ARB: ARB_edge Class Reference

ARB

#include <TreeNode.h>

Public Member Functions
void	virtually_distribute_length (GBT_LEN len, TreeNode::LengthCollector &collect) const

	ARB_edge (TreeNode From, TreeNode To)

	ARB_edge (TreeNode From, TreeNode To, ARB_edge_type Type)

	ARB_edge (const ARB_edge &otherEdge)

	DECLARE_ASSIGNMENT_OPERATOR (ARB_edge)

ARB_edge_type	get_type () const

TreeNode *	source () const

TreeNode *	dest () const

TreeNode *	son () const

TreeNode *	other () const

GBT_LEN	length () const

void	set_length (GBT_LEN len)

GBT_LEN	eliminate ()

ARB_edge	inverse () const

ARB_edge	next () const

ARB_edge	previous () const

ARB_edge	counter_next () const

ARB_edge	counter_previous () const

bool	operator== (const ARB_edge &otherEdge) const

bool	operator!= (const ARB_edge &otherEdge) const

bool	is_edge_to_leaf () const

bool	is_edge_from_leaf () const

bool	is_inner_edge () const

void	set_root ()

void	multifurcate ()

Static Public Member Functions
static int	iteration_count (int leafs_in_tree)

Detailed Description

Definition at line 771 of file TreeNode.h.

Constructor & Destructor Documentation

ARB_edge::ARB_edge	(	TreeNode *	From,
		TreeNode *	To
	)

inline

Definition at line 811 of file TreeNode.h.

Referenced by counter_next(), counter_previous(), inverse(), next(), and previous().

ARB_edge::ARB_edge	(	TreeNode *	From,
		TreeNode *	To,
		ARB_edge_type	Type
	)

inline

Definition at line 816 of file TreeNode.h.

References rt_assert.

ARB_edge::ARB_edge ( const ARB_edge & otherEdge )

inline

Definition at line 823 of file TreeNode.h.

References rt_assert.

Member Function Documentation

void ARB_edge::virtually_distribute_length	(	GBT_LEN	len,
		TreeNode::LengthCollector &	collect
	)		const

distribute length to all adjacent edges. Longer edges receive more than shorter ones.

Edges with length zero will not be changed, instead both edges "beyond" the edge will be affected (they will be affected equally to direct edges, because edges at multifurcations are considered to BE direct edges).

Note: length will not be distributed to tree-struction itself (yet), but collected in 'collect'

Definition at line 522 of file TreeNode.cxx.

References inverse(), and is_normal().

Referenced by TreeNode::LengthCollector::independent_distribution().

ARB_edge::DECLARE_ASSIGNMENT_OPERATOR ( ARB_edge )

ARB_edge_type ARB_edge::get_type ( ) const

inline

Definition at line 833 of file TreeNode.h.

Referenced by GroupSearch::perform_search().

TreeNode* ARB_edge::source ( ) const

inline

Definition at line 834 of file TreeNode.h.

Referenced by eliminate(), is_edge_from_leaf(), and GroupSearch::perform_search().

TreeNode* ARB_edge::dest ( ) const

inline

Definition at line 835 of file TreeNode.h.

Referenced by eliminate(), is_edge_to_leaf(), GroupIterator::node(), and GroupSearch::perform_search().

TreeNode* ARB_edge::son ( ) const

inline

Definition at line 837 of file TreeNode.h.

References EDGE_TO_ROOT.

Referenced by eliminate(), length(), multifurcate(), randomMixTree(), set_length(), and set_root().

TreeNode* ARB_edge::other ( ) const

inline

Definition at line 838 of file TreeNode.h.

References EDGE_TO_ROOT.

GBT_LEN ARB_edge::length ( ) const

inline

Definition at line 840 of file TreeNode.h.

References TreeNode::get_branchlength(), ROOT_EDGE, and son().

Referenced by TreeNode::LengthCollector::independent_distribution().

void ARB_edge::set_length ( GBT_LEN len )

inline

Definition at line 844 of file TreeNode.h.

References ROOT_EDGE, TreeNode::set_branchlength(), and son().

Referenced by TreeNode::LengthCollector::independent_distribution().

GBT_LEN ARB_edge::eliminate ( )

inline

eliminates edge (zeroes length and bootstrap). returns eliminated length.

Definition at line 853 of file TreeNode.h.

References dest(), TreeNode::reset_length_and_bootstrap(), ROOT_EDGE, son(), and source().

Referenced by TreeNode::LengthCollector::eliminate_parent_edge().

ARB_edge ARB_edge::inverse ( ) const

inline

Definition at line 861 of file TreeNode.h.

References ARB_edge(), EDGE_TO_LEAF, EDGE_TO_ROOT, and ROOT_EDGE.

Referenced by counter_next(), counter_previous(), leafEdge(), next(), previous(), and virtually_distribute_length().

ARB_edge ARB_edge::next ( ) const

inline

Definition at line 871 of file TreeNode.h.

References ARB_edge(), EDGE_TO_LEAF, EDGE_TO_ROOT, TreeNode::get_brother(), inverse(), is_edge_to_leaf(), TreeNode::is_rightson(), TreeNode::is_root_node(), TreeNode::is_son_of(), ROOT_EDGE, and rt_assert.

Referenced by GroupSearch::perform_search().

ARB_edge ARB_edge::previous ( ) const

inline

Definition at line 882 of file TreeNode.h.

References ARB_edge(), EDGE_TO_LEAF, EDGE_TO_ROOT, TreeNode::get_brother(), inverse(), is_edge_from_leaf(), TreeNode::is_leftson(), TreeNode::is_root_node(), TreeNode::is_son_of(), ROOT_EDGE, and rt_assert.

ARB_edge ARB_edge::counter_next ( ) const

inline

Definition at line 894 of file TreeNode.h.

References ARB_edge(), EDGE_TO_LEAF, EDGE_TO_ROOT, TreeNode::get_brother(), inverse(), is_edge_to_leaf(), TreeNode::is_leftson(), TreeNode::is_root_node(), TreeNode::is_son_of(), ROOT_EDGE, and rt_assert.

ARB_edge ARB_edge::counter_previous ( ) const

inline

Definition at line 905 of file TreeNode.h.

References ARB_edge(), EDGE_TO_LEAF, EDGE_TO_ROOT, TreeNode::get_brother(), inverse(), is_edge_from_leaf(), TreeNode::is_rightson(), TreeNode::is_root_node(), TreeNode::is_son_of(), ROOT_EDGE, and rt_assert.

static int ARB_edge::iteration_count ( int leafs_in_tree )

inlinestatic

returns number of different edges produced by next() / previous():

each edge is visited twice (once in each direction)

Definition at line 917 of file TreeNode.h.

References leafs_2_edges(), and UNROOTED.

Referenced by SearchedTree::get_edge_iteration_count().

bool ARB_edge::operator== ( const ARB_edge & otherEdge ) const

inline

Definition at line 924 of file TreeNode.h.

Referenced by operator!=().

bool ARB_edge::operator!= ( const ARB_edge & otherEdge ) const

inline

Definition at line 927 of file TreeNode.h.

References operator==().

bool ARB_edge::is_edge_to_leaf ( ) const

inline

true if edge is leaf edge AND points towards the leaf

Definition at line 931 of file TreeNode.h.

References dest(), and TreeNode::is_leaf().

Referenced by counter_next(), is_inner_edge(), and next().

bool ARB_edge::is_edge_from_leaf ( ) const

inline

true if edge is leaf edge AND points away from the leaf

Definition at line 935 of file TreeNode.h.

References TreeNode::is_leaf(), and source().

Referenced by counter_previous(), is_inner_edge(), and previous().

bool ARB_edge::is_inner_edge ( ) const

inline

true for inner edges

Definition at line 939 of file TreeNode.h.

References is_edge_from_leaf(), and is_edge_to_leaf().

void ARB_edge::set_root ( )

inline

Definition at line 944 of file TreeNode.h.

References TreeNode::set_root(), and son().

Referenced by AWT_graphic_tree::handle_command(), and nt_add().

void ARB_edge::multifurcate ( )

eliminate edge and distribute length to adjacent edges

sets its length to zero
removes remark (bootstrap)
distributes length to neighbour-branches

Definition at line 580 of file TreeNode.cxx.

References TreeNode::LengthCollector::eliminate_parent_edge(), TreeNode::LengthCollector::independent_distribution(), and son().

Referenced by TreeNode::multifurcate().

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

ARBDB/TreeNode.h
ARBDB/TreeNode.cxx