nodeseq_t Class Reference

A sequence of nodes. More...

#include <nodeseq.h>

Inheritance diagram for nodeseq_t:

Collaboration diagram for nodeseq_t:

Public Member Functions
	~nodeseq_t (void)
	destructor
size_t	bytesize (void) const
	size of serialized binary form
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	move (ball_t *b, node_t *p, node_t *q)
	move ball b from p to q
void	swap (ball_t *a, ball_t *b)
	swap balls a and b, wherever they lie
void	attach (node_t *p, node_t *q)
void	detach (node_t *p)
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	weed (void)
	drop all dead roots
void	comb (void)
void	trace_lineages (void)
string_t	yaml (string_t tab="") const
	human/machine-readable info
SEXP	structure (void) const
	R list description.
string_t	newick (slate_t t, bool showdeme, bool extended) const
	put genealogy at time t into Newick format.

Static Public Member Functions
static bool	compare (node_t *p, node_t *q)

Private Member Functions
void	clean (void)
	clean up: delete all nodes, reset globals
void	repair_owners (std::unordered_map< name_t, ball_t * > &names)
slate_t	dawn (void) const
	Earliest time in the sequence.
slate_t	dusk (void) const
	Latest time in the sequence.
void	trace_lineage (ball_t *b, name_t u)

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

Detailed Description

A sequence of nodes.

Definition at line 17 of file nodeseq.h.

Constructor & Destructor Documentation

~nodeseq_t()

nodeseq_t::~nodeseq_t ( void )

inline

destructor

Definition at line 30 of file nodeseq.h.

                    {
    clean();
  };

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Member Function Documentation

add()

void nodeseq_t::add ( node_t * p, ball_t * a )

inline

add node p; take as parent the node holding ball a. the deme of p is changed to match that of a

Definition at line 184 of file nodeseq.h.

                                  {
    swap(a,p->green_ball());
    p->deme() = a->deme();
    push_back(p);
  };

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attach()

void nodeseq_t::attach ( node_t * p, node_t * q )

inline

attach node q as descendant of node p. note that this does not push q into the nodeseq.

Definition at line 174 of file nodeseq.h.

                                     {
    move(q->green_ball(),q,p);
  };

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bytesize()

size_t nodeseq_t::bytesize ( void ) const

inline

size of serialized binary form

Definition at line 38 of file nodeseq.h.

                               {
    size_t s = sizeof(size_t);
    for (node_t *p : *this)
      s += p->bytesize();
    return s;
  };

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clean()

void nodeseq_t::clean ( void )

inlineprivate

clean up: delete all nodes, reset globals

Definition at line 22 of file nodeseq.h.

                    {
    for (node_t *p : *this) delete p;
    clear();
  };

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colored()

pocket_t * nodeseq_t::colored ( color_t col ) const

inline

Get all balls of a color.

Definition at line 121 of file nodeseq.h.

                                        {
    pocket_t *p = new pocket_t;
    for (node_t *q : *this) {
      for (ball_t *b : *q ) {
        if (b->is(col)) p->insert(b);
      }
    }
    return p;
  };

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comb()

void nodeseq_t::comb ( void )

inline

drop all inline nodes i.e., those holding just one ball that is green.

Definition at line 226 of file nodeseq.h.

                   {
    for (node_t *p : *this) {
      if (p->size() == 1 && p->holds(green)) {
        swap(p->last_ball(),p->green_ball());
      }
    }
    weed();
  };

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compare()

static bool nodeseq_t::compare ( node_t * p, node_t * q )

inlinestatic

Order relation among nodes. An ancestor node should always come before its descendants. Nodes should be ordered by time, then arbitrarily.

Definition at line 95 of file nodeseq.h.

                                             {
    return (p->slate < q->slate) ||
      ((p->slate == q->slate) &&
       ((p==q->green_ball()->holder()) ||
        ((q!=p->green_ball()->holder()) && (p->uniq < q->uniq))));
  };

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dawn()

slate_t nodeseq_t::dawn ( void ) const

inlineprivate

Earliest time in the sequence.

Definition at line 110 of file nodeseq.h.

                            {
    return (empty()) ? R_NaReal : front()->slate;
  };

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destroy_node()

void nodeseq_t::destroy_node ( node_t * p )

inline

remove a dead root node

Definition at line 208 of file nodeseq.h.

                                {
    assert(p->dead_root());
    remove(p);
    delete p;
  };

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detach()

void nodeseq_t::detach ( node_t * p )

inline

detach node p from its parent. note that this does not remove q from the nodeseq.

Definition at line 179 of file nodeseq.h.

                          {
    move(p->green_ball(),p->parent(),p);
  };

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drop()

void nodeseq_t::drop ( ball_t * a )

inline

drop the black ball 'a' and the node if either (1) the node becomes thereby a dead root, or (2) the node's pocket becomes thereby empty.

Definition at line 192 of file nodeseq.h.

                        {
    assert(a->is(black));
    node_t *p = a->holder();
    if (p->size() > 1) {
      p->erase(a);
      delete a;
      if (p->dead_root()) {     // remove isolated root
        destroy_node(p);
      }
    } else {
      swap(a,p->green_ball());
      destroy_node(p);
      drop(a);                  // recurse
    }
  };

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dusk()

slate_t nodeseq_t::dusk ( void ) const

inlineprivate

Latest time in the sequence.

Definition at line 114 of file nodeseq.h.

                            {
    return (empty()) ? R_NaReal : back()->slate;
  }

length()

size_t nodeseq_t::length ( void ) const

inline

Number of nodes in the sequence.

Definition at line 142 of file nodeseq.h.

                             {
    return this->size();
  };

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move()

void nodeseq_t::move ( ball_t * b, node_t * p, node_t * q )

inline

move ball b from p to q

Definition at line 159 of file nodeseq.h.

                                              {
    assert(b->holder() == p);
    p->erase(b); q->insert(b);
  };

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newick()

string_t nodeseq_t::newick	(	slate_t	t,
		bool	showdeme,
		bool	extended ) const

put genealogy at time t into Newick format.

Definition at line 78 of file newick.cc.

{
  slate_t te = dawn();
  string_t o = "";
  for (node_t *p : *this) {
    if (p->is_root()) {
      o += p->newick(t,te,showdeme,extended) + ";";
    }
  }
  return o;
}

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ntime()

size_t nodeseq_t::ntime ( slate_t t ) const

inline

Number of distinct timepoints.

Definition at line 131 of file nodeseq.h.

                                 {
    size_t count = 1;
    for (node_t *p : *this) {
      if (t < p->slate) {
        t = p->slate;
        count++;
      }
    }
    return count;
  };

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position()

node_t * nodeseq_t::position ( int n )

inline

traverse to nth node, retrieve pointer

Definition at line 146 of file nodeseq.h.

                           {
    int i = 0;
    node_it k = cbegin();
    while (i < n && k != cend()) {
      i++; k++;
    }
    assert(k != cend());
    return *k;
  };

repair_owners()

void nodeseq_t::repair_owners ( std::unordered_map< name_t, ball_t * > & names )

inlineprivate

Needed in deserialization. This function repairs the links green balls and their names.

Definition at line 80 of file nodeseq.h.

                                                               {
    std::unordered_map<name_t,ball_t*>::const_iterator n;
    for (node_t *p : *this) {
      n = names.find(p->uniq);
      assert(n != names.end());
      ball_t *b = n->second;
      p->green_ball() = b;
    }
  };

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sort()

void nodeseq_t::sort ( void )

inline

order nodes in order of increasing time

Definition at line 103 of file nodeseq.h.

                   {
    std::list<node_t*>::sort(compare);
  };

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structure()

SEXP nodeseq_t::structure

(

void

)

const

R list description.

Definition at line 70 of file structure.cc.

{
  SEXP Nodes;
  PROTECT(Nodes = NEW_LIST(size()));
  int k = 0;
  for (node_t *p : *this) {
    SET_ELEMENT(Nodes,k++,p->structure());
  }
  UNPROTECT(1);
  return Nodes;
}

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swap()

void nodeseq_t::swap ( ball_t * a, ball_t * b )

inline

swap balls a and b, wherever they lie

Definition at line 164 of file nodeseq.h.

                                   {
    node_t *p = a->holder();
    node_t *q = b->holder();
    if (p != q) {
      p->erase(a); q->insert(a);
      q->erase(b); p->insert(b);
    }
  };

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trace_lineage()

void nodeseq_t::trace_lineage ( ball_t * b, name_t u )

inlineprivate

trace back a single lineage. this results in the deme slot for all green balls along the lineage of 'b' begin replaced by the lineage of 'b'.

Definition at line 240 of file nodeseq.h.

                                           {
    node_t *p = b->holder();
    while (p->lineage() == null_lineage) {
      p->lineage() = u;
      p = p->parent();
    }
  };

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trace_lineages()

void nodeseq_t::trace_lineages ( void )

inline

trace back all sample lineages. this results in the deme slots of all green balls being replaced by the unique names of the lineages they trace.

Definition at line 253 of file nodeseq.h.

                             {
    // we trace each lineage in turn.
    // because we move from early to late,
    // the order is guaranteed to be valid.
    name_t u = 0;
    for (node_t *p : *this ) {
      for (ball_t *b : *p) {
        if (b->color==blue) {
          trace_lineage(b,u);
          u++;
        }
      }
    }
  };

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weed()

void nodeseq_t::weed ( void )

inline

drop all dead roots

Definition at line 214 of file nodeseq.h.

                   {
    node_nit j = begin();
    while (j != end()) {
      if ((*j)->dead_root()) {
        destroy_node(*(j++));
      } else {
        j++;
      }
    }
  };

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yaml()

string_t nodeseq_t::yaml

(

string_t

tab = ""

)

const

human/machine-readable info

Definition at line 51 of file yaml.cc.

{
  string_t o = "";
  string_t t = tab + "  ";
  for (node_t *p : *this) {
    o += tab + "- " + p->yaml(t);
  }
  return o;
}

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Friends And Related Symbol Documentation

operator>> [1/2]

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

friend

binary serialization

Definition at line 45 of file nodeseq.h.

                                                          {
    size_t nnode = G.size();
    memcpy(o,&nnode,sizeof(size_t)); o += sizeof(size_t);
    for (node_t *p : G) {
      o = (*p >> o);
    }
    return o;
  };

operator>> [2/2]

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

friend

binary deserialization

Definition at line 54 of file nodeseq.h.

                                                    {
    G.clean();
    std::unordered_map<name_t,node_t*> node_names;
    std::unordered_map<name_t,ball_t*> ball_names;
    size_t nnode = 0;
    memcpy(&nnode,o,sizeof(size_t)); o += sizeof(size_t);
    node_names.reserve(nnode);
    ball_names.reserve(nnode);
    for (size_t i = 0; i < nnode; i++) {
      node_t *p = new node_t();
      o = (o >> *p);
      G.push_back(p);
      node_names.insert({p->uniq,p});
    }
    for (node_t *q : G) {
      q->repair_owners(node_names,&ball_names);
    }
    G.repair_owners(ball_names);
    G.trace_lineages();
    return o;
  };

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

• src/nodeseq.h
• src/newick.cc
• src/structure.cc
• src/yaml.cc