Public Member Functions | List of all members
GroupMatchScorer Class Reference

#include <NT_tree_cmp.h>

Public Member Functions

 GroupMatchScorer ()
GB_ERROR check_validity () const
void setLimits (const RatioLimits &ingroupLimits, const RatioLimits &outgroupLimits)
void setPerErrorPenalties (double ingroup_pep, double outgroup_pep, double unfound_pep)
void setRelativePenalties (double ingroup_inv_relpen, double outgroup_relpen)
GroupPenalty matchGroups (const TSpecSet &sourceSet, const RSpecSet &targetSet, long commonSpecies, long overallSpecies)
double calcUnknownMembersPenalty (const TSpecSet &sourceSet) const

Detailed Description

Definition at line 112 of file NT_tree_cmp.h.

Constructor & Destructor Documentation

GroupMatchScorer::GroupMatchScorer ( )

Definition at line 135 of file NT_tree_cmp.h.

Member Function Documentation

GB_ERROR GroupMatchScorer::check_validity ( ) const

Definition at line 146 of file NT_tree_cmp.cxx.

References RatioLimits::isValid(), and NULp.

Referenced by NTREE_move_tree_info().

void GroupMatchScorer::setLimits ( const RatioLimits ingroupLimits,
const RatioLimits outgroupLimits 

Definition at line 147 of file NT_tree_cmp.h.

References RatioLimits::insideLimits(), and nt_assert.

Referenced by ad_move_tree_info().

void GroupMatchScorer::setPerErrorPenalties ( double  ingroup_pep,
double  outgroup_pep,
double  unfound_pep 

Definition at line 154 of file NT_tree_cmp.h.

Referenced by ad_move_tree_info().

void GroupMatchScorer::setRelativePenalties ( double  ingroup_inv_relpen,
double  outgroup_relpen 

Definition at line 159 of file NT_tree_cmp.h.

Referenced by ad_move_tree_info().

GroupPenalty GroupMatchScorer::matchGroups ( const TSpecSet sourceSet,
const RSpecSet targetSet,
long  commonSpecies,
long  overallSpecies 

calculate score of group match (tests normal and keeled insertion, reports better)

sourceSettested set (= named group in source tree (if moving groups))
targetSetregistered set (= subtree of target tree (if moving groups))
commonSpeciesnumber of species common in sourceSet and targetSet
overallSpeciesnumber of registered species (in SpecSetRegistry)
better GroupPenalty

Definition at line 106 of file NT_tree_cmp.cxx.

References GroupPenalty::addPenalty(), GroupPenalty::betterThan(), GroupPenalty::doesMatch(), SpecSet::get_known_members(), implicated, GroupPenalty::mark_as_keeled(), and nt_assert.

Referenced by SpecSetRegistry::search_best_match().

double GroupMatchScorer::calcUnknownMembersPenalty ( const TSpecSet sourceSet) const

Definition at line 142 of file NT_tree_cmp.cxx.

References TSpecSet::get_unknown_members().

Referenced by GroupPenalty::registerUnfound().

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