ARB: ARB_seqtree_root Class Reference

ARB

#include <ARB_Tree.hxx>

Inheritance diagram for ARB_seqtree_root:

Inheritance graph

Collaboration diagram for ARB_seqtree_root:

Collaboration graph

Public Member Functions
	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

virtual GB_ERROR	loadFromDB (const char *name) __ATTR__USERESULT

virtual GB_ERROR	saveToDB () __ATTR__USERESULT

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 ()

virtual void	change_root (TreeNode old, TreeNode newroot)

void	delete_by_node ()

bool	has_bootstrap () const

void	set_bootstrap_seen (bool seen)

virtual TreeNode *	makeNode () const =0

virtual void	destroyNode (TreeNode *node) const =0

	DEFINE_READ_ACCESSORS (TreeNode *, get_root_node, rootNode)

ARB_edge	find_innermost_edge ()

Protected Member Functions
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 44 of file ARB_Tree.hxx.

Constructor & Destructor Documentation

ARB_seqtree_root::ARB_seqtree_root	(	AliView *	aliView,
		AP_sequence *	seqTempl,
		bool	add_delete_callbacks
	)

Definition at line 28 of file ARB_Tree.cxx.

References at_assert, AP_sequence::get_aliview(), and AliView::has_data().

ARB_seqtree_root::~ARB_seqtree_root ( )

Definition at line 49 of file ARB_Tree.cxx.

References GB_CB_DELETE, GB_remove_callback(), and tree_deleted_cbwrapper().

Member Function Documentation

void ARB_seqtree_root::set_gb_tree ( GBDATA * gbTree )

inlineprotected

Definition at line 57 of file ARB_Tree.hxx.

References at_assert, and implicated.

Referenced by AP_tree_root::change_root().

void ARB_seqtree_root::set_gb_tree_and_name	(	GBDATA *	gbTree,
		const char *	name
	)

inlineprotected

Definition at line 62 of file ARB_Tree.hxx.

References ARB_strdup(), and at_assert.

Referenced by AP_tree_root::saveToDB().

ARB_seqtree_root::DEFINE_TREE_ROOT_ACCESSORS	(	ARB_seqtree_root	,
		ARB_seqtree
	)

const AliView* ARB_seqtree_root::get_aliview ( ) const

inline

Definition at line 75 of file ARB_Tree.hxx.

const AP_filter* ARB_seqtree_root::get_filter ( ) const

inline

Definition at line 77 of file ARB_Tree.hxx.

References AliView::get_filter().

Referenced by ST_ML::get_filter().

const AP_weights* ARB_seqtree_root::get_weights ( ) const

inline

Definition at line 78 of file ARB_Tree.hxx.

References AliView::get_weights().

GBDATA* ARB_seqtree_root::get_gb_main ( ) const

inline

Definition at line 80 of file ARB_Tree.hxx.

References AliView::get_gb_main().

Referenced by AP_tree_root::AP_tree_root(), AP_tree_root::check_update(), AP_tree::compute_tree(), AWT_graphic_tree::handle_command(), linkToDB(), loadFromDB(), AP_tree_root::remove_leafs(), saveToDB(), and AP_tree_root::saveToDB().

GBDATA* ARB_seqtree_root::get_gb_tree ( ) const

inline

Definition at line 82 of file ARB_Tree.hxx.

Referenced by AP_tree_root::change_root(), group_awar_changed_cb(), AWT_graphic_tree::handle_command(), AP_tree_root::is_tree_updated(), NT_reload_tree_event(), NTREE_move_tree_info(), AP_tree::recompute_and_write_folding(), AP_tree_root::saveToDB(), AWT_graphic_tree::show_ruler(), and AP_tree_root::update_timers().

void ARB_seqtree_root::tree_deleted_cb ( GBDATA * gb_tree_del )

Definition at line 57 of file ARB_Tree.cxx.

References at_assert, and NULp.

Referenced by tree_deleted_cbwrapper().

const char* ARB_seqtree_root::get_tree_name ( ) const

inline

Definition at line 85 of file ARB_Tree.hxx.

Referenced by AWT_graphic_tree::check_for_DB_update(), AWT_graphic_tree::load_from_DB(), AWT_graphic_tree::save_to_DB(), and tree_size_ok().

GB_ERROR ARB_seqtree_root::loadFromDB ( const char * name )

virtual

Reimplemented in AP_tree_root.

Definition at line 66 of file ARB_Tree.cxx.

References at_assert, TreeRoot::change_root(), DOWNCAST, error(), GB_add_callback(), GB_await_error(), GB_CB_DELETE, GB_end_transaction(), gb_main, GB_push_transaction(), GB_remove_callback(), GBT_find_tree(), GBT_read_tree(), get_gb_main(), TreeNode::get_root_node(), NULp, and tree_deleted_cbwrapper().

Referenced by AP_tree_root::loadFromDB().

GB_ERROR ARB_seqtree_root::saveToDB ( )

virtual

Reimplemented in AP_tree_root, and FINAL_TYPE< SEQTYPE >.

Definition at line 107 of file ARB_Tree.cxx.

References at_assert, error(), GB_end_transaction(), gb_main, GB_push_transaction(), GBT_overwrite_tree(), and get_gb_main().

Referenced by AP_tree_root::saveToDB().

const AP_sequence* ARB_seqtree_root::get_seqTemplate ( ) const

inline

Definition at line 90 of file ARB_Tree.hxx.

Referenced by linkToDB().

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

Definition at line 130 of file ARB_Tree.cxx.

References arb_tree_species_deleted_cb(), at_assert, error(), GBT_link_tree(), get_gb_main(), get_seqTemplate(), AliView::has_data(), and NULp.

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

void ARB_seqtree_root::unlinkFromDB ( )

Definition at line 147 of file ARB_Tree.cxx.

References arb_tree_species_deleted_cb(), GBT_unlink_tree(), and AliView::has_data().

ARB_seqtree_root::PREPARE_MARK_NONFINAL_CLASS ( ARB_seqtree_root )

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

SL/ARB_TREE/ARB_Tree.hxx
SL/ARB_TREE/ARB_Tree.cxx