ArbParsimony Class Reference

#include <pars_main.hxx>

Public Member Functions
	ArbParsimony ()
AWT_graphic_parsimony *	get_tree () const
	DEFINE_READ_ACCESSORS (AP_tree_nlen *, get_root_node, get_tree() ->get_root_node())
void	generate_tree (WeightedFilter *pars_weighted_filter)
void	set_tree (AWT_graphic_parsimony *tree_)
void	optimize_tree (AP_tree_nlen *at, const KL_Settings &settings, arb_progress &progress)
void	kernighan_optimize_tree (AP_tree_nlen *at, const KL_Settings &settings, const Mutations *pars_global_start, bool dumpPerf)

Detailed Description

Definition at line 25 of file pars_main.hxx.

Constructor & Destructor Documentation

ArbParsimony::ArbParsimony ( )

inline

Definition at line 29 of file pars_main.hxx.

Member Function Documentation

AWT_graphic_parsimony* ArbParsimony::get_tree ( ) const

inline

Definition at line 31 of file pars_main.hxx.

Referenced by global_tree().

ArbParsimony::DEFINE_READ_ACCESSORS	(	AP_tree_nlen *	,
		get_root_node	,
		get_tree() ->get_root_node()
	)

void ArbParsimony::generate_tree

(

WeightedFilter *

pars_weighted_filter

)

Definition at line 295 of file PARS_dtree.cxx.

References gb_main, GBT_is_alignment_protein(), AliView::get_aliname(), AliView::get_gb_main(), AWT_graphic_tree::init(), NULp, pars_generate_aliview(), PARS_map_viewer(), set_tree(), and ta.

Referenced by pars_start_cb().

void ArbParsimony::set_tree

(

AWT_graphic_parsimony *

tree_

)

Definition at line 67 of file PARS_main.cxx.

References ap_assert, and AP_main::set_tree_root().

Referenced by generate_tree().

void ArbParsimony::optimize_tree	(	AP_tree_nlen *	at,
		const KL_Settings &	settings,
		arb_progress &	progress
	)

Definition at line 190 of file PARS_dtree.cxx.

References arb_progress::aborted(), ap_assert, AP_BL_NNI_ONLY, OptiPerfMeter::dump(), OptiPerfMeter::dumpCustom(), GBS_global_string(), kernighan_optimize_tree(), NULp, rootNode(), settings, arb_progress::subtitle(), and KL_Settings::whichEdges.

Referenced by optimizeTree().

void ArbParsimony::kernighan_optimize_tree	(	AP_tree_nlen *	at,
		const KL_Settings &	settings,
		const Mutations *	pars_global_start,
		bool	dumpPerf
	)

Definition at line 96 of file PARS_dtree.cxx.

References AP_main::accept(), ap_assert, AP_DYNAMIK, ap_main, AP_STATIC, QuadraticThreshold::change_parsimony_start(), CUSTOM_DEPTHS, KL_Settings::depth, OptiPerfMeter::dump(), KL_Settings::Dynamic, KL_Settings::enabled, GBS_global_string(), implicated, KL_params::inc_rec_depth, KL_Settings::incdepth, AP_tree_edge::is_leaf_edge(), AP_tree_edge::kl_rec(), KL_params::max_rec_depth, KL_Settings::maxdepth, KL_Settings::maxx, KL_Settings::maxy, AP_tree_edge::next_to_folded_group(), NULp, AP_tree_edge::otherNode(), KL_params::rec_type, KL_params::rec_width, AP_main::remember(), AP_main::revert(), rootEdge(), AP_tree_edge::set_visited(), EdgeChain::size(), SKIP_FOLDED_EDGES, SKIP_LEAF_EDGES, KL_Settings::start, KL_Settings::Static, KL_params::stopAtFoldedGroups, arb_progress::subtitle(), KL_params::thresFunctor, KL_Settings::type, and KL_Settings::whichEdges.

Referenced by optimize_tree().

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

• PARSIMONY/pars_main.hxx
• PARSIMONY/PARS_dtree.cxx
• PARSIMONY/PARS_main.cxx