SpecSetRegistry Class Reference

#include <NT_species_set.h>

Inheritance diagram for SpecSetRegistry:

Collaboration diagram for SpecSetRegistry:

Public Member Functions
	SpecSetRegistry (long nspecies_, arb_progress *progress_, const GroupMatchScorer &scorer_)
	~SpecSetRegistry ()
void	finish (GB_ERROR &error)
long	bitstring_bytes () const
long	bitstring_longs () const
unsigned char *	allocate_bitstring () const
long	get_species_index (const char *species_name) const
RSpecSet *	registerTree (AP_tree *node)
RSpecSet *	search_best_match (const TSpecSet *tset, GroupPenalty &min_penalty)
TSpecSet *	find_best_matches_info (AP_tree *node, FILE *log, bool compare_node_info)
GB_ERROR	write_node_information (FILE *log, bool delete_old_nodes, GroupsToTransfer what, const char *aci)
void	setScorer (const GroupMatchScorer &newScorer)

Detailed Description

Definition at line 33 of file NT_species_set.h.

Constructor & Destructor Documentation

SpecSetRegistry::SpecSetRegistry	(	long	nspecies_,
		arb_progress *	progress_,
		const GroupMatchScorer &	scorer_
	)

Definition at line 23 of file NT_tree_cmp.cxx.

References allocate_bitstring().

SpecSetRegistry::~SpecSetRegistry

(

)

Definition at line 44 of file NT_tree_cmp.cxx.

References GBS_free_hash().

Member Function Documentation

void SpecSetRegistry::finish

(

GB_ERROR &

error

)

Definition at line 598 of file NT_tree_cmp.cxx.

Referenced by NTREE_move_tree_info().

long SpecSetRegistry::bitstring_bytes ( ) const

inline

Definition at line 64 of file NT_species_set.h.

Referenced by bitstring_longs(), search_best_match(), and SpecSet::SpecSet().

long SpecSetRegistry::bitstring_longs ( ) const

inline

Definition at line 65 of file NT_species_set.h.

References bitstring_bytes(), and long.

Referenced by allocate_bitstring(), search_best_match(), and SpecSet::SpecSet().

unsigned char* SpecSetRegistry::allocate_bitstring ( ) const

inline

Definition at line 67 of file NT_species_set.h.

References bitstring_longs(), and long.

Referenced by SpecSet::init(), and SpecSetRegistry().

long SpecSetRegistry::get_species_index ( const char *  species_name ) const

inline

Definition at line 69 of file NT_species_set.h.

References GBS_read_hash().

Referenced by SpecSet::SpecSet().

RSpecSet * SpecSetRegistry::registerTree

(

AP_tree *

node

)

Definition at line 318 of file NT_tree_cmp.cxx.

References add(), TreeNode::is_leaf(), SpecSet::is_leaf_set(), TreeNode::name, and nt_assert.

Referenced by NTREE_move_tree_info().

RSpecSet * SpecSetRegistry::search_best_match	(	const TSpecSet *	tset,
		GroupPenalty &	min_penalty
	)

Definition at line 165 of file NT_tree_cmp.cxx.

References GroupPenalty::betterThan(), SpecSet::bitstring, bitstring_bytes(), bitstring_longs(), arb_progress::inc(), GroupMatchScorer::matchGroups(), GroupPenalty::NoMatch(), and NULp.

Referenced by NTREE_move_tree_info().

TSpecSet * SpecSetRegistry::find_best_matches_info	(	AP_tree *	node,
		FILE *	log,
		bool	compare_node_info
	)

Definition at line 343 of file NT_tree_cmp.cxx.

References arb_progress::aborted(), GBS_global_string_copy(), TreeNode::is_leaf(), TreeNode::name, nt_assert, NULp, TreeNode::remove_remark(), TreeNode::set_remark(), and TreeNode::use_as_remark().

Referenced by NTREE_move_tree_info().

GB_ERROR SpecSetRegistry::write_node_information	(	FILE *	log,
		bool	delete_old_nodes,
		GroupsToTransfer	what,
		const char *	aci
	)

Definition at line 464 of file NT_tree_cmp.cxx.

References ARB_strdup(), RSpecSet::bestMatch(), ARB_seqtree::contains_marked_species(), error(), fputc(), fputs(), GB_await_error(), GB_command_interpreter_in_env(), GB_copy_dropProtectMarksAndTempstate(), GB_create_container(), GB_delete(), GB_entry(), TreeNode::gb_node, GB_read_string(), GBS_global_string_copy(), GBT_write_group_name(), GroupPenalty::get_groupsize(), get_GroupXfer_customized_ACI_commands(), GroupPenalty::get_ingroup_ratio(), GroupPenalty::get_outgroup_ratio(), GroupPenalty::get_penalty(), TreeNode::get_tree_root(), implicated, GroupPenalty::isPerfectMatch(), RSpecSet::matchedNode(), TreeNode::name, nt_assert, NULp, SpecSet::set_node, GroupPenalty::shouldHaveBeenKeeled(), RSpecSet::size(), and XFER_GROUPS_WITH_MARKED.

Referenced by NTREE_move_tree_info().

void SpecSetRegistry::setScorer ( const GroupMatchScorer &  newScorer )

inline

Definition at line 76 of file NT_species_set.h.

Referenced by NTREE_move_tree_info().

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

• NTREE/NT_species_set.h
• NTREE/NT_tree_cmp.cxx