t(p,unique(),black,d);
    p->insert(b);
    return b;
  };

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bytesize()

size_t genealogy_t::bytesize ( void ) const

inline

size of serialized binary form

Definition at line 73 of file genealogy.h.

                               {
    return 3*sizeof(name_t) +
      2*sizeof(slate_t) + nodeseq_t::bytesize();
  };

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check_genealogy_size()

bool genealogy_t::check_genealogy_size ( size_t grace = 0 ) const

inline

check the size of the genealogy (to prevent memory exhaustion).

Definition at line 379 of file genealogy.h.

                                                     {
    static size_t maxq = MEMORY_MAX/(sizeof(node_t)+2*sizeof(ball_t));
    bool ok = true;
    if (size() > maxq+grace) {
      err("maximum genealogy size exceeded!"); // #nocov
    } else if (size() > maxq) {
      ok = false;               // #nocov
    }
    return ok;
  };

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clean()

void genealogy_t::clean ( void )

inlineprivate

clean up

Definition at line 53 of file genealogy.h.

                    {
    _unique = 0;
    _t0 = _time = R_NaReal;
  };

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curtail()

void genealogy_t::curtail ( slate_t tnew, slate_t troot )

inline

curtail the genealogy by removing nodes with times later than tnew and/or earlier than troot

Definition at line 511 of file genealogy.h.

                                             {
    if (tnew < troot) troot = tnew;
    if (!empty() && tnew < time()) {
      node_t *p = back();
      while (!empty() && p->slate > tnew) {
        ball_t *b;
        while (p->size() > 1) {
          b = p->last_ball();
          switch (b->color) {
          case black:
            p->erase(b); delete b;
            break;
          case green: case blue: // #nocov
            assert(0);           // #nocov
            break;               // #nocov
          }
        }
        b = p->last_ball();
        switch (b->color) {
        case blue:
          b->color = black;
        case black:
          b->deme() = p->deme();
          swap(b,p->green_ball());
        case green:
          destroy_node(p);
          break;
        }
        if (!empty()) p = back();
      }
    }
    time() = tnew;
    if (!empty() && troot > timezero()) {
      node_t *p = front();
      node_t *q;
      while (!empty() && p->slate < troot) {
        ball_t *b;
        assert(p->holds_own());
        while (p->size() > 1) {
          b = p->last_ball();
          switch (b->color) {
          case blue:
            p->erase(b); delete b;
            break;
          case black:
            q = make_node(b->deme());
            q->slate = troot;
            q->insert(b); p->erase(b);
            b->holder() = q;
            push_back(q);
            break;
          case green:
            q = b->child();
            if (q == p) {
              b = p->first_ball();
              q = b->child();
            }
            if (q->slate < troot) {
              q->insert(b); p->erase(b);
              b->holder() = q;
            } else {
              node_t *pp = make_node(b->deme());
              pp->slate = troot;
              pp->insert(b); p->erase(b);
              b->holder() = pp;
              push_back(pp);
            }
            break;
          }
        }
        destroy_node(p);
        if (!empty()) p = front();
      }
      sort();
    }
    if (troot > timezero()) timezero() = troot;
  };

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death()

void genealogy_t::death ( ball_t * a, slate_t t )

inline

death

Definition at line 423 of file genealogy.h.

                                    {
    time() = t;
    drop(a);
  };

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describe()

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

inline

human-readable info

Definition at line 348 of file genealogy.h.

                                  {
    std::string o = "t0 = " + std::to_string(double(timezero()))
      + "\ntime = " + std::to_string(double(time())) + "\n"
      + nodeseq_t::describe();
    return o;
  };

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extant()

std::pair< node_it, node_it > genealogy_t::extant ( void ) const

inline

set up for extraction of black balls (see 'inventory.h')

Definition at line 476 of file genealogy.h.

                                                {
    return std::pair<node_it,node_it>(cbegin(),cend());
  };

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gendat() [1/2]

void genealogy_t::gendat ( double * tout, int * anc, int * lin, int * sat, int * type, int * deme, int * index, int * child ) const

inline

genealogy information in list format

Definition at line 233 of file genealogy.h.

                                             {
    int m, n, k;
    node_it i, j;
    for (k = 0, n = 0, i = begin(); i != end(); i++, n++) {
      node_t *p = *i;
      assert(!p->holds(black)); // tree should be pruned first
      tout[n] = p->slate;
      deme[n] = p->deme();
      if (p->is_root()) {
        type[n] = 0;            // root node
      } else if (p->holds(blue)) {
        type[n] = 1;            // sample node
        deme[n] = p->ball(blue)->deme();
      } else {
        type[n] = 2;            // internal node
      }
      lin[n] = p->lineage();    // 0-based indexing
      sat[n] = p->nchildren();
      index[n] = k;
      k += sat[n];
      child[n] = NA_INTEGER;
      if (p->is_root()) {
        anc[n] = n;             // 0-based indexing
      } else {
        for (m = 0, j = begin(); j != i; j++, m++) {
          node_t *q = *j;
          if (p->parent()->uniq == q->uniq) {
            anc[n] = m;
            break;
          }
        }
      }
    }
    tout[n] = time();
    for (k = 0, n = 0, i = begin(); i != end(); i++, n++) {
      node_t *p = *i;
      j = i; j++;
      for (m = n+1; j != end(); m++, j++) {
        node_t *q = *j;
        if (p->uniq == q->parent()->uniq) {
          child[k++] = m;
        }
      }
    }
  };

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gendat() [2/2]

SEXP genealogy_t::gendat ( void ) const

inline

genealogy information in list format

Definition at line 281 of file genealogy.h.

                           {
    SEXP tout, anc, lin, sat, type, deme, index, child, ns, nn;
    SEXP out, outn;
    size_t n = length();
    PROTECT(tout = NEW_NUMERIC(n+1));
    PROTECT(type = NEW_INTEGER(n));
    PROTECT(deme = NEW_INTEGER(n));
    PROTECT(lin = NEW_INTEGER(n));
    PROTECT(sat = NEW_INTEGER(n));
    PROTECT(index = NEW_INTEGER(n));
    PROTECT(child = NEW_INTEGER(n));
    PROTECT(anc = NEW_INTEGER(n));
    PROTECT(ns = NEW_INTEGER(1));
    PROTECT(nn = NEW_INTEGER(1));
    PROTECT(out = NEW_LIST(10));
    PROTECT(outn = NEW_CHARACTER(10));
    set_list_elem(out,outn,tout,"nodetime",0);
    set_list_elem(out,outn,type,"nodetype",1);
    set_list_elem(out,outn,deme,"deme",2);
    set_list_elem(out,outn,lin,"lineage",3);
    set_list_elem(out,outn,sat,"saturation",4);
    set_list_elem(out,outn,index,"index",5);
    set_list_elem(out,outn,child,"child",6);
    set_list_elem(out,outn,anc,"ancestor",7);
    set_list_elem(out,outn,ns,"nsample",8);
    set_list_elem(out,outn,nn,"nnode",9);
    SET_NAMES(out,outn);
    gendat(REAL(tout),INTEGER(anc),INTEGER(lin),INTEGER(sat),
           INTEGER(type),INTEGER(deme),INTEGER(index),INTEGER(child));
    *INTEGER(ns) = nsample();   // number of samples
    *INTEGER(nn) = length();    // number of nodes
    UNPROTECT(12);
    return out;
  };

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graft()

ball_t * genealogy_t::graft ( slate_t t, name_t d )

inline

graft a new lineage into deme d

Definition at line 428 of file genealogy.h.

                                      {
    time() = t;
    node_t *p = make_node(d);
    ball_t *b = new ball_t (p,p->uniq,black,d);
    p->insert(b);
    p->slate = timezero();
    push_front(p);
    return b;
  };

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lineage_count() [1/2]

void genealogy_t::lineage_count ( double * tout, int * deme, int * ell, 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
• 3 = end of interval

Definition at line 175 of file genealogy.h.

                                                            {
    slate_t tcur = timezero();
    for (size_t j = 0; j < _ndeme; j++) {
      tout[j] = tcur;
      deme[j] = j+1;
      sat[j] = ell[j] = 0;
      etype[j] = 0;
    }
    for (const node_t *p : *this) {
      if (tcur < p->slate) {
        tout += _ndeme; ell += _ndeme; sat += _ndeme;
        deme += _ndeme; etype += _ndeme;
        tcur = p->slate;
        for (size_t j = 0; j < _ndeme; j++) {
          tout[j] = tcur;
          deme[j] = j+1;
          ell[j] = (ell-_ndeme)[j];
          sat[j] = 0;
          etype[j] = 0;
        }
      }
      p->lineage_incr(ell,sat,etype);
    }
    tout += _ndeme; ell += _ndeme; sat += _ndeme;
    deme += _ndeme; etype += _ndeme;
    tcur = time();
    for (size_t j = 0; j < _ndeme; j++) {
      tout[j] = tcur;
      sat[j] = ell[j] = 0;
      deme[j] = j+1;
      etype[j] = 3;
    }
  };

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lineage_count() [2/2]

SEXP genealogy_t::lineage_count ( void ) const

inline

lineage count and saturation

Definition at line 210 of file genealogy.h.

                                  {
    SEXP tout, deme, ell, sat, etype, out, outn;
    int nt = ntime(timezero())+1;
    int nl = _ndeme*nt;
    PROTECT(tout = NEW_NUMERIC(nl));
    PROTECT(deme = NEW_INTEGER(nl));
    PROTECT(ell = NEW_INTEGER(nl));
    PROTECT(sat = NEW_INTEGER(nl));
    PROTECT(etype = NEW_INTEGER(nl));
    PROTECT(out = NEW_LIST(5));
    PROTECT(outn = NEW_CHARACTER(5));
    set_list_elem(out,outn,tout,"time",0);
    set_list_elem(out,outn,deme,"deme",1);
    set_list_elem(out,outn,ell,"lineages",2);
    set_list_elem(out,outn,sat,"saturation",3);
    set_list_elem(out,outn,etype,"event_type",4);
    SET_NAMES(out,outn);
    lineage_count(REAL(tout),INTEGER(deme),INTEGER(ell),
                  INTEGER(sat),INTEGER(etype));
    UNPROTECT(7);
    return out;
  };

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make_node()

node_t * genealogy_t::make_node ( name_t d )

inline

create a node holding its own green ball. insert into the genealogy.

Definition at line 394 of file genealogy.h.

                               {
    check_genealogy_size(0);
    name_t u = unique();
    node_t *p = new node_t(u,_time);
    ball_t *g = new ball_t(p,u,green,d);
    p->green_ball() = g;
    p->insert(g);
    return p;
  };

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migrate()

void genealogy_t::migrate ( ball_t * a, slate_t t, name_t d = 0 )

inline

movement into deme d

Definition at line 457 of file genealogy.h.

                                                    {
    time() = t;
    node_t *p = make_node(a->deme());
    p->slate = time();
    add(p,a);
    a->deme() = d;
  };

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ndeme() [1/2]

size_t & genealogy_t::ndeme ( void )

inline

number of demes

Definition at line 65 of file genealogy.h.

                       {
    return _ndeme;
  };

ndeme() [2/2]

size_t genealogy_t::ndeme ( void ) const

inline

number of demes

Definition at line 61 of file genealogy.h.

                            {
    return _ndeme;
  };

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newick()

std::string genealogy_t::newick ( void ) const

inline

put genealogy at current time into Newick format.

Definition at line 370 of file genealogy.h.

                                {
    return nodeseq_t::newick(time());
  };

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nsample()

size_t genealogy_t::nsample ( void ) const

inline

number of samples

Definition at line 317 of file genealogy.h.

                              {
    size_t n = 0;
    for (const node_t *p : *this) {
      if (p->holds(blue)) n++;
    }
    return n;
  };

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obscure()

genealogy_t & genealogy_t::obscure ( void )

inline

erase all deme information

Definition at line 491 of file genealogy.h.

                              {
    // erase deme information from black balls.
    pocket_t *blacks = colored(black);
    while (!blacks->empty()) {
      ball_t *a = *(blacks->begin());
      a->deme() = 0;
      blacks->erase(a);
    }
    delete blacks;
    // erase deme information from nodes.
    for (node_t *p : *this) {
      p->deme() = 0;
    }
    // drop superfluous nodes (holding just one ball).
    comb();
    _ndeme = 1;
    return *this;
  };

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operator+=()

genealogy_t & genealogy_t::operator+= ( genealogy_t & G )

inline

merge two genealogies:

1. the node-sequences are merged;
2. the root time retreats as necessary;
3. the current time advances as necessary;
4. the unique-name stack advances as necessary.

Definition at line 593 of file genealogy.h.

                                           {
    reinterpret_cast<nodeseq_t&>(*this) += reinterpret_cast<nodeseq_t&>(G);
    _t0 = (_t0 > G._t0) ? G._t0 : _t0;
    _time = (_time < G._time) ? G._time : _time;
    _unique = (_unique < G._unique) ? G._unique : _unique;
    _ndeme = (_ndeme < G.ndeme()) ? G.ndeme() : _ndeme;
    return *this;
  };

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operator=() [1/2]

genealogy_t & genealogy_t::operator= ( const genealogy_t & G )

inline

copy assignment operator

Definition at line 132 of file genealogy.h.

                                                {
    clean();
    raw_t *o = new raw_t[G.bytesize()];
    G >> o;
    o >> *this;
    delete[] o;
    return *this;
  };

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operator=() [2/2]

genealogy_t & genealogy_t::operator= ( genealogy_t && )

default

move assignment operator

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parse()

genealogy_t & genealogy_t::parse ( const std::string & s, slate_t t0, node_t * p = 0 )

inline

Parse a Newick string and create the indicated genealogy.

Definition at line 754 of file genealogy.h.

                                                                     {
    size_t i = 0;
    size_t n = s.size();
    while (i < n) {
      switch (s[i]) {
      case '(':
        {
          genealogy_t G(t0,unique());
          node_t *q = 0;
          i += G.scan_tree(s.substr(i),t0,&q);
          *this += G;
          if (p != 0) {
            ball_t *g = q->green_ball();
            q->erase(g); p->insert(g); g->holder() = p;
          }
        }
        break;
      case 'b':
        {
          node_t *q = 0;
          i += scan_node(s.substr(i),t0,&q);
          if (p != 0) {
            ball_t *g = q->green_ball();
            q->erase(g); p->insert(g); g->holder() = p;
          }
        }
        break;
      case 'o':
        i += scan_ball(s.substr(i),t0,p);
        break;
      case ',': case ';': case ' ': case '\n': case '\t':
        i++;
        break;
      case ')':
        err("in '%s': invalid Newick string: unbalanced parentheses.",__func__);
        break;
      default:
        err("in '%s': invalid Newick string.",__func__);
        break;
      }
    }
    sort();
    return *this;
  };

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prune()

genealogy_t & genealogy_t::prune ( void )

inline

prune the tree (drop all black balls)

Definition at line 480 of file genealogy.h.

                            {
    pocket_t *blacks = colored(black);
    while (!blacks->empty()) {
      ball_t *b = *(blacks->begin());
      blacks->erase(b);
      drop(b);
    }
    delete blacks;
    return *this;
  };

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sample()

void genealogy_t::sample ( ball_t * a, slate_t t )

inline

insert a sample node

Definition at line 438 of file genealogy.h.

                                     {
    time() = t;
    node_t *p = make_node(a->deme());
    ball_t *b = new ball_t (p,p->uniq,blue,a->deme());
    p->insert(b);
    p->slate = time();
    add(p,a);
  };

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sample_death()

void genealogy_t::sample_death ( ball_t * a, slate_t t )

inline

insert a sample node and simultaneously terminate the lineage

Definition at line 447 of file genealogy.h.

                                           {
    time() = t;
    node_t *p = make_node(a->deme());
    ball_t *b = new ball_t (p,p->uniq,blue,a->deme());
    p->insert(b);
    p->slate = time();
    add(p,a);
    drop(a);
  };

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sample_migrate()

void genealogy_t::sample_migrate ( ball_t * a, slate_t t, name_t d = 0 )

inline

insert a sample node and simultaneously migrate the lineage

Definition at line 465 of file genealogy.h.

                                                           {
    time() = t;
    node_t *p = make_node(a->deme());
    ball_t *b = new ball_t (p,p->uniq,blue,a->deme());
    p->insert(b);
    p->slate = time();
    add(p,a);
    a->deme() = d;
  };

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scan_ball()

size_t genealogy_t::scan_ball ( const std::string & s, const slate_t t0, node_t * p )

inlineprivate

Scan the Newick string and put the ball into the indicated pocket, as appropriate.

Definition at line 683 of file genealogy.h.

                                                                     {
    color_t col;
    name_t deme;
    slate_t t;
    ball_t *b;
    size_t i = scan_label(s,&col,&deme,&t);
    t += t0;
    _time = (_time < t) ? t : _time;
    _ndeme = (_ndeme <= deme) ? deme+1 : _ndeme;
    if (col != black) err("in '%s': bad Newick string (1)",__func__);
    if (p == 0) err("in '%s': bad Newick string (2)",__func__);
    b = new ball_t(p,unique(),col,deme);
    p->insert(b);
    return i;
  };

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scan_color()

size_t genealogy_t::scan_color ( const std::string & s, color_t * col ) const

inlineprivate

Definition at line 604 of file genealogy.h.

                                                             {
    return 1;
  };

scan_label()

size_t genealogy_t::scan_label ( const std::string & s, color_t * col, name_t * deme, slate_t * time ) const

inlineprivate

Scan the Newick-format label string. This has format c_d_d:f

Definition at line 609 of file genealogy.h.

                                                        {
    size_t n = s.size();
    if (n < 1)
      err("in '%s' (%s line %d): invalid Newick format: empty label.",__func__,__FILE__,__LINE__);
    size_t sz, i = 1;
    switch (s[0]) {
    case 'o':
      *col = black;
      break;
    case 'b':
      *col = blue;
      break;
    case 'g': case 'm':
      *col = green;
      break;
    default:
      err("in '%s' (%s line %d): invalid Newick label: expected one of 'b','g','m', or 'o', got '%c'.",
          __func__,__FILE__,__LINE__,s[0]);
      break;
    }
    while (i < n && s[i] == '_') i++;
    if (i == n)
      err("in '%s': invalid Newick format: premature termination.",__func__);
    if (s[i] == '(' || s[i] == ')' || s[i] == ',' || s[i] == ';')
      err("in '%s' (%s line %d): invalid Newick format.",__func__,__FILE__,__LINE__);
    if (s[i] == ':') {
      *deme = 0;
    } else {
      try {
        *deme = name_t(stoi(s.substr(i),&sz));
        i += sz;
      }
      catch (const std::invalid_argument& e) {
        err("in '%s' (%s line %d): invalid Newick format: deme should be indicated with an integer.",
            __func__,__FILE__,__LINE__);
      }
      catch (const std::out_of_range& e) {
        err("in '%s': invalid Newick format: deme out of range.",__func__);
      }
      catch (const std::exception& e) {
        err("in '%s': parsing deme label: %s.",__func__,e.what());
      }
      catch (...) {
        err("in '%s': other deme-parsing error.",__func__);
      }
    }
    // skip to branch length
    while (i < n && s[i] != ':' &&
           s[i] != '(' && s[i] != ')' && s[i] != ',' && s[i] != ';') i++;
    if (i == n || s[i] != ':')
      err("in '%s': invalid Newick format: missing or invalid branch length.",__func__);
    i++;
    try {
      *time = slate_t(stod(s.substr(i),&sz));
    }
    catch (const std::invalid_argument& e) {
      err("in '%s': invalid Newick format: branch length should be a non-negative decimal number.",__func__);
    }
    catch (const std::out_of_range& e) {
      err("in '%s': invalid Newick format: branch length out of range.",__func__);
    }
    catch (const std::exception& e) {
      err("in '%s': parsing branch-length: %s.",__func__,e.what());
    }
    catch (...) {
      err("in '%s': other branch-length parsing error.",__func__);
    }
    if (*time < 0.0) err("in '%s': negative branch length detected.",__func__);
    i += sz;
    return i;
  };

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scan_node()

size_t genealogy_t::scan_node ( const std::string & s, const slate_t t0, node_t ** q )

inlineprivate

Scan the Newick string and create the indicated node.

Definition at line 699 of file genealogy.h.

                                                                      {
    size_t i;
    color_t col;
    name_t deme;
    slate_t t;
    name_t u = unique();
    i = scan_label(s,&col,&deme,&t);
    t += t0;
    _ndeme = (_ndeme <= deme) ? deme+1 : _ndeme;
    _time = (_time < t) ? t : _time;
    node_t *p = new node_t(u,t);
    ball_t *g = new ball_t(p,u,green,deme);
    p->green_ball() = g;
    p->insert(g);
    if (col==blue) {
      ball_t *b = new ball_t(p,p->uniq,blue,deme);
      p->insert(b);
    }
    push_back(p);
    *q = p;
    return i;
  };

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scan_tree()

size_t genealogy_t::scan_tree ( const std::string & s, const slate_t t0, node_t ** root )

inlineprivate

Parse a single-root Newick tree. This assumes the string starts with a '('.

Definition at line 723 of file genealogy.h.

                                                     {
    size_t n = s.size();
    size_t i = 1, j = 1, k;
    size_t stack = 1;
    while (j < n && stack > 0) {
      switch (s[j]) {
      case '(':
        stack++;
        break;
      case ')':
        stack--;
        break;
      default:
        break;
      }
      j++;
    }
    if (stack > 0)
      err("in '%s': premature end of Newick string.",__func__);
    node_t *p = 0;
    k = j;
    k += scan_node(s.substr(j),t0,&p);
    parse(s.substr(i,j-i-1),p->slate,p);
    *root = p;
    return k;
  };

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structure()

SEXP genealogy_t::structure ( void ) const

inline

R list description.

Definition at line 328 of file genealogy.h.

                              {
    SEXP O, On, T0, Time, Nodes;
    PROTECT(O = NEW_LIST(3));
    PROTECT(On = NEW_CHARACTER(3));
    PROTECT(Time = NEW_NUMERIC(1));
    *REAL(Time) = double(time());
    PROTECT(T0 = NEW_NUMERIC(1));
    *REAL(T0) = double(timezero());
    PROTECT(Nodes = nodeseq_t::structure());
    set_list_elem(O,On,Time,"time",0);
    set_list_elem(O,On,T0,"t0",1);
    set_list_elem(O,On,Nodes,"nodes",2);
    SET_NAMES(O,On);
    UNPROTECT(5);
    return O;
  };

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time() [1/2]

slate_t & genealogy_t::time ( void )

inline

view/set current time.

Definition at line 150 of file genealogy.h.

                       {
    return _time;
  };

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time() [2/2]

slate_t genealogy_t::time ( void ) const

inline

view current time.

Definition at line 154 of file genealogy.h.

                            {
    return _time;
  };

timezero() [1/2]

slate_t & genealogy_t::timezero ( void )

inline

view/set zero time.

Definition at line 158 of file genealogy.h.

                           {
    return _t0;
  };

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timezero() [2/2]

slate_t genealogy_t::timezero ( void ) const

inline

get zero time.

Definition at line 162 of file genealogy.h.

                                {
    return _t0;
  };

unique()

name_t genealogy_t::unique ( void )

inlineprivate

get the next unique name

Definition at line 46 of file genealogy.h.

                       {
    name_t u = _unique;
    _unique++;
    return u;
  };

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valid()

void genealogy_t::valid ( void ) const

inline

check the validity of the genealogy.

Definition at line 377 of file genealogy.h.

{};

yaml()

virtual std::string genealogy_t::yaml ( std::string tab = "" ) const

inlinevirtual

machine-readable info

Reimplemented from nodeseq_t.

Definition at line 358 of file genealogy.h.

                                                    {
    std::string o;
    std::string t = tab + "  ";
    o = tab + "t0: " + std::to_string(timezero()) + "\n"
      + tab + "time: " + std::to_string(time()) + "\n"
      + tab + "nodes:\n" + nodeseq_t::yaml(tab);
    return o;
  };

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Friends And Related Symbol Documentation

operator>> [1/2]

raw_t * operator>> ( const genealogy_t & G, raw_t * o )

friend

binary serialization

Definition at line 78 of file genealogy.h.

                                                            {
    name_t A[3]; A[0] = magic; A[1] = G._unique; A[2] = name_t(G._ndeme);
    slate_t B[2]; B[0] = G.timezero(); B[1] = G.time();
    memcpy(o,A,sizeof(A)); o += sizeof(A);
    memcpy(o,B,sizeof(B)); o += sizeof(B);
    return reinterpret_cast<const nodeseq_t&>(G) >> o;
  };

operator>> [2/2]

raw_t * operator>> ( raw_t * o, genealogy_t & G )

friend

binary deserialization

Definition at line 86 of file genealogy.h.

                                                      {
    G.clean();
    name_t A[3];
    slate_t B[2];
    memcpy(A,o,sizeof(A)); o += sizeof(A);
    memcpy(B,o,sizeof(B)); o += sizeof(B);
    if (A[0] != magic)
      err("in %s (%s line %d) corrupted genealogy serialization.",
          __func__,__FILE__,__LINE__);
    G._unique = A[1]; G._ndeme = size_t(A[2]);
    G.timezero() = B[0]; G.time() = B[1];
    return o >> reinterpret_cast<nodeseq_t&>(G);
  };

Field Documentation

_ndeme

size_t genealogy_t::_ndeme

private

The number of demes.

Definition at line 39 of file genealogy.h.

_t0

slate_t genealogy_t::_t0

private

The initial time.

Definition at line 35 of file genealogy.h.

_time

slate_t genealogy_t::_time

private

The current time.

Definition at line 37 of file genealogy.h.

_unique

name_t genealogy_t::_unique

private

The next unique name.

Definition at line 33 of file genealogy.h.

magic

const name_t genealogy_t::magic = 1123581321

staticprivate

Definition at line 41 of file genealogy.h.

---

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

• src/genealogy.h