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protocols::frag_picker::scores::ProfileScoreL1 Class Reference

a fragment candidate More...

#include <ProfileScoreL1.hh>

Inheritance diagram for protocols::frag_picker::scores::ProfileScoreL1:
Inheritance graph
Collaboration diagram for protocols::frag_picker::scores::ProfileScoreL1:
Collaboration graph

Public Member Functions

 ProfileScoreL1 (Size, Real, bool, sequence::SequenceProfileOP, utility::vector1< Size > &, Size)
 ~ProfileScoreL1 ()
void do_caching_simple (VallChunkOP)
void do_caching (VallChunkOP)
void clean_up ()
bool score (FragmentCandidateOP, FragmentScoreMapOP)
bool cached_score (FragmentCandidateOP, FragmentScoreMapOP)
- Public Member Functions inherited from protocols::frag_picker::scores::CachingScoringMethod
 CachingScoringMethod (Size priority, Real lowest_acceptable_value, bool use_lowest, std::string name)
- Public Member Functions inherited from protocols::frag_picker::scores::FragmentScoringMethod
 FragmentScoringMethod (Size priority, Real lowest_acceptable_value, bool use_lowest, std::string name)
std::string & get_score_name ()
 Returns a name of this scoring method. More...
Size get_id ()
 Returns an integer index assigned to this scoring method by a scoring manager. More...
void set_id (Size id)
 Sets a new integer index for this scoring method. More...
Size get_priority ()
 Returns a priority of this scoring method. More...
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 (Real lowest_acceptable_value)
 Sets a new value of the lowest acceptable score. More...

Protected Attributes

Matrix scores_
utility::vector1< Matrixcache_

Private Member Functions

void clear ()

Private Attributes

sequence::SequenceProfileOP query_profile_
std::string cached_scores_id_

Detailed Description

a fragment candidate

Constructor & Destructor Documentation

protocols::frag_picker::scores::ProfileScoreL1::ProfileScoreL1 ( Size  priority,
Real  lowest_acceptable_value,
bool  use_lowest,
sequence::SequenceProfileOP  query_profile,
utility::vector1< Size > &  frag_sizes,
Size  longest_vall_chunk 
protocols::frag_picker::scores::ProfileScoreL1::~ProfileScoreL1 ( )

Member Function Documentation

bool protocols::frag_picker::scores::ProfileScoreL1::cached_score ( FragmentCandidateOP  f,
FragmentScoreMapOP  empty_map 
void protocols::frag_picker::scores::ProfileScoreL1::clean_up ( )
void protocols::frag_picker::scores::ProfileScoreL1::clear ( )
void protocols::frag_picker::scores::ProfileScoreL1::do_caching ( VallChunkOP  chunk)
void protocols::frag_picker::scores::ProfileScoreL1::do_caching_simple ( VallChunkOP  chunk)
bool protocols::frag_picker::scores::ProfileScoreL1::score ( FragmentCandidateOP  f,
FragmentScoreMapOP  empty_map 

Member Data Documentation

utility::vector1< Matrix > protocols::frag_picker::scores::ProfileScoreL1::cache_
std::string protocols::frag_picker::scores::ProfileScoreL1::cached_scores_id_

Referenced by cached_score(), and do_caching().

sequence::SequenceProfileOP protocols::frag_picker::scores::ProfileScoreL1::query_profile_
Matrix protocols::frag_picker::scores::ProfileScoreL1::scores_

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