#include <ap_main_type.hxx>

Inheritance diagram for AP_main:

Collaboration diagram for AP_main:

Public Member Functions
	AP_main ()

	~AP_main ()

void	set_tree_root (AWT_graphic_parsimony *agt_)

AWT_graphic_parsimony *	get_graphic_tree ()

AP_pars_root *	get_tree_root () const

	DEFINE_READ_ACCESSORS (AP_tree_nlen *, get_root_node, agt->get_root_node())

GBDATA *	get_gb_main () const

const char *	get_aliname () const

size_t	get_user_push_counter () const

Level	get_frameLevel () const

GB_ERROR	open (const char *db_server)

bool	push_node (AP_tree_nlen *node, AP_STACK_MODE)

void	remember_user_state ()

void	revert_user_state ()

void	remember ()

void	revert ()

void	accept ()

void	accept_all ()

void	accept_if (bool cond)

void	revert_if (bool cond)

bool	remember_and_rollback_to (Level wanted_frameLevel)

bool	remember_and_rollback_to_previous ()

Validity	revert_will_produce_valid_tree ()

Validity	all_available_reverts_will_produce_valid_trees ()

AP_tree_nlen *	makeNode (AP_pars_root *proot)

AP_tree_edge *	makeEdge (AP_tree_nlen n1, AP_tree_nlen n2)

void	destroyNode (AP_tree_nlen *node)

void	destroyEdge (AP_tree_edge *edge)

Detailed Description

Definition at line 31 of file ap_main_type.hxx.

Constructor & Destructor Documentation

AP_main::AP_main ( )

inline

Definition at line 44 of file ap_main_type.hxx.

AP_main::~AP_main ( )

inline

Definition at line 51 of file ap_main_type.hxx.

References ap_assert, and GB_close().

Member Function Documentation

void AP_main::set_tree_root ( AWT_graphic_parsimony * agt_ )

Definition at line 299 of file AP_main.cxx.

References ap_assert.

Referenced by ArbParsimony::set_tree().

AWT_graphic_parsimony* AP_main::get_graphic_tree ( )

inline

Definition at line 58 of file ap_main_type.hxx.

Referenced by delete_kept_ghostnodes(), and PARS_tree_init().

AP_pars_root* AP_main::get_tree_root ( ) const

inline

Definition at line 59 of file ap_main_type.hxx.

References AWT_graphic_parsimony::get_tree_root().

Referenced by delete_kept_ghostnodes(), insert_all_species_into_tree(), set_keep_ghostnodes(), and transform_gbd_to_leaf().

AP_main::DEFINE_READ_ACCESSORS	(	AP_tree_nlen *	,
		get_root_node	,
		agt->	get_root_node()
	)

GBDATA* AP_main::get_gb_main ( ) const

inline

Definition at line 63 of file ap_main_type.hxx.

References ap_assert.

Referenced by ARB_main(), create_pars_init_window(), PARSIMONY_testenv< SEQTYPE >::gbmain(), PARSIMONY_testenv< SEQTYPE >::load_tree(), pars_check_size(), pars_exit(), pars_start_cb(), PARS_tree_init(), and PARSIMONY_testenv< SEQTYPE >::PARSIMONY_testenv().

const char * AP_main::get_aliname ( ) const

Definition at line 304 of file AP_main.cxx.

Referenced by nt_add_partial(), and PARS_tree_init().

size_t AP_main::get_user_push_counter ( ) const

inline

Definition at line 68 of file ap_main_type.hxx.

References AP_STACK< ELEM >::count_elements().

Referenced by AP_user_pop_cb(), AP_user_push_cb(), and PARSIMONY_testenv< SEQTYPE >::get_user_push_counter().

Level AP_main::get_frameLevel ( ) const

inline

Definition at line 69 of file ap_main_type.hxx.

Referenced by all_available_reverts_will_produce_valid_trees(), and PARSIMONY_testenv< SEQTYPE >::get_frame_level().

GB_ERROR AP_main::open ( const char * db_server )

Definition at line 20 of file AP_main.cxx.

References error(), GB_await_error(), gb_main, GB_open(), and NULp.

Referenced by ARB_main().

bool AP_main::push_node	(	AP_tree_nlen *	node,
		AP_STACK_MODE	mode
	)

stores node in currFrame (if exists) if (mode&SEQUENCE) => sequence gets invalidated

Returns: true, if a new entry has been created. false, if existing entry was extended or no stack exists.

Definition at line 252 of file AP_main.cxx.

References ap_assert, BOTH, GBK_terminate(), ROOT, and SEQUENCE.

Referenced by AP_tree_edge::nni_rec(), push_all_upnode_sequences(), and undefine_branchlengths().

void AP_main::remember_user_state ( )

Definition at line 27 of file AP_main.cxx.

Referenced by AP_user_push_cb().

void AP_main::revert_user_state ( )

Definition at line 32 of file AP_main.cxx.

References aw_message(), and UserFrame::get_level().

Referenced by AP_user_pop_cb().

void AP_main::remember ( )

remember current tree state

See also: revert() and accept()

Definition at line 50 of file AP_main.cxx.

References ap_assert, and DOWNCAST.

Referenced by insert_species_into_tree(), ArbParsimony::kernighan_optimize_tree(), AP_tree_edge::kl_rec(), AP_tree_edge::nni_mutPerSite(), PARSIMONY_testenv< SEQTYPE >::push(), remember_and_rollback_to(), and update_undefined_leaf_branchlength().

void AP_main::revert ( )

revert tree to last remembered state

See also: remember() and accept()

Definition at line 66 of file AP_main.cxx.

References ap_assert, and GBK_terminate().

Referenced by accept_if(), all_available_reverts_will_produce_valid_trees(), insert_species_into_tree(), ArbParsimony::kernighan_optimize_tree(), AP_tree_edge::kl_rec(), AP_tree_edge::nni_mutPerSite(), PARSIMONY_testenv< SEQTYPE >::pop(), revert_will_produce_valid_tree(), and update_undefined_leaf_branchlength().

void AP_main::accept ( )

accept changes performed on tree (since last remember())

See also: revert()

Definition at line 205 of file AP_main.cxx.

References ap_assert, ASSERT_RESULT, GBK_terminate(), ResourceStack::has_node(), NULp, AP_STACK< ELEM >::pop(), and AP_STACK< ELEM >::push().

Referenced by PARSIMONY_testenv< SEQTYPE >::accept(), accept_all(), accept_if(), and ArbParsimony::kernighan_optimize_tree().

void AP_main::accept_all ( )

inline

Definition at line 82 of file ap_main_type.hxx.

References accept().

Referenced by pars_exit().

void AP_main::accept_if ( bool cond )

inline

Definition at line 88 of file ap_main_type.hxx.

References accept(), and revert().

Referenced by PARSIMONY_testenv< SEQTYPE >::accept_if(), AP_tree_edge::kl_rec(), AP_tree_edge::nni_mutPerSite(), and revert_if().

void AP_main::revert_if ( bool cond )

inline

Definition at line 89 of file ap_main_type.hxx.

References accept_if().

bool AP_main::remember_and_rollback_to ( Level wanted_frameLevel )

inline

Definition at line 91 of file ap_main_type.hxx.

References remember().

Referenced by all_available_reverts_will_produce_valid_trees(), and remember_and_rollback_to_previous().

bool AP_main::remember_and_rollback_to_previous ( )

inline

tree is modified into the same (or equiv) state as it would be done by calling pop(), but the current state is pushed onto the stack. Calling pop() afterwards will undo this operation.

Definition at line 100 of file ap_main_type.hxx.

References remember_and_rollback_to().

Referenced by revert_will_produce_valid_tree().

Validity AP_main::revert_will_produce_valid_tree ( )

inline

Definition at line 126 of file ap_main_type.hxx.

References ASSERT_RESULT, ASSERT_VALID_TREE, remember_and_rollback_to_previous(), revert(), and valid().

Referenced by PARSIMONY_testenv< SEQTYPE >::pop_will_produce_valid_tree().

Validity AP_main::all_available_reverts_will_produce_valid_trees ( )

inline

Definition at line 134 of file ap_main_type.hxx.

References ASSERT_RESULT, ASSERT_VALID_TREE, get_frameLevel(), remember_and_rollback_to(), revert(), and valid().