ARB
Public Member Functions | List of all members
SpecSetRegistry Class Reference

#include <NT_species_set.h>

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Collaboration diagram for SpecSetRegistry:
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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 charallocate_bitstring () const
 
long get_species_index (const char *species_name) const
 
RSpecSetregisterTree (AP_tree *node)
 
RSpecSetsearch_best_match (const TSpecSet *tset, GroupPenalty &min_penalty)
 
TSpecSetfind_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 22 of file NT_tree_cmp.cxx.

References allocate_bitstring().

SpecSetRegistry::~SpecSetRegistry ( )

Definition at line 43 of file NT_tree_cmp.cxx.

References GBS_free_hash().

Member Function Documentation

void SpecSetRegistry::finish ( GB_ERROR error)

Definition at line 596 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)
RSpecSet * SpecSetRegistry::search_best_match ( const TSpecSet tset,
GroupPenalty min_penalty 
)
TSpecSet * SpecSetRegistry::find_best_matches_info ( AP_tree node,
FILE *  log,
bool  compare_node_info 
)
GB_ERROR SpecSetRegistry::write_node_information ( FILE *  log,
bool  delete_old_nodes,
GroupsToTransfer  what,
const char aci 
)
void SpecSetRegistry::setScorer ( const GroupMatchScorer newScorer)
inline

Definition at line 76 of file NT_species_set.h.

Referenced by NTREE_move_tree_info().


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