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protocols::frag_picker::scores::ProfileScoreBlosum62 Class Reference

a fragment candidate More...

#include <ProfileScoreBlosum62.hh>

Inheritance diagram for protocols::frag_picker::scores::ProfileScoreBlosum62:
Inheritance graph
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Public Member Functions

 ProfileScoreBlosum62 (core::Size priority, core::Real lowest_acceptable_value, bool use_lowest, core::sequence::SequenceProfileOP query_profile, core::Size longest_vall_chunk)
 
 ~ProfileScoreBlosum62 () override
 
void do_caching (VallChunkOP) override
 
void clean_up () override
 
bool score (FragmentCandidateOP, FragmentScoreMapOP) override
 
bool cached_score (FragmentCandidateOP, FragmentScoreMapOP) override
 
- Public Member Functions inherited from protocols::frag_picker::scores::CachingScoringMethod
 CachingScoringMethod (core::Size priority, core::Real lowest_acceptable_value, bool use_lowest, std::string name)
 
- Public Member Functions inherited from protocols::frag_picker::scores::FragmentScoringMethod
 FragmentScoringMethod (core::Size priority, core::Real lowest_acceptable_value, bool use_lowest, std::string name)
 
std::string & get_score_name ()
 Returns a name of this scoring method. More...
 
core::Size get_id ()
 Returns an integer index assigned to this scoring method by a scoring manager. More...
 
void set_id (core::Size id)
 Sets a new integer index for this scoring method. More...
 
core::Size get_priority ()
 Returns a priority of this scoring method. More...
 
core::Real get_min_allowed_score ()
 Returns the lowest acceptable score value for this scoring method. More...
 
bool get_use_lowest ()
 Returns the boolean choice on using the above lowest acceptable score value. More...
 
void set_min_allowed_score (core::Real lowest_acceptable_value)
 Sets a new value of the lowest acceptable score. More...
 

Protected Attributes

Matrix scores_
 
- Protected Attributes inherited from protocols::frag_picker::scores::FragmentScoringMethod
core::Size id_
 
core::Size priority_
 
std::string name_
 
core::Real lowest_acceptable_value_
 
bool use_lowest_
 

Private Member Functions

void clear ()
 

Private Attributes

core::sequence::SequenceProfileOP query_profile_
 
utility::vector1
< utility::vector1< core::Real > > 
blosum_matrix_
 
std::string cached_scores_id_
 

Detailed Description

a fragment candidate

Constructor & Destructor Documentation

protocols::frag_picker::scores::ProfileScoreBlosum62::ProfileScoreBlosum62 ( core::Size  priority,
core::Real  lowest_acceptable_value,
bool  use_lowest,
core::sequence::SequenceProfileOP  query_profile,
core::Size  longest_vall_chunk 
)
protocols::frag_picker::scores::ProfileScoreBlosum62::~ProfileScoreBlosum62 ( )
overridedefault

Member Function Documentation

bool protocols::frag_picker::scores::ProfileScoreBlosum62::cached_score ( FragmentCandidateOP  f,
FragmentScoreMapOP  empty_map 
)
overridevirtual
void protocols::frag_picker::scores::ProfileScoreBlosum62::clean_up ( )
inlineoverridevirtual
void protocols::frag_picker::scores::ProfileScoreBlosum62::clear ( )
private
void protocols::frag_picker::scores::ProfileScoreBlosum62::do_caching ( VallChunkOP  chunk)
overridevirtual
bool protocols::frag_picker::scores::ProfileScoreBlosum62::score ( FragmentCandidateOP  f,
FragmentScoreMapOP  empty_map 
)
overridevirtual

Member Data Documentation

utility::vector1< utility::vector1< core::Real > > protocols::frag_picker::scores::ProfileScoreBlosum62::blosum_matrix_
private

Referenced by do_caching(), and ProfileScoreBlosum62().

std::string protocols::frag_picker::scores::ProfileScoreBlosum62::cached_scores_id_
private

Referenced by cached_score(), and do_caching().

core::sequence::SequenceProfileOP protocols::frag_picker::scores::ProfileScoreBlosum62::query_profile_
private

Referenced by do_caching(), and ProfileScoreBlosum62().

Matrix protocols::frag_picker::scores::ProfileScoreBlosum62::scores_
protected

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