#include <SyncRoot.hxx>

Inheritance diagram for RootSynchronizer:

Collaboration diagram for RootSynchronizer:

Public Member Functions
	RootSynchronizer ()

int	add (SizeAwareTree &tree, const char treename)

SizeAwareTree *	take_tree (int idx)

void	beginDeconstructionPhase ()

bool	deconstructionPhase () const

GB_ERROR	deconstruct_all_trees (bool provideProgress)

bool	allTreesDeconstructed () const

ErrorOrSizeAwareTreePtr	find_best_root_candidate (int inTree, int accordingToTree, int &best_dist, bool provideProgress)

MultirootPtr	get_innermost_edges () const

ErrorOrMultirootPtr	get_current_roots () const

ErrorOrMultirootPtr	find_good_roots_for_trees (const int MAX_DEPTH, arb_progress *progress=NULp)

const SpeciesSpace &	get_SpeciesSpace () const

ErrorOrDeconstructedTreePtr	get_DeconstructedTree (int treeIdx)

const PART *	get_tree_PART (int treeIdx) const

const PART *	get_edge_PART (int treeIdx, const SizeAwareTree *sonOfEdge) const

int	calcEdgeDistance (int i1, const SizeAwareTree n1, int i2, const SizeAwareTree n2) const

int	calcTreeDistance (int i1, int i2) const

int	minDistanceSum () const

Public Member Functions inherited from TreeContainer
	~TreeContainer ()

size_t	get_tree_count () const

bool	valid_tree_index (int idx) const

const TreeInfo &	get_tree_info (int idx) const

const SizeAwareTree *	get_tree (int idx) const

SizeAwareTree *	take_tree (int idx)

void	get_species_names (ConstStrArray &species_names) const

size_t	get_species_count () const

int	add (SizeAwareTree &tree, const char treename)

Static Public Member Functions
static void	find_best_matching_PART_in (int &best_dist, int &best_idx, const PART part, const DeconstructedTree &in, const PART tree_part, const PART *tree_in, bool provideProgress)

static void	find_worst_matching_PART_in (int &worst_dist, int &worst_idx, const PART part, const DeconstructedTree &in, const PART tree_part, const PART *tree_in)

Detailed Description

Definition at line 100 of file SyncRoot.hxx.

Constructor & Destructor Documentation

RootSynchronizer::RootSynchronizer ( )

inline

Definition at line 116 of file SyncRoot.hxx.

Member Function Documentation

int RootSynchronizer::add	(	SizeAwareTree *&	tree,
		const char *	treename
	)

inline

Definition at line 118 of file SyncRoot.hxx.

References TreeContainer::add(), arb_assert, and deconstructionPhase().

Referenced by load_and_add_tree().

SizeAwareTree* RootSynchronizer::take_tree ( int idx )

inline

Definition at line 122 of file SyncRoot.hxx.

References deconstructionPhase(), and TreeContainer::take_tree().

Referenced by adjustTreeRoot().

void RootSynchronizer::beginDeconstructionPhase ( )

Definition at line 18 of file SyncRoot.cxx.

References arb_assert.

bool RootSynchronizer::deconstructionPhase ( ) const

inline

Definition at line 131 of file SyncRoot.hxx.

References SmartPtr< T, C >::isSet().

Referenced by add(), allTreesDeconstructed(), Multiroot::distanceSum(), get_SpeciesSpace(), get_tree_PART(), and take_tree().

GB_ERROR RootSynchronizer::deconstruct_all_trees ( bool provideProgress )

Definition at line 274 of file SyncRoot.cxx.

References arb_progress::done(), error(), arb_progress::inc_and_check_user_abort(), NULp, and showDeconstructingSubtitle().

Referenced by multiroot_sync_subsetTrees().

bool RootSynchronizer::allTreesDeconstructed ( ) const

inline

Definition at line 135 of file SyncRoot.hxx.

References arb_assert, deconstructionPhase(), and TreeContainer::get_tree_count().

Referenced by get_edge_PART().

ErrorOrSizeAwareTreePtr RootSynchronizer::find_best_root_candidate	(	int	inTree,
		int	accordingToTree,
		int &	best_dist,
		bool	provideProgress
	)

Definition at line 58 of file SyncRoot.cxx.

References arb_assert, arb_progress::done(), DOWNCAST, PART_FWD::get_origin(), arb_progress::inc_and_check_user_abort(), SmartPtr< T, C >::isSet(), NULp, result, showDeconstructingSubtitle(), and arb_progress::subtitle().

Referenced by rootsync_subsetTrees_vs_selected().

MultirootPtr RootSynchronizer::get_innermost_edges ( ) const

Definition at line 419 of file SyncRoot.cxx.

References arb_assert, DOWNCAST, and PART_FWD::get_origin().

ErrorOrMultirootPtr RootSynchronizer::get_current_roots ( ) const

Definition at line 407 of file SyncRoot.cxx.

References NULp, and result.

Referenced by multiroot_sync_subsetTrees().

ErrorOrMultirootPtr RootSynchronizer::find_good_roots_for_trees	(	const int	MAX_DEPTH,
		arb_progress *	progress = `NULp`
	)

Definition at line 297 of file SyncRoot.cxx.

References arb_progress::aborted(), arb_assert, GBS_global_string(), ErrorOr< TYPE >::getValue(), ErrorOr< TYPE >::hasError(), SmartPtr< T, C >::isNull(), arb_test::none(), NULp, and arb_progress::subtitle().

Referenced by multiroot_sync_subsetTrees().

const SpeciesSpace& RootSynchronizer::get_SpeciesSpace ( ) const

inline

Definition at line 149 of file SyncRoot.hxx.

References arb_assert, and deconstructionPhase().

ErrorOrDeconstructedTreePtr RootSynchronizer::get_DeconstructedTree ( int treeIdx )

inline

Definition at line 153 of file SyncRoot.hxx.

References error().

const PART* RootSynchronizer::get_tree_PART ( int treeIdx ) const

inline

Definition at line 157 of file SyncRoot.hxx.

References arb_assert, deconstructionPhase(), and TreeParts::get_tree_PART().

const PART* RootSynchronizer::get_edge_PART	(	int	treeIdx,
		const SizeAwareTree *	sonOfEdge
	)		const

inline

Definition at line 161 of file SyncRoot.hxx.

References allTreesDeconstructed(), arb_assert, and TreeContainer::valid_tree_index().

Referenced by Multiroot::distanceToCenterSum().

int RootSynchronizer::calcEdgeDistance	(	int	i1,
		const SizeAwareTree *	n1,
		int	i2,
		const SizeAwareTree *	n2
	)		const

Definition at line 436 of file SyncRoot.cxx.

References arb_assert, and PART_FWD::calcDistance().

int RootSynchronizer::calcTreeDistance	(	int	i1,
		int	i2
	)		const

Definition at line 457 of file SyncRoot.cxx.

References PART_FWD::calcDistance().

int RootSynchronizer::minDistanceSum ( ) const

Definition at line 464 of file SyncRoot.cxx.

void RootSynchronizer::find_best_matching_PART_in	(	int &	best_dist,
		int &	best_idx,
		const PART *	part,
		const DeconstructedTree &	in,
		const PART *	tree_part,
		const PART *	tree_in,
		bool	provideProgress
	)

static

Definition at line 116 of file SyncRoot.cxx.

References arb_progress::aborted(), arb_assert, PART_FWD::calcDistance(), DeconstructedTree::get_part_count(), DeconstructedTree::peek_part(), and represents_existing_edge().

void RootSynchronizer::find_worst_matching_PART_in	(	int &	worst_dist,
		int &	worst_idx,
		const PART *	part,
		const DeconstructedTree &	in,
		const PART *	tree_part,
		const PART *	tree_in
	)

static

Definition at line 147 of file SyncRoot.cxx.

References arb_assert, PART_FWD::calcDistance(), DeconstructedTree::get_part_count(), DeconstructedTree::peek_part(), and represents_existing_edge().

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

CONSENSUS_TREE/SyncRoot.hxx
CONSENSUS_TREE/SyncRoot.cxx

Public Member Functions

Static Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation