ARB: AP_tree_root Class Reference

ARB

#include <AP_Tree.hxx>

Inheritance diagram for AP_tree_root:

Inheritance graph

Collaboration diagram for AP_tree_root:

Collaboration graph

Public Member Functions
	AP_tree_root (AliView aliView, AP_sequence seq_proto, bool add_delete_callbacks, const group_scaling *scaling)

	~AP_tree_root () OVERRIDE

	DEFINE_TREE_ROOT_ACCESSORS (AP_tree_root, AP_tree)

TreeNode *	makeNode () const OVERRIDE

void	destroyNode (TreeNode *node) const OVERRIDE

void	change_root (TreeNode old, TreeNode newroot) FINAL_OVERRIDE

GB_ERROR	loadFromDB (const char *name) FINAL_OVERRIDE

GB_ERROR	saveToDB () OVERRIDE

virtual AP_UPDATE_FLAGS	check_update ()

void	update_timers ()

bool	is_tree_updated ()

bool	is_species_updated ()

const group_scaling *	get_group_scaling () const

void	inform_about_delete (AP_tree *old)

void	set_root_changed_callback (AP_rootChangedCb cb, void *cd)

void	set_node_deleted_callback (AP_nodeDelCb cb, void *cd)

long	remove_leafs (AWT_RemoveType awt_remove_type)

	PREPARE_MARK_NONFINAL_CLASS (AP_tree_root)

Public Member Functions inherited from ARB_seqtree_root
	ARB_seqtree_root (AliView aliView, AP_sequence seqTempl, bool add_delete_callbacks)

	~ARB_seqtree_root () OVERRIDE

	DEFINE_TREE_ROOT_ACCESSORS (ARB_seqtree_root, ARB_seqtree)

const AliView *	get_aliview () const

const AP_filter *	get_filter () const

const AP_weights *	get_weights () const

GBDATA *	get_gb_main () const

GBDATA *	get_gb_tree () const

void	tree_deleted_cb (GBDATA *gb_tree_del)

const char *	get_tree_name () const

const AP_sequence *	get_seqTemplate () const

GB_ERROR	linkToDB (int zombies, int duplicates) __ATTR__USERESULT

void	unlinkFromDB ()

	PREPARE_MARK_NONFINAL_CLASS (ARB_seqtree_root)

Public Member Functions inherited from TreeRoot
	TreeRoot (bool deleteWithNodes_)

virtual	~TreeRoot ()

void	delete_by_node ()

bool	has_bootstrap () const

void	set_bootstrap_seen (bool seen)

	DEFINE_READ_ACCESSORS (TreeNode *, get_root_node, rootNode)

ARB_edge	find_innermost_edge ()

Public Attributes
GBDATA *	gb_tree_gone

char *	gone_tree_name

long	tree_timer

long	species_timer

AP_rates *	rates

Additional Inherited Members
Protected Member Functions inherited from ARB_seqtree_root
void	set_gb_tree (GBDATA *gbTree)

void	set_gb_tree_and_name (GBDATA gbTree, const char name)

Protected Member Functions inherited from TreeRoot
void	predelete ()

Detailed Description

Definition at line 81 of file AP_Tree.hxx.

Constructor & Destructor Documentation

AP_tree_root::AP_tree_root	(	AliView *	aliView,
		AP_sequence *	seq_proto,
		bool	add_delete_callbacks,
		const group_scaling *	scaling
	)

AP_tree_root **********

Definition at line 85 of file AP_Tree.cxx.

References gb_main, GBT_get_species_data(), ARB_seqtree_root::get_gb_main(), and ta.

AP_tree_root::~AP_tree_root ( )

Definition at line 102 of file AP_Tree.cxx.

References ap_assert, gone_tree_name, and TreeRoot::predelete().

Member Function Documentation

AP_tree_root::DEFINE_TREE_ROOT_ACCESSORS	(	AP_tree_root	,
		AP_tree
	)

TreeNode * AP_tree_root::makeNode ( ) const

inlinevirtual

Implements TreeRoot.

Reimplemented in FINAL_TYPE< SEQTYPE >.

Definition at line 386 of file AP_Tree.hxx.

Referenced by AP_tree::initial_insert().

void AP_tree_root::destroyNode ( TreeNode * node ) const

inlinevirtual

Implements TreeRoot.

Reimplemented in FINAL_TYPE< SEQTYPE >.

Definition at line 387 of file AP_Tree.hxx.

References DOWNCAST.

Referenced by remove_leafs().

void AP_tree_root::change_root	(	TreeNode *	old,
		TreeNode *	newroot
	)

virtual

Reimplemented from TreeRoot.

Definition at line 223 of file AP_Tree.cxx.

References ap_assert, TreeRoot::change_root(), DOWNCAST, gb_tree_gone, ARB_seqtree_root::get_gb_tree(), NULp, and ARB_seqtree_root::set_gb_tree().

Referenced by AP_tree::initial_insert(), AP_tree::insert(), and AP_tree::REMOVE().

GB_ERROR AP_tree_root::loadFromDB ( const char * name )

virtual

Reimplemented from ARB_seqtree_root.

Definition at line 891 of file AP_Tree.cxx.

References error(), ARB_seqtree_root::loadFromDB(), and update_timers().

Referenced by ST_ML::calc_st_ml(), AWT_graphic_tree::load_from_DB(), and NTREE_move_tree_info().

GB_ERROR AP_tree_root::saveToDB ( )

virtual

Reimplemented from ARB_seqtree_root.

Definition at line 536 of file AP_Tree.cxx.

References ap_assert, aw_message(), error(), GB_end_transaction(), GB_push_transaction(), gb_tree_gone, GBS_global_string(), GBT_find_tree(), GBT_write_tree(), ARB_seqtree_root::get_gb_main(), ARB_seqtree_root::get_gb_tree(), gone_tree_name, ARB_seqtree_root::saveToDB(), ARB_seqtree_root::set_gb_tree_and_name(), and update_timers().

Referenced by AWT_graphic_tree::save_to_DB().

AP_UPDATE_FLAGS AP_tree_root::check_update ( )

virtual

Reimplemented in FINAL_TYPE< SEQTYPE >.

Definition at line 907 of file AP_Tree.cxx.

References AP_UPDATE_OK, AP_UPDATE_RELINKED, AP_UPDATE_RELOADED, gb_main, ARB_seqtree_root::get_gb_main(), is_species_updated(), is_tree_updated(), and ta.

Referenced by AWT_graphic_tree::check_for_DB_update().

void AP_tree_root::update_timers ( )

Definition at line 125 of file AP_Tree.cxx.

References GB_get_root(), GB_read_clock(), ARB_seqtree_root::get_gb_tree(), species_timer, ta, and tree_timer.

Referenced by AWT_graphic_tree::handle_command(), loadFromDB(), AWT_graphic_tree::notify_synchronized(), and saveToDB().

bool AP_tree_root::is_tree_updated ( )

Definition at line 108 of file AP_Tree.cxx.

References GB_read_clock(), ARB_seqtree_root::get_gb_tree(), ta, and tree_timer.

Referenced by check_update().

bool AP_tree_root::is_species_updated ( )

Definition at line 117 of file AP_Tree.cxx.

References GB_read_clock(), species_timer, and ta.

Referenced by check_update().

const group_scaling* AP_tree_root::get_group_scaling ( ) const

inline

Definition at line 122 of file AP_Tree.hxx.

Referenced by AP_tree::compute_tree(), and AP_tree::recompute_and_write_folding().

void AP_tree_root::inform_about_delete ( AP_tree * old )

Definition at line 244 of file AP_Tree.cxx.

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

void AP_tree_root::set_root_changed_callback	(	AP_rootChangedCb	cb,
		void *	cd
	)

Definition at line 248 of file AP_Tree.cxx.

References cb.

Referenced by AWT_graphic_tree::load_from_DB().

void AP_tree_root::set_node_deleted_callback	(	AP_nodeDelCb	cb,
		void *	cd
	)

Definition at line 253 of file AP_Tree.cxx.

References cb.

Referenced by AWT_graphic_tree::load_from_DB().

long AP_tree_root::remove_leafs ( AWT_RemoveType awt_remove_type )

Definition at line 944 of file AP_Tree.cxx.

References ASSERT_VALID_TREE, ASSERT_VALID_TREE_OR_NULL, AWT_REMOVE_MARKED, AWT_REMOVE_NO_SEQUENCE, AWT_REMOVE_UNMARKED, AWT_REMOVE_ZOMBIES, AP_tree::buildLeafList(), destroyNode(), TreeNode::gb_node, GB_read_flag(), ARB_seqtree_root::get_gb_main(), ARB_seqtree::get_seq(), and ta.

Referenced by ST_ML::calc_st_ml().

AP_tree_root::PREPARE_MARK_NONFINAL_CLASS ( AP_tree_root )

Member Data Documentation

GBDATA* AP_tree_root::gb_tree_gone

Definition at line 92 of file AP_Tree.hxx.

Referenced by change_root(), AWT_graphic_tree::save_to_DB(), and saveToDB().

char* AP_tree_root::gone_tree_name

Definition at line 93 of file AP_Tree.hxx.

Referenced by AWT_graphic_tree::load_from_DB(), AWT_graphic_tree::save_to_DB(), saveToDB(), and ~AP_tree_root().

long AP_tree_root::tree_timer

Definition at line 95 of file AP_Tree.hxx.

Referenced by is_tree_updated(), and update_timers().

long AP_tree_root::species_timer

Definition at line 96 of file AP_Tree.hxx.

Referenced by is_species_updated(), and update_timers().

AP_rates* AP_tree_root::rates

Definition at line 98 of file AP_Tree.hxx.

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

SL/AP_TREE/AP_Tree.hxx
SL/AP_TREE/AP_Tree.cxx