#include <TreeNode.h>

Inheritance diagram for TreeNode:

Collaboration diagram for TreeNode:

Classes
class	LengthCollector

struct	multifurc_limits

Public Member Functions
bool	is_leaf () const

void	markAsLeaf ()

	DEFINE_READ_ACCESSORS (TreeNode *, get_father, father)

	DEFINE_READ_ACCESSORS (TreeNode *, get_leftson, leftson)

	DEFINE_READ_ACCESSORS (TreeNode *, get_rightson, rightson)

bool	is_son_of (const TreeNode *Father) const

bool	is_leftson () const

bool	is_rightson () const

bool	is_inside (const TreeNode *subtree) const

bool	is_ancestor_of (const TreeNode *descendant) const

bool	in_same_branch_as (const TreeNode *other) const

bool	in_other_branch_than (const TreeNode *other) const

const TreeNode *	ancestor_common_with (const TreeNode *other) const

TreeNode *	ancestor_common_with (TreeNode *other)

bool	is_son_of_root () const

GBT_LEN	get_branchlength () const

void	set_branchlength (GBT_LEN newlen)

GBT_LEN	get_branchlength_unrooted () const

void	set_branchlength_unrooted (GBT_LEN newlen)

GBT_LEN	sum_child_lengths () const

GBT_LEN	root_distance () const

GBT_LEN	intree_distance_to (const TreeNode *other) const

void	remove_bootstrap ()

GB_ERROR	apply_aci_to_remarks (const char *aci, const GBL_call_env &callEnv)

void	reset_branchlengths ()

void	scale_branchlengths (double factor)

void	bootstrap2branchlen ()

void	branchlen2bootstrap ()

GBT_RemarkType	parse_bootstrap (double &bootstrap) const

const char *	get_remark () const

const SmartCharPtr &	get_remark_ptr () const

bool	is_inner_node_with_remark () const

void	use_as_remark (const SmartCharPtr &newRemark)

void	set_remark (const char *newRemark)

void	set_bootstrap (double bootstrap)

void	remove_remark ()

bool	has_no_remark () const

bool	has_valid_root_remarks () const

	TreeNode (TreeRoot *root)

TreeNode *	fixDeletedSon ()

void	unlink_from_DB ()

void	announce_tree_constructed ()

virtual unsigned	get_leaf_count () const =0

virtual void	compute_tree ()=0

void	forget_origin ()

void	forget_relatives ()

TreeRoot *	get_tree_root () const

const TreeNode *	get_root_node () const

TreeNode *	get_root_node ()

bool	is_root_node () const

virtual void	set_root ()

TreeNode *	get_brother ()

const TreeNode *	get_brother () const

bool	has_group_info () const

TreeNode *	keelTarget ()

const TreeNode *	keelTarget () const

bool	keelsDownGroup (const TreeNode *toSon) const

void	unkeelGroup ()

int	keeledStateInfo () const

void	setKeeledState (int keeledState)

bool	is_normal_group () const

bool	is_keeled_group () const

bool	is_clade () const

const char *	get_group_name () const

const TreeNode *	find_parent_with_groupInfo (bool skipKeeledBrothers=false) const

TreeNode *	find_parent_with_groupInfo (bool skipKeeledBrothers=false)

const TreeNode *	find_parent_clade () const

TreeNode *	find_parent_clade ()

int	calc_clade_level () const

int	count_clades () const

virtual void	swap_sons ()

void	rotate_subtree ()

void	reorder_tree (TreeOrder mode)

TreeNode *	findLeafNamed (const char *wantedName)

GBT_LEN	reset_length_and_bootstrap ()

void	multifurcate ()

void	set_branchlength_preserving (GBT_LEN new_len)

void	multifurcate_whole_tree (const multifurc_limits &below)

Public Member Functions inherited from Noncopyable
	Noncopyable ()

Static Public Member Functions
static void	destroy (TreeNode *that)

static void	destroy (TreeNode that, TreeRoot root)

Public Attributes
TreeNode *	father

TreeNode *	leftson

TreeNode *	rightson

GBT_LEN	leftlen

GBT_LEN	rightlen

GBDATA *	gb_node

char *	name

Protected Member Functions
TreeNode *&	self_ref ()

void	unlink_from_father ()

void	swap_node_info (TreeNode *other, bool ofKeeledGroups)

void	fixKeeledOrientation ()

void	set_tree_root (TreeRoot *new_root)

bool	at_root () const

virtual	~TreeNode ()

void	destroy ()

void	destroy (TreeRoot *viaRoot)

Friends
void	TreeRoot::change_root (TreeNode old, TreeNode newroot)

Detailed Description

Definition at line 170 of file TreeNode.h.

Constructor & Destructor Documentation

virtual TreeNode::~TreeNode ( )

inlineprotectedvirtual

Definition at line 353 of file TreeNode.h.

References TreeRoot::delete_by_node(), gb_assert, leftson, NULp, rightson, rt_assert, and unlink_from_father().

TreeNode::TreeNode ( TreeRoot * root )

inline

Definition at line 384 of file TreeNode.h.

Member Function Documentation

TreeNode*& TreeNode::self_ref ( )

inlineprotected

Definition at line 191 of file TreeNode.h.

References is_leftson(), leftson, and rightson.

Referenced by unlink_from_father().

void TreeNode::unlink_from_father ( )

inlineprotected

Definition at line 194 of file TreeNode.h.

References NULp, and self_ref().

Referenced by AP_tree::REMOVE(), and ~TreeNode().

void TreeNode::swap_node_info	(	TreeNode *	other,
		bool	ofKeeledGroups
	)

inlineprotected

Definition at line 575 of file AP_Tree.cxx.

References fixKeeledOrientation(), gb_assert, gb_node, get_father(), name, and swap().

void TreeNode::fixKeeledOrientation ( )

inlineprotected

Definition at line 202 of file TreeNode.h.

References is_keeled_group(), is_leftson(), and rt_assert.

Referenced by swap_node_info().

bool TreeNode::is_leaf ( ) const

inline

Definition at line 211 of file TreeNode.h.

Referenced by add_bootstrap(), ap_just_tree_rek(), ap_mark_degenerated(), ap_mark_duplicates_rek(), apply_aci_to_remarks(), ARB_main(), bootstrap2branchlen(), branchlen2bootstrap(), build_taxonomy_rek(), ARB_seqtree::calcTreeInfo(), collect_contained_groups(), collect_enclosing_groups(), AP_tree::colorize(), FINAL_TYPE< SEQTYPE >::compute_tree(), ARB_seqtree::contains_marked_species(), count_clades(), AP_tree::count_leafs(), countTaxLevel(), AWT_graphic_tree::detect_group_state(), BootstrapConfig::display_node_remark(), export_tree_node_print(), export_tree_node_print_xml(), export_tree_rek(), fill_species_name_array(), SpecSetRegistry::find_best_matches_info(), find_node_with_groupdata(), findLeafNamed(), findNode(), fixDeletedSon(), GBT_count_leafs(), gbt_is_invalid(), GBT_is_invalid(), gbt_link_tree_to_hash_rek(), GBT_remove_leafs(), gbt_rename_tree_rek(), GBT_TREE_order(), gbt_write_tree_nodes(), gbt_write_tree_rek_new(), get_downgroups(), get_group_name(), get_remark(), get_remark_ptr(), Cluster::get_upgroup_info(), AWT_graphic_tree::group_tree(), GroupIterator::GroupIterator(), AP_tree::has_correct_mark_flags(), has_group_info(), has_son(), has_valid_root_remarks(), AP_tree::initial_insert(), is_ancestor_of(), is_clade(), ARB_edge::is_edge_from_leaf(), ARB_edge::is_edge_to_leaf(), is_inner_node_with_remark(), AP_tree::is_inside_folded_group(), SpecSet::is_leaf_set(), is_normal_group(), leafEdge(), left_neighbour_leaf(), link_to_tree(), AP_tree::load_subtree_info(), main(), mapTree(), AWT_graphic_tree::mark_species_in_tree(), AWT_graphic_tree::mark_species_in_tree_that(), ARB_seqtree::mark_subtree(), markAsLeaf(), AP_tree::move_group_to(), AP_tree::moveNextTo(), nt_build_conf_string_rek(), NT_remove_species_in_tree_from_hash(), NT_resort_data_base_by_tree(), parse_bootstrap(), DepthMarker::perform_marking(), GroupSearch::perform_search(), FINAL_TYPE< SEQTYPE >::recalc_marked_from_sons(), SpecSetRegistry::registerTree(), relink_tree_rek(), AP_tree::REMOVE(), remove_bootstrap(), reset_branchlengths(), reset_length_and_bootstrap(), AP_tree::reset_subtree_angles(), AP_tree::reset_subtree_layout(), AP_tree::reset_subtree_linewidths(), AP_tree::reset_subtree_spreads(), rightmost_leaf(), rotate_subtree(), scale_branchlengths(), set_branchlength_preserving(), AP_tree::set_linewidth_recursive(), set_root(), SpeciesInTwoTrees::setSpecies(), BootstrapConfig::shall_show_remark_for(), sq_calc_seq_quality_cb(), SQ_check_tree_structure(), SQ_pass1_on_tree(), SQ_pass2_on_tree(), sum_child_lengths(), AP_tree::swap_sons(), swap_sons(), AWT_graphic_tree::toggle_group(), trackable_species(), tree2newick(), TREE_export_tree(), AWT_graphic_tree::tree_has_marks(), TREE_load(), TREE_scale(), tree_size_ok(), AP_tree::tree_write_tree_rek(), unlink_from_DB(), AP_tree::update_subtree_information(), use_as_remark(), and NodeTextBuilder::work().

void TreeNode::markAsLeaf ( )

inline

Definition at line 212 of file TreeNode.h.

References is_leaf(), and rt_assert.

Referenced by gbt_read_tree_rek(), and neighbourjoining().

TreeNode::DEFINE_READ_ACCESSORS	(	TreeNode *	,
		get_father	,
		father
	)

TreeNode::DEFINE_READ_ACCESSORS	(	TreeNode *	,
		get_leftson	,
		leftson
	)

TreeNode::DEFINE_READ_ACCESSORS	(	TreeNode *	,
		get_rightson	,
		rightson
	)

bool TreeNode::is_son_of ( const TreeNode * Father ) const

inline

Definition at line 224 of file TreeNode.h.

References leftson, and rightson.

Referenced by ARB_edge::counter_next(), ARB_edge::counter_previous(), is_leftson(), is_rightson(), ARB_edge::next(), and ARB_edge::previous().

bool TreeNode::is_leftson ( ) const

inline

Definition at line 228 of file TreeNode.h.

References gb_assert, get_father(), is_son_of(), and leftson.

Referenced by build_taxonomy_rek(), ARB_edge::counter_next(), fixKeeledOrientation(), get_brother(), ARB_seqtree::is_upper_son(), ARB_edge::previous(), AP_tree::REMOVE(), and self_ref().

bool TreeNode::is_rightson ( ) const

inline

Definition at line 233 of file TreeNode.h.

References gb_assert, get_father(), is_son_of(), and rightson.

Referenced by ARB_edge::counter_previous(), ARB_seqtree::is_lower_son(), and ARB_edge::next().

bool TreeNode::is_inside ( const TreeNode * subtree ) const

inline

Definition at line 238 of file TreeNode.h.

References get_father().

Referenced by AWT_graphic_tree_root_changed(), AP_tree::cantMoveNextTo(), TreeRoot::change_root(), get_root_node(), get_upgroup(), is_ancestor_of(), AP_tree::moveNextTo(), ARB_countedTree::relative_position_in(), and set_root().

bool TreeNode::is_ancestor_of ( const TreeNode * descendant ) const

inline

Definition at line 241 of file TreeNode.h.

References is_inside(), and is_leaf().

Referenced by ancestor_common_with(), find_parent_clade(), and in_same_branch_as().

bool TreeNode::in_same_branch_as ( const TreeNode * other ) const

inline

Definition at line 244 of file TreeNode.h.

References is_ancestor_of().

Referenced by find_parent_clade(), and in_other_branch_than().

bool TreeNode::in_other_branch_than ( const TreeNode * other ) const

inline

Definition at line 248 of file TreeNode.h.

References in_same_branch_as().

const TreeNode * TreeNode::ancestor_common_with ( const TreeNode * other ) const

Definition at line 792 of file TreeNode.cxx.

References get_father(), and is_ancestor_of().

Referenced by common_ancestor(), and intree_distance_to().

TreeNode* TreeNode::ancestor_common_with ( TreeNode * other )

inline

Definition at line 253 of file TreeNode.h.

References ancestor_common_with().

Referenced by ancestor_common_with().

bool TreeNode::is_son_of_root ( ) const

inline

Definition at line 255 of file TreeNode.h.

References father, and is_root_node().

Referenced by DeconstructedTree::find_part(), AP_tree::insert(), and AP_tree::REMOVE().

GBT_LEN TreeNode::get_branchlength ( ) const

inline

Definition at line 259 of file TreeNode.h.

Referenced by get_branchlength_unrooted(), ARB_edge::length(), AP_tree::REMOVE(), root_distance(), and tree2newick().

void TreeNode::set_branchlength ( GBT_LEN newlen )

inline

Definition at line 260 of file TreeNode.h.

References gb_assert, and is_nan_or_inf().

Referenced by set_branchlength_unrooted(), and ARB_edge::set_length().

GBT_LEN TreeNode::get_branchlength_unrooted ( ) const

inline

like get_branchlength, but root-edge is treated correctly

Definition at line 265 of file TreeNode.h.

References get_branchlength(), is_root_node(), leftlen, and rightlen.

Referenced by branchlen2bootstrap(), reset_length_and_bootstrap(), and set_branchlength_preserving().

void TreeNode::set_branchlength_unrooted ( GBT_LEN newlen )

inline

like set_branchlength, but root-edge is treated correctly

Definition at line 272 of file TreeNode.h.

References is_root_node(), leftlen, rightlen, and set_branchlength().

Referenced by bootstrap2branchlen(), reset_length_and_bootstrap(), and set_branchlength_preserving().

GBT_LEN TreeNode::sum_child_lengths ( ) const

Definition at line 697 of file TreeNode.cxx.

References is_leaf(), leftlen, and rightlen.

GBT_LEN TreeNode::root_distance ( ) const

inline

returns distance from node to root (including nodes own length)

Definition at line 284 of file TreeNode.h.

References get_branchlength(), and root_distance().

Referenced by intree_distance_to(), and root_distance().

GBT_LEN TreeNode::intree_distance_to ( const TreeNode * other ) const

inline

Definition at line 288 of file TreeNode.h.

References ancestor_common_with(), and root_distance().

Referenced by DI_MATRIX::extract_from_tree().

void TreeNode::remove_bootstrap ( )

Definition at line 644 of file TreeNode.cxx.

References is_leaf().

Referenced by NT_remove_bootstrap().

GB_ERROR TreeNode::apply_aci_to_remarks	(	const char *	aci,
		const GBL_call_env &	callEnv
	)

Definition at line 652 of file TreeNode.cxx.

References error(), GB_await_error(), GB_command_interpreter_in_env(), GBS_trim(), is_leaf(), and NULp.

Referenced by NT_edit_bootstrap().

void TreeNode::reset_branchlengths ( )

Definition at line 678 of file TreeNode.cxx.

References DEFAULT_BRANCH_LENGTH, is_leaf(), leftlen, and rightlen.

Referenced by NT_reset_branchlengths().

void TreeNode::scale_branchlengths ( double factor )

Definition at line 687 of file TreeNode.cxx.

References is_leaf(), leftlen, and rightlen.

Referenced by NT_scale_tree().

void TreeNode::bootstrap2branchlen ( )

copy bootstraps to branchlengths

Definition at line 706 of file TreeNode.cxx.

References DEFAULT_BRANCH_LENGTH, father, is_leaf(), parse_bootstrap(), REMARK_BOOTSTRAP, and set_branchlength_unrooted().

Referenced by NT_move_boot_branch().

void TreeNode::branchlen2bootstrap ( )

copy branchlengths to bootstraps

Definition at line 729 of file TreeNode.cxx.

References get_branchlength_unrooted(), has_no_remark(), is_leaf(), is_root_node(), remove_remark(), rt_assert, and set_bootstrap().

Referenced by NT_move_boot_branch().

GBT_RemarkType TreeNode::parse_bootstrap ( double & bootstrap ) const

inline

Definition at line 302 of file TreeNode.h.

References is_leaf(), parse_remark(), and rt_assert.

Referenced by bootstrap2branchlen(), export_tree_node_print(), export_tree_node_print_xml(), gbt_read_tree_rek(), and TREE_scale().

const char* TreeNode::get_remark ( ) const

inline

Definition at line 307 of file TreeNode.h.

References is_leaf(), and rt_assert.

Referenced by BootstrapConfig::display_node_remark(), export_tree_node_print(), fixDeletedSon(), gbt_write_tree_rek_new(), has_valid_root_remarks(), set_branchlength_preserving(), and tree2newick().

const SmartCharPtr& TreeNode::get_remark_ptr ( ) const

inline

Definition at line 311 of file TreeNode.h.

References is_leaf(), and rt_assert.

Referenced by fixDeletedSon(), is_inner_node_with_remark(), set_root(), and BootstrapConfig::shall_show_remark_for().

bool TreeNode::is_inner_node_with_remark ( ) const

inline

Definition at line 315 of file TreeNode.h.

References get_remark_ptr(), and is_leaf().

Referenced by gbt_read_tree_rek().

void TreeNode::use_as_remark ( const SmartCharPtr & newRemark )

inline

Definition at line 316 of file TreeNode.h.

References is_leaf(), and rt_assert.

Referenced by SpecSetRegistry::find_best_matches_info(), fixDeletedSon(), remove_remark(), set_bootstrap(), set_branchlength_preserving(), and set_remark().

void TreeNode::set_remark ( const char * newRemark )

inline

Definition at line 320 of file TreeNode.h.

References use_as_remark().

Referenced by SpecSetRegistry::find_best_matches_info(), and gbt_read_tree_rek().

void TreeNode::set_bootstrap ( double bootstrap )

inline

Definition at line 323 of file TreeNode.h.

References GBS_global_string_copy(), and use_as_remark().

Referenced by add_bootstrap(), branchlen2bootstrap(), and TREE_scale().

void TreeNode::remove_remark ( )

inline

Definition at line 326 of file TreeNode.h.

References use_as_remark().

Referenced by add_bootstrap(), branchlen2bootstrap(), SpecSetRegistry::find_best_matches_info(), fixDeletedSon(), gbt_read_tree_rek(), AP_tree::REMOVE(), reset_length_and_bootstrap(), and TREE_scale().

bool TreeNode::has_no_remark ( ) const

inline

Definition at line 331 of file TreeNode.h.

Referenced by branchlen2bootstrap(), gbt_write_tree_rek_new(), and set_branchlength_preserving().

bool TreeNode::has_valid_root_remarks ( ) const

Definition at line 805 of file TreeNode.cxx.

References ARB_strNULLcmp(), get_remark(), implicated, is_leaf(), is_root_node(), and rt_assert.

Referenced by AP_tree::insert(), AP_tree::moveNextTo(), and set_root().

void TreeNode::set_tree_root ( TreeRoot * new_root )

protected

Definition at line 84 of file TreeNode.cxx.

References leftson, and rightson.

Referenced by TreeRoot::change_root(), forget_origin(), AP_tree::initial_insert(), and AP_tree::insert().

bool TreeNode::at_root ( ) const

inlineprotected

return true for root-node and its sons

Definition at line 349 of file TreeNode.h.

References father.

Referenced by set_root().

void TreeNode::destroy ( )

inlineprotected

Definition at line 368 of file TreeNode.h.

References TreeRoot::destroyNode(), get_tree_root(), knownNonNull(), and rt_assert.

Referenced by destroy(), destroy(), and AP_tree::REMOVE().

void TreeNode::destroy ( TreeRoot * viaRoot )

inlineprotected

Definition at line 374 of file TreeNode.h.

References TreeRoot::destroyNode(), get_tree_root(), knownNonNull(), and rt_assert.

static void TreeNode::destroy ( TreeNode * that )

inlinestatic

Definition at line 394 of file TreeNode.h.

References destroy().

static void TreeNode::destroy	(	TreeNode *	that,
		TreeRoot *	root
	)

inlinestatic

Definition at line 397 of file TreeNode.h.

References destroy().

TreeNode * TreeNode::fixDeletedSon ( )

Definition at line 746 of file TreeNode.cxx.

References TreeRoot::change_root(), father, forget_origin(), forget_relatives(), gb_assert, gb_node, get_remark(), get_remark_ptr(), get_tree_root(), is_leaf(), is_root_node(), leftson, NULp, remove_remark(), result, rightson, and use_as_remark().

Referenced by GBT_remove_leafs().

void TreeNode::unlink_from_DB ( )

Unlink tree from the database.

See also: GBT_link_tree()

Definition at line 976 of file adtree.cxx.

References gb_node, is_leaf(), and NULp.

Referenced by GBT_unlink_tree().

void TreeNode::announce_tree_constructed ( )

inline

Definition at line 405 of file TreeNode.h.

References TreeRoot::change_root(), gb_assert, get_tree_root(), and NULp.

Referenced by GBT_read_tree_and_size(), and TreeReader::load().

virtual unsigned TreeNode::get_leaf_count ( ) const

pure virtual

Implemented in FINAL_TYPE< SEQTYPE >, AP_tree, FINAL_TYPE< SEQTYPE >, FINAL_TYPE< SEQTYPE >, FINAL_TYPE< SEQTYPE >, and FINAL_TYPE< SEQTYPE >.

Referenced by get_downgroups(), Cluster::get_upgroup_info(), and ARB_countedTree::relative_position_in().

virtual void TreeNode::compute_tree ( )

pure virtual

Implemented in FINAL_TYPE< SEQTYPE >, AP_tree, ARB_countedTree, FINAL_TYPE< SEQTYPE >, FINAL_TYPE< SEQTYPE >, and FINAL_TYPE< SEQTYPE >.

Referenced by reorder_tree().

void TreeNode::forget_origin ( )

inline

Definition at line 414 of file TreeNode.h.

References NULp, and set_tree_root().

Referenced by fixDeletedSon(), GBT_remove_leafs(), and AP_tree::REMOVE().

void TreeNode::forget_relatives ( )

inline

Definition at line 415 of file TreeNode.h.

References NULp.

Referenced by fixDeletedSon(), and GBT_remove_leafs().

TreeRoot* TreeNode::get_tree_root ( ) const

inline

Definition at line 421 of file TreeNode.h.

Referenced by announce_tree_constructed(), TreeRoot::change_root(), AP_tree::compute_tree(), destroy(), fixDeletedSon(), GBT_remove_leafs(), AP_tree::insert(), AP_tree::moveNextTo(), neighbourjoining(), AP_tree::recompute_and_write_folding(), AP_tree::relink(), AP_tree::REMOVE(), SpecSetRegistry::write_node_information(), and AP_tree::~AP_tree().

const TreeNode* TreeNode::get_root_node ( ) const

inline

Definition at line 423 of file TreeNode.h.

References is_inside(), NULp, and rt_assert.

Referenced by AP_tree::insert(), is_root_node(), ARB_seqtree_root::loadFromDB(), AP_tree::moveNextTo(), multifurcate_whole_tree(), NTREE_move_tree_info(), and set_root().

TreeNode* TreeNode::get_root_node ( )

inline

Definition at line 430 of file TreeNode.h.

References get_root_node().

Referenced by get_root_node().

bool TreeNode::is_root_node ( ) const

inline

void TreeNode::set_root ( )

virtual

set the root at parent edge of this pointers to tree-nodes remain valid, but all parent-nodes of this change their meaning (afterwards they will point to [father+brother] instead of [this+brother]) esp. pointers to the root-node will still point to the root-node (which only changed children)

Reimplemented in FINAL_TYPE< SEQTYPE >.

Definition at line 206 of file TreeNode.cxx.

References at_root(), father, get_father(), POS_TREE1::get_father(), get_remark_ptr(), get_root_node(), has_valid_root_remarks(), is_inside(), is_leaf(), leftlen, leftson, rightlen, rightson, rt_assert, and swap().

Referenced by ST_ML::get_ml_vectors(), nt_add(), NTREE_move_tree_info(), randomMixTree(), and ARB_edge::set_root().

TreeNode* TreeNode::get_brother ( )

inline

const TreeNode* TreeNode::get_brother ( ) const

inline

Definition at line 440 of file TreeNode.h.

References get_brother().

bool TreeNode::has_group_info ( ) const

inline

Definition at line 444 of file TreeNode.h.

References is_leaf(), name, and rt_assert.

Referenced by build_taxonomy_rek(), collect_contained_groups(), collect_enclosing_groups(), export_tree_node_print(), find_group_name_entry(), find_parent_with_groupInfo(), is_normal_group(), keelTarget(), AP_tree::moveNextTo(), GroupSearch::perform_search(), read_tree_and_size_internal(), AWT_graphic_tree::toggle_group(), and AP_tree_folding::unfold().

TreeNode* TreeNode::keelTarget ( )

inline

Definition at line 448 of file TreeNode.h.

References has_group_info(), and NULp.

Referenced by build_taxonomy_rek(), collect_enclosing_groups(), export_tree_node_print(), find_parent_clade(), find_parent_with_groupInfo(), isCorrectParent(), keelsDownGroup(), keelTarget(), read_tree_and_size_internal(), and unkeelGroup().

const TreeNode* TreeNode::keelTarget ( ) const

inline

Definition at line 451 of file TreeNode.h.

References keelTarget().

bool TreeNode::keelsDownGroup ( const TreeNode * toSon ) const

inline

Definition at line 454 of file TreeNode.h.

References keelTarget().

Referenced by Group::at_node(), and is_keeled_group().

void TreeNode::unkeelGroup ( )

inline

Definition at line 458 of file TreeNode.h.

References keelTarget(), and rt_assert.

Referenced by AWT_graphic_tree::toggle_group().

int TreeNode::keeledStateInfo ( ) const

inline

Definition at line 462 of file TreeNode.h.

Referenced by gbt_write_tree_nodes().

void TreeNode::setKeeledState ( int keeledState )

inline

Definition at line 465 of file TreeNode.h.

Referenced by gbt_read_tree_rek().

bool TreeNode::is_normal_group ( ) const

inline

Definition at line 470 of file TreeNode.h.

References has_group_info(), is_leaf(), and rt_assert.

Referenced by Group::at_node(), calcTaxDifference(), countTaxLevel(), AWT_graphic_tree::detect_group_state(), findParentGroup(), GBT_read_tree_and_size(), get_group_name(), Group::Group(), AWT_graphic_tree::group_tree(), is_clade(), AP_tree::is_folded_group(), isCorrectParent(), AP_tree::move_group_to(), GroupSearch::perform_search(), read_tree_and_size_internal(), and tree2newick().

bool TreeNode::is_keeled_group ( ) const

inline

Definition at line 475 of file TreeNode.h.

References keelsDownGroup().

Referenced by collect_enclosing_groups(), fixKeeledOrientation(), get_downgroups(), get_group_name(), Group::Group(), AWT_graphic_tree::group_tree(), is_clade(), AP_tree::is_folded_group(), isCorrectParent(), AP_tree::move_group_to(), GroupSearch::perform_search(), AWT_graphic_tree::toggle_group(), and tree2newick().

bool TreeNode::is_clade ( ) const

inline

Definition at line 480 of file TreeNode.h.

References is_keeled_group(), is_leaf(), and is_normal_group().

Referenced by calc_clade_level(), count_clades(), find_parent_clade(), GroupIterator::GroupIterator(), NT_jump_cb(), AWT_graphic_tree::select_group(), and AWT_graphic_tree::toggle_group().

const char* TreeNode::get_group_name ( ) const

inline

Definition at line 486 of file TreeNode.h.

References is_keeled_group(), is_leaf(), is_normal_group(), name, and NULp.

Referenced by get_downgroups(), and get_upgroup().

const TreeNode* TreeNode::find_parent_with_groupInfo ( bool skipKeeledBrothers = false ) const

inline

Definition at line 493 of file TreeNode.h.

References get_father(), has_group_info(), and keelTarget().

Referenced by find_parent_clade(), find_parent_with_groupInfo(), and isCorrectParent().

TreeNode* TreeNode::find_parent_with_groupInfo ( bool skipKeeledBrothers = false )

inline

Definition at line 511 of file TreeNode.h.

References find_parent_with_groupInfo().

const TreeNode* TreeNode::find_parent_clade ( ) const

inline

Definition at line 515 of file TreeNode.h.

References find_parent_with_groupInfo(), get_brother(), implicated, in_same_branch_as(), is_ancestor_of(), is_clade(), keelTarget(), and rt_assert.

Referenced by calc_clade_level(), and find_parent_clade().

TreeNode* TreeNode::find_parent_clade ( )

inline

Definition at line 541 of file TreeNode.h.

References find_parent_clade().

int TreeNode::calc_clade_level ( ) const

inline

Definition at line 544 of file TreeNode.h.

References calc_clade_level(), find_parent_clade(), and is_clade().

Referenced by calc_clade_level(), and GroupIterator::get_clade_level().

int TreeNode::count_clades ( ) const

Definition at line 799 of file TreeNode.cxx.

References is_clade(), and is_leaf().

Referenced by NTREE_move_tree_info().

virtual void TreeNode::swap_sons ( )

inlinevirtual

Reimplemented in AP_tree, and FINAL_TYPE< SEQTYPE >.

Definition at line 553 of file TreeNode.h.

References is_leaf(), rt_assert, and swap().

Referenced by rotate_subtree(), and AP_tree::swap_sons().

void TreeNode::rotate_subtree ( )

Definition at line 164 of file TreeNode.cxx.

References is_leaf(), and swap_sons().

void TreeNode::reorder_tree ( TreeOrder mode )

beautify tree (does not change topology, only swaps branches)

Definition at line 157 of file TreeNode.cxx.

References compute_tree().

Referenced by AWT_graphic_tree::reorderTree().

TreeNode * TreeNode::findLeafNamed ( const char * wantedName )

Definition at line 274 of file TreeNode.cxx.

References findLeafNamed(), is_leaf(), name, and NULp.

Referenced by findLeafNamed(), and NT_jump_cb().

GBT_LEN TreeNode::reset_length_and_bootstrap ( )

inline

remove remark + zero but return branchlen

Definition at line 565 of file TreeNode.h.

References get_branchlength_unrooted(), is_leaf(), remove_remark(), and set_branchlength_unrooted().

Referenced by ARB_edge::eliminate().

void TreeNode::multifurcate ( )

eliminate branch from 'this' to 'father' (or brother @ root)

See also: ARB_edge::multifurcate()

Definition at line 588 of file TreeNode.cxx.

References father, ARB_edge::multifurcate(), parentEdge(), and rt_assert.

Referenced by set_branchlength_preserving().

void TreeNode::set_branchlength_preserving ( GBT_LEN new_len )

set branchlength to 'new_len' while preserving overall distance in tree.

Always works on unrooted tree (i.e. lengths @ root are treated correctly). Length is preserved as in multifurcate()

Definition at line 596 of file TreeNode.cxx.

References get_branchlength_unrooted(), get_remark(), has_no_remark(), is_leaf(), multifurcate(), NULp, rt_assert, set_branchlength_unrooted(), and use_as_remark().

void TreeNode::multifurcate_whole_tree ( const multifurc_limits & below )

multifurcate all branches specified by 'below'

step 1: eliminate all branches, store eliminated lengths
step 2: calculate length distribution for all adjacent branches (proportionally to original length of each branch)
step 3: apply distributed length

Definition at line 623 of file TreeNode.cxx.

References get_root_node(), TreeNode::LengthCollector::independent_distribution(), and arb_progress::subtitle().

Referenced by NT_multifurcate_tree().