#include <ARB_Tree.hxx>

Inheritance diagram for ARB_seqtree:

Collaboration diagram for ARB_seqtree:

Public Member Functions
	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 ()

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 ()

Protected Member Functions
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
GB_ERROR	ARB_seqtree_root::loadFromDB (const char *name)

GB_ERROR	ARB_seqtree_root::linkToDB (int zombies, int duplicates)

void	ARB_seqtree_root::unlinkFromDB ()

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

static void	destroy (TreeNode that, TreeRoot root)

Public Attributes inherited from TreeNode
TreeNode *	father

TreeNode *	leftson

TreeNode *	rightson

GBT_LEN	leftlen

GBT_LEN	rightlen

GBDATA *	gb_node

char *	name