 |
Rosetta
2021.16
|
All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
|
Rosetta
2021.16
|
Keeps the N best fragments candidates for the final selection. More...
#include <BoundedCollector.hh>
Public Types | |
| typedef utility::pointer::shared_ptr < BoundedCollector < StrictWeakOrdering > > | BoundedCollectorOP |
| typedef utility::pointer::shared_ptr < BoundedCollector < StrictWeakOrdering > const > | BoundedCollectorCOP |
Public Member Functions | |
| BoundedCollector (core::Size query_size, core::Size max_frags_per_pos, StrictWeakOrdering fragment_comparator, core::Size n_score_terms, core::Size buffer_factor=5) | |
| create a collector for a given size of a query sequence More... | |
| bool | add (ScoredCandidate new_canditate) override |
| Insert a fragment candidate to the container. More... | |
| core::Size | count_candidates (core::Size seq_pos) const override |
| Check how many candidates have been already collected for a given position APL Note: you cannot have inlined virtual functions. More... | |
| core::Size | count_candidates () const override |
| Check how many candidates have been already collected for all positions APL Note: you cannot have inlined virtual functions. More... | |
| core::Size | query_length () const override |
| Check the size of query sequence that this object knows. This is mainly to be able to check if it is the same as in the other parts of fragment picking machinery. More... | |
| void | insert (core::Size pos, CandidatesCollectorOP collector) override |
| Inserts candidates from another Collector for a give position in the query Candidates may or may not get inserted depending on the candidate. More... | |
| ScoredCandidatesVector1 & | get_candidates (core::Size position_in_query) override |
| returns all stored fragment candidates that begins at a given position in a query More... | |
| void | clear () override |
| removes all candidates from the container More... | |
| void | print_report (std::ostream &out, scores::FragmentScoreManagerOP scoring) const override |
| prints how many candidates have been collected for each position and how good they are More... | |
Private Attributes | |
| utility::vector1 < LazySortedVector1< std::pair < FragmentCandidateOP, scores::FragmentScoreMapOP > , StrictWeakOrdering > > | storage_ |
Keeps the N best fragments candidates for the final selection.
The purpose of a collector is to keep the best fragment candidates to the end of vall processing. In particular, the capacity of this collector may be larger than the number of fragments one wants to get
| typedef utility::pointer::shared_ptr< BoundedCollector< StrictWeakOrdering > const> protocols::frag_picker::BoundedCollector< StrictWeakOrdering >::BoundedCollectorCOP |
| typedef utility::pointer::shared_ptr< BoundedCollector< StrictWeakOrdering > > protocols::frag_picker::BoundedCollector< StrictWeakOrdering >::BoundedCollectorOP |
|
inline |
create a collector for a given size of a query sequence
|
inlineoverridevirtual |
Insert a fragment candidate to the container.
Implements protocols::frag_picker::CandidatesCollector.
|
inlineoverridevirtual |
removes all candidates from the container
Implements protocols::frag_picker::CandidatesCollector.
|
inlineoverridevirtual |
Check how many candidates have been already collected for a given position APL Note: you cannot have inlined virtual functions.
Implements protocols::frag_picker::CandidatesCollector.
|
inlineoverridevirtual |
Check how many candidates have been already collected for all positions APL Note: you cannot have inlined virtual functions.
Implements protocols::frag_picker::CandidatesCollector.
|
inlineoverridevirtual |
returns all stored fragment candidates that begins at a given position in a query
Implements protocols::frag_picker::CandidatesCollector.
|
inlineoverridevirtual |
Inserts candidates from another Collector for a give position in the query Candidates may or may not get inserted depending on the candidate.
Implements protocols::frag_picker::CandidatesCollector.
|
inlineoverridevirtual |
prints how many candidates have been collected for each position and how good they are
Implements protocols::frag_picker::CandidatesCollector.
|
inlineoverridevirtual |
Check the size of query sequence that this object knows. This is mainly to be able to check if it is the same as in the other parts of fragment picking machinery.
Implements protocols::frag_picker::CandidatesCollector.
|
private |
Referenced by protocols::frag_picker::BoundedCollector< CompareTotalScore >::add(), protocols::frag_picker::BoundedCollector< CompareTotalScore >::BoundedCollector(), protocols::frag_picker::BoundedCollector< CompareTotalScore >::clear(), protocols::frag_picker::BoundedCollector< CompareTotalScore >::count_candidates(), protocols::frag_picker::BoundedCollector< CompareTotalScore >::get_candidates(), protocols::frag_picker::BoundedCollector< CompareTotalScore >::insert(), protocols::frag_picker::BoundedCollector< CompareTotalScore >::print_report(), and protocols::frag_picker::BoundedCollector< CompareTotalScore >::query_length().
1.8.7