A base class for collecting fragments. More...

#include <QuotaCollector.hh>

Inheritance diagram for protocols::frag_picker::quota::QuotaCollector:

Public Member Functions
	QuotaCollector (core::Size query_size, core::Size frag_size)

bool	add (std::pair< FragmentCandidateOP, scores::FragmentScoreMapOP >) override
	Insert a fragment candidate to the container. More...

void	clear () override
	removes all candidates from the container More...

core::Size	count_candidates (core::Size) const override
	Check how many candidates have been already collected for a given position. More...

core::Size	count_candidates () const override
	Check how many candidates have been already collected for all positions. More...

core::Size	query_length () const override
	Check the size of query sequence that this object knows. This is mainly to be ale to check if it is the same as in the other parts of fragment picking machinery. More...

ScoredCandidatesVector1 &	get_candidates (core::Size position_in_query) override

void	print_report (std::ostream &output, scores::FragmentScoreManagerOP scoring) const override
	Describes what has been collected. More...

void	insert (core::Size pos, CandidatesCollectorOP collector) override
	Inserts candidates from another QuotaCollector for a give position in the query Candidates may or may not get inserted depending on the candidate. More...

void	list_pools (std::ostream &where) const
	list all registered pools with their capacity More...

core::Size	count_pools (core::Size position) const
	prints the number of quota pools for a given positio in query More...

QuotaPoolCOP	get_pool (core::Size position, core::Size pool_id) const

QuotaPoolOP	get_pool (core::Size position, core::Size pool_id)

void	add_pool (core::Size position, QuotaPoolOP the_pool)

void	renormalize_quota_pools ()

void	attach_secondary_structure_pools (core::Real, core::fragment::SecondaryStructureOP, std::string, core::Size, utility::vector1< core::Size >, utility::vector1< core::Real >, core::Size)

Public Member Functions inherited from protocols::frag_picker::CandidatesCollector
virtual bool	add (ScoredCandidate)=0
	Insert a fragment candidate to the container. More...

Private Attributes
core::Size	frag_size_

ScoredCandidatesVector1	frags_for_pos_

utility::vector1 < utility::vector1 < QuotaPoolOP > >	storage_

Detailed Description

A base class for collecting fragments.

The purpose of a collector is to keep fragment candidates to the end of vall processing. Then a selector will go through all the candidates stored in a collector and select the final fragments

See also: GrabAll collector for a possible implementation

Constructor & Destructor Documentation

protocols::frag_picker::quota::QuotaCollector::QuotaCollector	(	core::Size	query_size,
		core::Size	frag_size
	)

inline

References frag_size_, and storage_.

Member Function Documentation

bool protocols::frag_picker::quota::QuotaCollector::add ( std::pair< FragmentCandidateOP, scores::FragmentScoreMapOP > candidate )

override

Insert a fragment candidate to the container.

References storage_.

void protocols::frag_picker::quota::QuotaCollector::add_pool	(	core::Size	position,
		QuotaPoolOP	the_pool
	)

inline

References storage_.

void protocols::frag_picker::quota::QuotaCollector::attach_secondary_structure_pools	(	core::Real	prediction_fraction,
		core::fragment::SecondaryStructureOP	prediction,
		std::string	name,
		core::Size	n_candidates,
		utility::vector1< core::Size >	components,
		utility::vector1< core::Real >	weights,
		core::Size	n_scores
	)

References frag_size_, storage_, and protocols::frag_picker::quota::trQuotaCollector().

void protocols::frag_picker::quota::QuotaCollector::clear ( )

overridevirtual

removes all candidates from the container

Implements protocols::frag_picker::CandidatesCollector.

References storage_.

core::Size protocols::frag_picker::quota::QuotaCollector::count_candidates ( core::Size pos ) const

overridevirtual

Check how many candidates have been already collected for a given position.

Implements protocols::frag_picker::CandidatesCollector.

References storage_.

core::Size protocols::frag_picker::quota::QuotaCollector::count_candidates ( ) const

overridevirtual

Check how many candidates have been already collected for all positions.

Implements protocols::frag_picker::CandidatesCollector.

References storage_.

core::Size protocols::frag_picker::quota::QuotaCollector::count_pools ( core::Size position ) const

inline

prints the number of quota pools for a given positio in query

References storage_.

Referenced by protocols::frag_picker::QuotaDebug::setup_summary().

ScoredCandidatesVector1 & protocols::frag_picker::quota::QuotaCollector::get_candidates ( core::Size position_in_query )

overridevirtual

Implements protocols::frag_picker::CandidatesCollector.

References frags_for_pos_, storage_, and protocols::frag_picker::quota::trQuotaCollector().

QuotaPoolCOP protocols::frag_picker::quota::QuotaCollector::get_pool	(	core::Size	position,
		core::Size	pool_id
	)		const

inline

References storage_.

Referenced by protocols::frag_picker::QuotaDebug::setup_summary().

QuotaPoolOP protocols::frag_picker::quota::QuotaCollector::get_pool	(	core::Size	position,
		core::Size	pool_id
	)

inline

References storage_.

void protocols::frag_picker::quota::QuotaCollector::insert	(	core::Size	pos,
		CandidatesCollectorOP	collector
	)

inlineoverridevirtual

Inserts candidates from another QuotaCollector for a give position in the query Candidates may or may not get inserted depending on the candidate.

Implements protocols::frag_picker::CandidatesCollector.

References core::pack::dunbrack::c, and storage_.

void protocols::frag_picker::quota::QuotaCollector::list_pools ( std::ostream & where ) const

list all registered pools with their capacity

References storage_.

void protocols::frag_picker::quota::QuotaCollector::print_report	(	std::ostream &	output,
		scores::FragmentScoreManagerOP	scoring
	)		const

overridevirtual

Describes what has been collected.

Implements protocols::frag_picker::CandidatesCollector.

References core::chemical::element::I, and storage_.

core::Size protocols::frag_picker::quota::QuotaCollector::query_length ( ) const

inlineoverridevirtual

Check the size of query sequence that this object knows. This is mainly to be ale to check if it is the same as in the other parts of fragment picking machinery.

Implements protocols::frag_picker::CandidatesCollector.

References storage_.

Referenced by protocols::frag_picker::QuotaDebug::setup_summary().

void protocols::frag_picker::quota::QuotaCollector::renormalize_quota_pools ( )

References storage_, and core::simple_metrics::metrics::sum.