haplo::ScoreProvider Class Reference

#include <haplotypes.hpp>

Inheritance diagram for haplo::ScoreProvider:

Public Member Functions
virtual pair< double, bool >	score (const vg::Path &, haploMath::RRMemo &memo)=0
	Score the given path usign the given memo. More...
virtual int64_t	get_haplotype_count () const
virtual bool	has_incremental_search () const
virtual IncrementalSearchState	incremental_find (const vg::Position &pos) const
virtual IncrementalSearchState	incremental_extend (const IncrementalSearchState &state, const vg::Position &pos) const
virtual	~ScoreProvider ()=default

Detailed Description

Interface abstracting over the various ways of generating haplotype scores. You probably want the implementations: GBWTScoreProvider, LinearScoreProvider TODO: Const-ify the indexes used

Constructor & Destructor Documentation

~ScoreProvider()

virtual haplo::ScoreProvider::~ScoreProvider ( )

virtualdefault

Member Function Documentation

get_haplotype_count()

int64_t haplo::ScoreProvider::get_haplotype_count ( ) const

virtual

Return the haplotype count (number of expected haplotypes that agree with a path that is fixed in the population) that should be used to construct the memo to pass to score, or -1 if the indexes backing the ScoreProvider do not make this information available.

Reimplemented in haplo::GBWTScoreProvider< GBWTType >.

has_incremental_search()

bool haplo::ScoreProvider::has_incremental_search ( ) const

virtual

Return true if this ScoreProvider supports incremental search for counting haplotypes.

Reimplemented in haplo::GBWTScoreProvider< GBWTType >.

incremental_extend()

IncrementalSearchState haplo::ScoreProvider::incremental_extend ( const IncrementalSearchState &  state, const vg::Position &  pos  ) const

virtual

Extend the given search state with the node visit described by the given Position, if incremental search is supported.

Reimplemented in haplo::GBWTScoreProvider< GBWTType >.

incremental_find()

IncrementalSearchState haplo::ScoreProvider::incremental_find ( const vg::Position &  pos ) const

virtual

Start a new search state with the node visit described by the given Position, if incremental search is supported.

Reimplemented in haplo::GBWTScoreProvider< GBWTType >.

score()

virtual pair<double, bool> haplo::ScoreProvider::score ( const vg::Path &  , haploMath::RRMemo &  memo  )

pure virtual

Score the given path usign the given memo.

Implemented in haplo::LinearScoreProvider, and haplo::GBWTScoreProvider< GBWTType >.

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

• src/haplotypes.hpp
• src/haplotypes.cpp