ARB
Public Member Functions | List of all members
Candidate Class Reference
Inheritance diagram for Candidate:
Inheritance graph
[legend]
Collaboration diagram for Candidate:
Collaboration graph
[legend]

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 charget_name () const
 
const charget_entry () const
 
bool operator< (const Candidate &other) const
 
 Candidate (const FoundGroup &group_, GroupSearchTree *node_)
 
 Candidate (GBDATA *gb_group_, GroupSearchTree *node_)
 
FoundGroupget_group ()
 
const FoundGroupget_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_)
 
GBDATAget_pointer () const
 
GBDATAget_tree_data () const
 
const charget_name () const
 
const charget_tree_name () const
 
int get_tree_order () const
 
const std::stringget_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< GBDATAgb_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 588 of file group_search.cxx.

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

Definition at line 592 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 597 of file group_search.cxx.

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

const FoundGroup& Candidate::get_group ( ) const
inline

Definition at line 598 of file group_search.cxx.

GroupSearchTree* Candidate::get_clade ( )
inline

Definition at line 600 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 604 of file group_search.cxx.

References get_clade().

int Candidate::get_keeledStateInfo ( ) const
inline

Definition at line 608 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

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