ARB: Candidate Class Reference

ARB

Inheritance diagram for Candidate:

Inheritance graph

Collaboration diagram for Candidate:

Collaboration graph

Public Member Functions
	Candidate (bool is_species, const char name_, GBDATA gb_src, GBDATA *gb_dst, const CharPtrArray &ali_names)

	~Candidate ()

int	has_alignments () const

double	get_score () const

const char *	get_name () const

const char *	get_entry () const

bool	operator< (const Candidate &other) const

	Candidate (const FoundGroup &group_, GroupSearchTree *node_)

	Candidate (GBDATA gb_group_, GroupSearchTree node_)

FoundGroup &	get_group ()

const FoundGroup &	get_group () const

GroupSearchTree *	get_clade ()

const GroupSearchTree *	get_clade () const

int	get_keeledStateInfo () const

void	inform_group (const GroupSearch &group_search, const string &hitReason)

Public Member Functions inherited from FoundGroup
	FoundGroup (GBDATA *gb_group_)

GBDATA *	get_pointer () const

GBDATA *	get_tree_data () const

const char *	get_name () const

const char *	get_tree_name () const

int	get_tree_order () const

const std::string &	get_hit_reason () const

void	set_cluster_id (int id)

void	forget_cluster_id ()

int	get_cluster_id () const

bool	overlap_is_folded () const

bool	is_folded () const

bool	knows_details () const

void	track_max_widths (ColumnWidths &widths) const

int	get_nesting () const

int	get_size () const

int	get_marked () const

int	get_marked_pc () const

int	get_keeled () const

double	get_aid () const

bool	operator== (const FoundGroup &other) const

GB_ERROR	delete_from_DB ()

ARB_ERROR	rename_by_ACI (const char *acisrt, const QueriedGroups &results, int hit_idx)

ARB_ERROR	change_folding (GroupFoldingMode mode)

Additional Inherited Members
Protected Attributes inherited from FoundGroup
std::string	hit_reason

Lazy< int,-1 >	nesting

Lazy< int,-1 >	size

Lazy< int,-1 >	marked

LazyFloat< double >	aid

Lazy< int,-1 >	keeled

RefPtr< GBDATA >	gb_overlap_group

int	clusterID

Detailed Description

Definition at line 106 of file MG_preserves.cxx.

Constructor & Destructor Documentation

Candidate::Candidate	(	bool	is_species,
		const char *	name_,
		GBDATA *	gb_src,
		GBDATA *	gb_dst,
		const CharPtrArray &	ali_names
	)

inline

Definition at line 113 of file MG_preserves.cxx.

References count_bases(), GB_have_error(), GBT_find_sequence(), mg_assert, and valid().

Candidate::~Candidate ( )

inline

Definition at line 146 of file MG_preserves.cxx.

Candidate::Candidate	(	const FoundGroup &	group_,
		GroupSearchTree *	node_
	)

inline

Definition at line 591 of file group_search.cxx.

Candidate::Candidate	(	GBDATA *	gb_group_,
		GroupSearchTree *	node_
	)

inline

Definition at line 595 of file group_search.cxx.

Member Function Documentation

int Candidate::has_alignments ( ) const

inline

Definition at line 148 of file MG_preserves.cxx.

Referenced by find_SAI_candidates(), and find_species_candidates().

double Candidate::get_score ( ) const

inline

Definition at line 149 of file MG_preserves.cxx.

Referenced by find_SAI_candidates(), and find_species_candidates().

const char* Candidate::get_name ( ) const

inline

Definition at line 151 of file MG_preserves.cxx.

const char* Candidate::get_entry ( ) const

inline

Definition at line 152 of file MG_preserves.cxx.

References GBS_global_string().

bool Candidate::operator< ( const Candidate & other ) const

inline

Definition at line 156 of file MG_preserves.cxx.

FoundGroup& Candidate::get_group ( )

inline

Definition at line 600 of file group_search.cxx.

Referenced by QueriedGroups::add_candidate(), and TargetGroup::get_group().

const FoundGroup& Candidate::get_group ( ) const

inline

Definition at line 601 of file group_search.cxx.

GroupSearchTree* Candidate::get_clade ( )

inline

Definition at line 603 of file group_search.cxx.

References DOWNCAST.

Referenced by get_clade(), TargetGroup::get_clade(), and inform_group().

const GroupSearchTree* Candidate::get_clade ( ) const

inline

Definition at line 607 of file group_search.cxx.

References get_clade().

int Candidate::get_keeledStateInfo ( ) const

inline

Definition at line 611 of file group_search.cxx.

Referenced by TargetGroup::get_keeledStateInfo(), and inform_group().

void Candidate::inform_group	(	const GroupSearch &	group_search,
		const string &	hitReason
	)

inline

Definition at line 613 of file group_search.cxx.

References FoundGroup::aid, GroupSearch::calc_nesting_level(), FoundGroup::gb_overlap_group, get_clade(), get_keeledStateInfo(), FoundGroup::get_pointer(), gs_assert, FoundGroup::hit_reason, FoundGroup::keeled, FoundGroup::knows_details(), FoundGroup::marked, Lazy< T, UNDEFINED >::needs_eval(), LazyFloat< T >::needs_eval(), FoundGroup::nesting, and FoundGroup::size.

Referenced by QueriedGroups::add_candidate().

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

MERGE/MG_preserves.cxx
SL/GROUP_SEARCH/group_search.cxx