A base class for collecting fragments. More...

#include <CandidatesCollector.hh>

Public Member Functions
virtual bool	add (ScoredCandidate)=0
	Insert a fragment candidate to the container. More...

virtual void	clear ()=0
	removes all candidates from the container More...

virtual void	insert (Size, CandidatesCollectorOP)=0
	inserts candidates from another collector Candidates may or may not get inserted depending on the candidate and type of storage More...

virtual Size	count_candidates (Size) const =0
	Check how many candidates have been already collected for a given position. More...

virtual Size	count_candidates () const =0
	Check how many candidates have been already collected for all positions. More...

virtual Size	query_length () const =0
	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...

virtual ScoredCandidatesVector1 &	get_candidates (Size position_in_query)=0

virtual void	print_report (std::ostream &output, scores::FragmentScoreManagerOP scoring) const =0
	Describes what has been collected. More...

Detailed Description

A base class for collecting fragments.

TODO write collector for mixed fragment lengths

Detailed: 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

Member Function Documentation

virtual bool protocols::frag_picker::CandidatesCollector::add ( ScoredCandidate )

pure virtual

Insert a fragment candidate to the container.

Implemented in protocols::frag_picker::quota::ABEGO_SS_Pool, protocols::frag_picker::BoundedCollector< StrictWeakOrdering >, protocols::frag_picker::BoundedCollector< CompareTotalScore >, protocols::frag_picker::quota::SecondaryStructurePool, and protocols::frag_picker::GrabAllCollector.

virtual void protocols::frag_picker::CandidatesCollector::clear ( )

pure virtual

removes all candidates from the container

Implemented in protocols::frag_picker::BoundedCollector< StrictWeakOrdering >, protocols::frag_picker::BoundedCollector< CompareTotalScore >, protocols::frag_picker::quota::ABEGO_SS_Pool, protocols::frag_picker::quota::SecondaryStructurePool, protocols::frag_picker::GrabAllCollector, protocols::frag_picker::quota::QuotaPool, and protocols::frag_picker::quota::QuotaCollector.

virtual Size protocols::frag_picker::CandidatesCollector::count_candidates ( Size ) const

pure virtual

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

Implemented in protocols::frag_picker::quota::ABEGO_SS_Pool, protocols::frag_picker::BoundedCollector< StrictWeakOrdering >, protocols::frag_picker::BoundedCollector< CompareTotalScore >, protocols::frag_picker::quota::SecondaryStructurePool, protocols::frag_picker::GrabAllCollector, and protocols::frag_picker::quota::QuotaCollector.

virtual Size protocols::frag_picker::CandidatesCollector::count_candidates ( ) const

pure virtual

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

Implemented in protocols::frag_picker::quota::ABEGO_SS_Pool, protocols::frag_picker::BoundedCollector< StrictWeakOrdering >, protocols::frag_picker::BoundedCollector< CompareTotalScore >, protocols::frag_picker::GrabAllCollector, protocols::frag_picker::quota::SecondaryStructurePool, protocols::frag_picker::quota::QuotaPool, and protocols::frag_picker::quota::QuotaCollector.

virtual ScoredCandidatesVector1& protocols::frag_picker::CandidatesCollector::get_candidates ( Size position_in_query )

pure virtual

Implemented in protocols::frag_picker::quota::ABEGO_SS_Pool, protocols::frag_picker::BoundedCollector< StrictWeakOrdering >, protocols::frag_picker::BoundedCollector< CompareTotalScore >, protocols::frag_picker::GrabAllCollector, protocols::frag_picker::quota::SecondaryStructurePool, and protocols::frag_picker::quota::QuotaCollector.

virtual void protocols::frag_picker::CandidatesCollector::insert	(	Size	,
		CandidatesCollectorOP
	)

pure virtual

inserts candidates from another collector Candidates may or may not get inserted depending on the candidate and type of storage

Implemented in protocols::frag_picker::quota::ABEGO_SS_Pool, protocols::frag_picker::BoundedCollector< StrictWeakOrdering >, protocols::frag_picker::BoundedCollector< CompareTotalScore >, protocols::frag_picker::GrabAllCollector, protocols::frag_picker::quota::SecondaryStructurePool, and protocols::frag_picker::quota::QuotaCollector.

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

pure virtual

Describes what has been collected.

Implemented in protocols::frag_picker::BoundedCollector< StrictWeakOrdering >, protocols::frag_picker::BoundedCollector< CompareTotalScore >, protocols::frag_picker::quota::ABEGO_SS_Pool, protocols::frag_picker::quota::SecondaryStructurePool, protocols::frag_picker::GrabAllCollector, and protocols::frag_picker::quota::QuotaCollector.

virtual Size protocols::frag_picker::CandidatesCollector::query_length ( ) const

pure virtual

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.

Implemented in protocols::frag_picker::quota::ABEGO_SS_Pool, protocols::frag_picker::BoundedCollector< StrictWeakOrdering >, protocols::frag_picker::BoundedCollector< CompareTotalScore >, protocols::frag_picker::GrabAllCollector, protocols::frag_picker::quota::SecondaryStructurePool, and protocols::frag_picker::quota::QuotaCollector.

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

src/protocols/frag_picker/CandidatesCollector.hh

Public Member Functions

Detailed Description

Member Function Documentation