ARB: AP_tree_edge Class Reference

ARB

#include <ap_tree_nlen.hxx>

Inheritance diagram for AP_tree_edge:

Inheritance graph

Collaboration diagram for AP_tree_edge:

Collaboration graph

Public Member Functions
	AP_tree_edge (AP_tree_nlen node1, AP_tree_nlen node2)

bool	isConnectedTo (const AP_tree_nlen *n) const

int	indexOf (const AP_tree_nlen *n) const

AP_tree_nlen *	otherNode (const AP_tree_nlen *n) const

AP_tree_nlen *	sonNode () const

AP_tree_nlen *	notSonNode () const

long	Age () const

bool	is_root_edge () const

bool	is_leaf_edge () const

bool	next_to_folded_group () const

bool	has_marked () const

void	set_root ()

Mutations	nni_rec (EdgeSpec whichEdges, AP_BL_MODE mode, AP_tree_nlen *skipNode, bool includeStartEdge)

bool	kl_rec (const KL_params &KL, const int rec_depth, Mutations pars_best)

Mutations	calc_branchlengths ()

Mutations	nni_mutPerSite (Mutations pars_one, AP_BL_MODE mode, MutationsPerSite *mps)

void	mixTree (int repeat, int percent, EdgeSpec whichEdges)

void	set_visited (bool vis)

Static Public Member Functions
static void	initialize (AP_tree_nlen *root)

static void	destroy (AP_tree_nlen *root)

Protected Member Functions
	~AP_tree_edge ()

void	relink (AP_tree_nlen node1, AP_tree_nlen node2)

AP_tree_edge *	unlink ()

Friends
class	AP_tree_nlen

class	EdgeChain

std::ostream &	operator<< (std::ostream &, const AP_tree_edge *)

AP_tree_edge *	StackFrameData::makeEdge (AP_tree_nlen n1, AP_tree_nlen n2)

void	AP_main::destroyEdge (AP_tree_edge *edge)

void	ResourceStack::destroy_edges ()

Detailed Description

Definition at line 260 of file ap_tree_nlen.hxx.

Constructor & Destructor Documentation

AP_tree_edge::~AP_tree_edge ( )

protected

Definition at line 35 of file AP_tree_edge.cxx.

References unlink().

AP_tree_edge::AP_tree_edge	(	AP_tree_nlen *	node1,
		AP_tree_nlen *	node2
	)

Definition at line 25 of file AP_tree_edge.cxx.

References NULp, and relink().

Referenced by initialize().

Member Function Documentation

void AP_tree_edge::relink	(	AP_tree_nlen *	node1,
		AP_tree_nlen *	node2
	)

protected

Definition at line 101 of file AP_tree_edge.cxx.

References ap_assert.

Referenced by AP_tree_edge(), and StackFrameData::makeEdge().

AP_tree_edge * AP_tree_edge::unlink ( )

protected

Definition at line 88 of file AP_tree_edge.cxx.

References ap_assert, and NULp.

Referenced by ~AP_tree_edge().

void AP_tree_edge::initialize ( AP_tree_nlen * root )

static

Builds all edges in the whole tree. The root node is skipped - instead his two sons are connected with an edge

Definition at line 57 of file AP_tree_edge.cxx.

References AP_tree_edge(), and buildSonEdges().

Referenced by PARSIMONY_testenv< SEQTYPE >::load_tree(), and pars_start_cb().

void AP_tree_edge::destroy ( AP_tree_nlen * root )

static

Destroys all edges in the whole tree

Definition at line 71 of file AP_tree_edge.cxx.

References ANY_EDGE, ap_assert, and NULp.

Referenced by PARSIMONY_testenv< SEQTYPE >::~PARSIMONY_testenv().

bool AP_tree_edge::isConnectedTo ( const AP_tree_nlen * n ) const

inline

Definition at line 312 of file ap_tree_nlen.hxx.

Referenced by indexOf(), and insert_species_into_tree().

int AP_tree_edge::indexOf ( const AP_tree_nlen * n ) const

inline

Definition at line 313 of file ap_tree_nlen.hxx.

References ap_assert, and isConnectedTo().

Referenced by otherNode().

AP_tree_nlen* AP_tree_edge::otherNode ( const AP_tree_nlen * n ) const

inline

Definition at line 314 of file ap_tree_nlen.hxx.

References indexOf().

Referenced by EdgeChain::EdgeChain(), insert_species_into_tree(), ArbParsimony::kernighan_optimize_tree(), and notSonNode().

AP_tree_nlen* AP_tree_edge::sonNode ( ) const

inline

Definition at line 315 of file ap_tree_nlen.hxx.

Referenced by EdgeChain::EdgeChain(), has_marked(), insert_species_into_tree(), kl_rec(), nni_mutPerSite(), nni_rec(), notSonNode(), and set_root().

AP_tree_nlen* AP_tree_edge::notSonNode ( ) const

inline

Definition at line 316 of file ap_tree_nlen.hxx.

References otherNode(), and sonNode().

Referenced by insert_species_into_tree().

long AP_tree_edge::Age ( ) const

inline

Definition at line 318 of file ap_tree_nlen.hxx.

bool AP_tree_edge::is_root_edge ( ) const

inline

Definition at line 322 of file ap_tree_nlen.hxx.

Referenced by EdgeChain::EdgeChain(), and has_marked().

bool AP_tree_edge::is_leaf_edge ( ) const

inline

Definition at line 323 of file ap_tree_nlen.hxx.

Referenced by insert_species_into_tree(), ArbParsimony::kernighan_optimize_tree(), kl_rec(), nni_mutPerSite(), and nni_rec().

bool AP_tree_edge::next_to_folded_group ( ) const

inline

Definition at line 324 of file ap_tree_nlen.hxx.

Referenced by ArbParsimony::kernighan_optimize_tree(), and kl_rec().

bool AP_tree_edge::has_marked ( ) const

inline

Definition at line 325 of file ap_tree_nlen.hxx.

References is_root_edge(), and sonNode().

void AP_tree_edge::set_root ( )

inline

Definition at line 333 of file ap_tree_nlen.hxx.

References sonNode().

Referenced by insert_all_species_into_tree(), insert_species_into_tree(), and nni_rec().

Mutations AP_tree_edge::nni_rec	(	EdgeSpec	whichEdges,
		AP_BL_MODE	mode,
		AP_tree_nlen *	skipNode,
		bool	includeStartEdge
	)

Definition at line 438 of file AP_tree_edge.cxx.

References allBranchlengthsAreDefined(), ANY_EDGE, ap_assert, AP_BL_BL_ONLY, AP_BL_BOOTSTRAP_LIMIT, ap_calc_bootstrap_remark(), ap_main, AP_tree_nlen, implicated, is_leaf(), is_leaf_edge(), nni_mutPerSite(), NULp, AP_main::push_node(), EdgeChain::restart(), rootEdge(), rootNode(), set_root(), EdgeChain::size(), SKIP_LEAF_EDGES, sonNode(), STRUCTURE, and undefine_branchlengths().

Referenced by calc_branchlengths(), and insert_species_into_tree().

bool AP_tree_edge::kl_rec	(	const KL_params &	KL,
		const int	rec_depth,
		Mutations	pars_best
	)

does K.L. recursion

Parameters

KL	parameters defining how recursion is done
rec_depth	current recursion depth (starts with 0)
pars_best	current parsimony value of topology

Definition at line 1096 of file AP_tree_nlen.cxx.

References AP_main::accept_if(), ap_assert, AP_DYNAMIK, ap_main, AP_STATIC, QuadraticThreshold::calculate(), CUSTOM_DEPTHS, idx2side(), implicated, KL_params::inc_rec_depth, is_leaf_edge(), kl_rec(), KL_params::max_rec_depth, min, next_to_folded_group(), NULp, KL_params::rec_type, KL_params::rec_width, AP_main::remember(), AP_main::revert(), rootNode(), sonNode(), KL_params::stopAtFoldedGroups, swap(), and KL_params::thresFunctor.

Referenced by ArbParsimony::kernighan_optimize_tree(), and kl_rec().

Mutations AP_tree_edge::calc_branchlengths ( )

inline

Definition at line 340 of file ap_tree_nlen.hxx.

References ANY_EDGE, AP_BL_BL_ONLY, nni_rec(), and NULp.

Mutations AP_tree_edge::nni_mutPerSite	(	Mutations	pars_one,
		AP_BL_MODE	mode,
		MutationsPerSite *	mps
	)

Definition at line 502 of file AP_tree_edge.cxx.

References AP_main::accept_if(), ap_assert, AP_BL_BL_ONLY, AP_BL_BOOTSTRAP_LIMIT, AP_BL_NNI_ONLY, AP_LEFT, ap_main, AP_RIGHT, AP_tree_nlen, MutationsPerSite::data(), is_leaf_edge(), NULp, AP_main::remember(), AP_main::revert(), rootNode(), and sonNode().

Referenced by nni_rec().

void AP_tree_edge::mixTree	(	int	repeat,
		int	percent,
		EdgeSpec	whichEdges
	)

Definition at line 592 of file AP_tree_edge.cxx.

References arb_progress::aborted(), ap_assert, AP_LEFT, AP_RIGHT, AP_tree_nlen, GB_random(), EdgeChain::restart(), EdgeChain::size(), and SKIP_LEAF_EDGES.

void AP_tree_edge::set_visited ( bool vis )

inline

Definition at line 346 of file ap_tree_nlen.hxx.

Referenced by ArbParsimony::kernighan_optimize_tree().

Friends And Related Function Documentation

friend class AP_tree_nlen

friend

Definition at line 283 of file ap_tree_nlen.hxx.

Referenced by mixTree(), nni_mutPerSite(), and nni_rec().

friend class EdgeChain

friend

Definition at line 284 of file ap_tree_nlen.hxx.

std::ostream& operator<<	(	std::ostream &	,
		const AP_tree_edge *
	)

friend

Definition at line 572 of file AP_tree_edge.cxx.

AP_tree_edge* StackFrameData::makeEdge	(	AP_tree_nlen *	n1,
		AP_tree_nlen *	n2
	)

friend

void AP_main::destroyEdge ( AP_tree_edge * edge )

friend

void ResourceStack::destroy_edges ( )

friend

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

PARSIMONY/ap_tree_nlen.hxx
PARSIMONY/AP_tree_edge.cxx
PARSIMONY/AP_tree_nlen.cxx