#include <AP_Tree.hxx>

Inheritance diagram for AP_tree:

Collaboration diagram for AP_tree:

Public Member Functions
	AP_tree (AP_tree_root *troot)

	DEFINE_TREE_ACCESSORS (AP_tree_root, AP_tree)

void	compute_tree () FINAL_OVERRIDE

void	recompute_and_write_folding ()

unsigned	count_leafs () const

unsigned	get_leaf_count () const OVERRIDE

void	load_subtree_info ()

int	colorize (GB_HASH *hashptr)

void	uncolorize ()

virtual void	insert (AP_tree *new_brother)

virtual void	initial_insert (AP_tree new_brother, AP_tree_root troot)

virtual AP_tree *	REMOVE ()

void	swap_sons () OVERRIDE

GB_ERROR	cantMoveNextTo (AP_tree *new_brother)

virtual void	moveNextTo (AP_tree *new_brother, AP_FLOAT rel_pos)

GB_ERROR	tree_write_tree_rek (GBDATA *gb_tree)

GB_ERROR	relink () __ATTR__USERESULT

int	get_linewidth () const

void	set_linewidth (int width)

void	reset_linewidth ()

void	set_linewidth_recursive (int width)

float	get_angle () const

void	set_angle (float angle)

void	reset_angle ()

void	buildLeafList (AP_tree **&list, long &num)

GB_ERROR	move_group_to (AP_tree *new_group) __ATTR__USERESULT

bool	is_folded_group () const

bool	is_inside_folded_group () const

void	mark_duplicates ()

const char *	mark_long_branches (double min_rel_diff, double min_abs_diff, double &found_max_abs_diff)

const char *	mark_deep_leafs (int min_depth, double min_rootdist, int &found_max_depth, double &found_max_rootdist)

double	mark_degenerated_branches (double degeneration_factor)

const char *	analyse_distances ()

void	justify_branch_lenghs (GBDATA *gb_main)

void	relink_tree (GBDATA gb_main, void(relinker)(GBDATA &ref_gb_node, char &ref_name, GB_HASH organism_hash), GB_HASH organism_hash)

void	reset_subtree_spreads ()

void	reset_subtree_angles ()

void	reset_subtree_linewidths ()

void	reset_subtree_layout ()

bool	hasName (const char *Name) const

bool	has_correct_mark_flags () const

	PREPARE_MARK_NONFINAL_CLASS (AP_tree)

template<>
ShadedValue	update_subtree_information (const group_scaling &gscaling)

Public Member Functions inherited from ARB_seqtree
	ARB_seqtree (ARB_seqtree_root *root)

	DEFINE_TREE_ACCESSORS (ARB_seqtree_root, ARB_seqtree)

void	calcTreeInfo (ARB_tree_info &info)

bool	is_upper_son () const

bool	is_lower_son () const

AP_sequence *	get_seq ()

const AP_sequence *	get_seq () const

AP_sequence *	set_seq (AP_sequence *sequence)

bool	hasSequence () const

void	mark_subtree ()

bool	contains_marked_species ()

Public Member Functions inherited from TreeNode
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 ()

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

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	set_tree_shader (AP_TreeShader *new_shader)

static const AP_TreeShader *	get_tree_shader ()

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

static void	destroy (TreeNode that, TreeRoot root)

Public Attributes
AP_tree_members	gr

Public Attributes inherited from TreeNode
TreeNode *	father

TreeNode *	leftson

TreeNode *	rightson

GBT_LEN	leftlen

GBT_LEN	rightlen

GBDATA *	gb_node

char *	name

Protected Member Functions
	~AP_tree () OVERRIDE

Protected Member Functions inherited from ARB_seqtree
AP_sequence *	take_seq ()

void	replace_seq (AP_sequence *sequence)

	~ARB_seqtree () OVERRIDE

Protected Member Functions inherited from TreeNode
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
class	AP_tree_root

Detailed Description

Definition at line 210 of file AP_Tree.hxx.

Constructor & Destructor Documentation

AP_tree::~AP_tree ( )

protected

Definition at line 142 of file AP_Tree.cxx.

References ap_tree_node_deleted(), AP_tree_members::callback_exists, GB_CB_DELETE, TreeNode::gb_node, GB_remove_callback(), TreeNode::get_tree_root(), gr, and AP_tree_root::inform_about_delete().

AP_tree::AP_tree ( AP_tree_root * troot )

inlineexplicit

Definition at line 285 of file AP_Tree.hxx.

References AP_tree_members::clear().

Member Function Documentation

AP_tree::DEFINE_TREE_ACCESSORS	(	AP_tree_root	,
		AP_tree
	)

void AP_tree::compute_tree ( )

virtual

Implements TreeNode.

Reimplemented in FINAL_TYPE< SEQTYPE >.

Definition at line 876 of file AP_Tree.cxx.

References ap_assert, fputs(), ARB_seqtree_root::get_gb_main(), AP_tree_root::get_group_scaling(), TreeNode::get_tree_root(), group_scaling::has_been_set(), ta, and AP_TreeShader::update_settings().

Referenced by AWT_graphic_tree::load_from_DB(), uncolorize(), and AWT_graphic_tree::update_structure().

void AP_tree::recompute_and_write_folding ( )

Definition at line 754 of file AP_Tree.cxx.

References ap_assert, aw_message(), GBS_global_string(), get_father(), ARB_seqtree_root::get_gb_tree(), AP_tree_root::get_group_scaling(), and TreeNode::get_tree_root().

Referenced by AWT_graphic_tree::fast_sync_changed_folding().

unsigned AP_tree::count_leafs ( ) const

Definition at line 840 of file AP_Tree.cxx.

References TreeNode::is_leaf().

Referenced by buildLeafList(), and NTREE_move_tree_info().

unsigned AP_tree::get_leaf_count ( ) const

inlinevirtual

Implements TreeNode.

Reimplemented in FINAL_TYPE< SEQTYPE >.

Definition at line 298 of file AP_Tree.hxx.

References AP_tree_members::leaf_sum.

void AP_tree::load_subtree_info ( )

Definition at line 454 of file AP_Tree.cxx.

References TreeNode::is_leaf().

int AP_tree::colorize ( GB_HASH * hashptr )

Definition at line 846 of file AP_Tree.cxx.

References AWT_GC_BLACK, AWT_GC_ONLY_ZOMBIES, AWT_GC_SOME_MARKED, TreeNode::gb_node, GB_read_flag(), GBS_read_hash(), AP_tree_members::gc, gr, TreeNode::is_leaf(), and TreeNode::name.

void AP_tree::uncolorize ( )

inline

Definition at line 306 of file AP_Tree.hxx.

References compute_tree().

Referenced by MP_close_main(), and MP_normal_colors_in_tree().

void AP_tree::insert ( AP_tree * new_brother )

virtual

Reimplemented in FINAL_TYPE< SEQTYPE >.

Definition at line 178 of file AP_Tree.cxx.

References ap_assert, ASSERT_VALID_TREE, AP_tree_root::change_root(), DOWNCAST, TreeNode::father, TreeNode::get_root_node(), TreeNode::get_tree_root(), TreeNode::has_valid_root_remarks(), TreeNode::is_son_of_root(), TreeNode::leftlen, TreeNode::leftson, TreeRoot::makeNode(), TreeNode::rightlen, TreeNode::rightson, and TreeNode::set_tree_root().

void AP_tree::initial_insert	(	AP_tree *	new_brother,
		AP_tree_root *	troot
	)

virtual

Reimplemented in FINAL_TYPE< SEQTYPE >.

Definition at line 151 of file AP_Tree.cxx.

References ap_assert, ASSERT_VALID_TREE, AP_tree_root::change_root(), DOWNCAST, TreeNode::father, TreeNode::is_leaf(), TreeNode::leftlen, TreeNode::leftson, AP_tree_root::makeNode(), NULp, TreeNode::rightlen, TreeNode::rightson, and TreeNode::set_tree_root().

AP_tree * AP_tree::REMOVE ( )

virtual

void AP_tree::swap_sons ( )

inlinevirtual

Reimplemented from TreeNode.

Definition at line 312 of file AP_Tree.hxx.

References ap_assert, TreeNode::is_leaf(), AP_tree_members::swap_son_layout(), and TreeNode::swap_sons().

GB_ERROR AP_tree::cantMoveNextTo ( AP_tree * new_brother )

Definition at line 338 of file AP_Tree.cxx.

References error(), TreeNode::father, TreeNode::is_inside(), and NULp.

void AP_tree::moveNextTo	(	AP_tree *	new_brother,
		AP_FLOAT	rel_pos
	)

virtual

Reimplemented in FINAL_TYPE< SEQTYPE >.

Definition at line 351 of file AP_Tree.cxx.

References ap_assert, TreeRoot::change_root(), TreeNode::father, TreeNode::get_brother(), get_father(), POS_TREE1::get_father(), TreeNode::get_root_node(), TreeNode::get_tree_root(), TreeNode::has_group_info(), TreeNode::has_valid_root_remarks(), TreeNode::is_inside(), TreeNode::is_leaf(), TreeNode::leftlen, TreeNode::leftson, NULp, TreeNode::rightlen, and TreeNode::rightson.

GB_ERROR AP_tree::tree_write_tree_rek ( GBDATA * gb_tree )

Definition at line 520 of file AP_Tree.cxx.

References error(), gr, AP_tree_members::grouped, TreeNode::is_leaf(), AP_tree_members::left_angle, AP_tree_members::left_linewidth, NULp, AP_tree_members::right_angle, AP_tree_members::right_linewidth, AP_tree_members::spread, tree_write_byte(), and tree_write_float().

GB_ERROR AP_tree::relink ( )

Definition at line 900 of file AP_Tree.cxx.

References error(), GBT_link_tree(), get_gb_main(), TreeNode::get_tree_root(), NULp, and ta.

Referenced by AWT_graphic_tree::check_for_DB_update().

int AP_tree::get_linewidth ( ) const

inline

Definition at line 326 of file AP_Tree.hxx.

References TreeNode::is_root_node().

Referenced by BranchLinewidthScaler::do_scale(), and AWT_graphic_tree::set_line_attributes_for().

void AP_tree::set_linewidth ( int width )

inline

Definition at line 327 of file AP_Tree.hxx.

References TreeNode::father.

Referenced by BranchLinewidthScaler::do_scale(), reset_linewidth(), and set_linewidth_recursive().

void AP_tree::reset_linewidth ( )

inline

Definition at line 328 of file AP_Tree.hxx.

References tree_defaults::LINEWIDTH, and set_linewidth().

Referenced by reset_subtree_layout(), and reset_subtree_linewidths().

void AP_tree::set_linewidth_recursive ( int width )

Definition at line 1601 of file AP_Tree.cxx.

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

Referenced by BranchLinewidthScaler::do_scale().

float AP_tree::get_angle ( ) const

inline

Definition at line 331 of file AP_Tree.hxx.

References TreeNode::is_root_node().

void AP_tree::set_angle ( float angle )

inline

Definition at line 332 of file AP_Tree.hxx.

References TreeNode::father, TreeNode::get_brother(), get_father(), and TreeNode::is_root_node().

Referenced by reset_angle().

void AP_tree::reset_angle ( )

inline

Definition at line 342 of file AP_Tree.hxx.

References tree_defaults::ANGLE, and set_angle().

Referenced by reset_subtree_angles(), and reset_subtree_layout().

void AP_tree::buildLeafList	(	AP_tree **&	list,
		long &	num
	)

Definition at line 933 of file AP_Tree.cxx.

References ap_assert, count_leafs(), and NULp.

Referenced by AP_tree_root::remove_leafs().

GB_ERROR AP_tree::move_group_to ( AP_tree * new_group )

Definition at line 627 of file AP_Tree.cxx.

References ap_assert, error(), find_group_name_entry(), GB_touch(), GBS_global_string(), get_father(), TreeNode::is_keeled_group(), TreeNode::is_leaf(), TreeNode::is_normal_group(), TreeNode::name, and NULp.

bool AP_tree::is_folded_group ( ) const

inline

Definition at line 348 of file AP_Tree.hxx.

References TreeNode::father, get_father(), AP_tree_members::grouped, TreeNode::is_keeled_group(), and TreeNode::is_normal_group().

Referenced by is_inside_folded_group().

bool AP_tree::is_inside_folded_group ( ) const

Definition at line 1640 of file AP_Tree.cxx.

References TreeNode::father, get_father(), is_folded_group(), and TreeNode::is_leaf().

Referenced by NT_jump_cb().

void AP_tree::mark_duplicates ( )

Definition at line 1530 of file AP_Tree.cxx.

References ap_mark_duplicates_rek(), aw_message(), GB_IGNORE_CASE, GBS_create_hash(), GBS_free_hash(), GBS_global_string(), gr, and AP_tree_members::leaf_sum.

Referenced by NT_mark_duplicates().

const char * AP_tree::mark_long_branches	(	double	min_rel_diff,
		double	min_abs_diff,
		double &	found_max_abs_diff
	)

Definition at line 1299 of file AP_Tree.cxx.

References LongBranchMarker::get_max_abs_diff(), and LongBranchMarker::get_report().

const char * AP_tree::mark_deep_leafs	(	int	min_depth,
		double	min_rootdist,
		int &	found_max_depth,
		double &	found_max_rootdist
	)

Definition at line 1305 of file AP_Tree.cxx.

References DepthMarker::get_max_depth(), DepthMarker::get_max_rootdist(), and DepthMarker::get_report().

double AP_tree::mark_degenerated_branches ( double degeneration_factor )

Definition at line 1496 of file AP_Tree.cxx.

References ap_mark_degenerated().

Referenced by BranchWindow::markDegeneratedBranches().

const char * AP_tree::analyse_distances ( )

Definition at line 1461 of file AP_Tree.cxx.

References EdgeDistances::get_report().

void AP_tree::justify_branch_lenghs ( GBDATA * gb_main )

Definition at line 1559 of file AP_Tree.cxx.

References ap_just_tree_rek(), and ta.

Referenced by NT_justify_branch_lenghs().

void AP_tree::relink_tree	(	GBDATA *	gb_main,
		void()(GBDATA &ref_gb_node, char &ref_name, GB_HASH organism_hash)	relinker,
		GB_HASH *	organism_hash
	)