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protocols::frag_picker::scores::ProfileScoreSubMatrix Class Reference

a fragment candidate More...

#include <ProfileScoreSubMatrix.hh>

Inheritance diagram for protocols::frag_picker::scores::ProfileScoreSubMatrix:
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Collaboration diagram for protocols::frag_picker::scores::ProfileScoreSubMatrix:
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Public Member Functions

 ProfileScoreSubMatrix (Size priority, Real lowest_acceptable_value, bool use_lowest, std::string sequence, Size longest_vall_chunk, std::string subMatrixFile)
 
 ~ProfileScoreSubMatrix ()
 
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_
 

Private Member Functions

void clear ()
 

Private Attributes

std::string sequence_
 
std::string subMatrixFile_
 
utility::vector1
< utility::vector1< Real > > 
sub_matrix_
 
std::string cached_scores_id_
 

Detailed Description

a fragment candidate

Constructor & Destructor Documentation

protocols::frag_picker::scores::ProfileScoreSubMatrix::ProfileScoreSubMatrix ( Size  priority,
Real  lowest_acceptable_value,
bool  use_lowest,
std::string  sequence,
Size  longest_vall_chunk,
std::string  subMatrixFile 
)
protocols::frag_picker::scores::ProfileScoreSubMatrix::~ProfileScoreSubMatrix ( )

Member Function Documentation

bool protocols::frag_picker::scores::ProfileScoreSubMatrix::cached_score ( FragmentCandidateOP  f,
FragmentScoreMapOP  empty_map 
)
virtual
void protocols::frag_picker::scores::ProfileScoreSubMatrix::clean_up ( )
inlinevirtual
void protocols::frag_picker::scores::ProfileScoreSubMatrix::clear ( )
private
void protocols::frag_picker::scores::ProfileScoreSubMatrix::do_caching ( VallChunkOP  chunk)
virtual
bool protocols::frag_picker::scores::ProfileScoreSubMatrix::score ( FragmentCandidateOP  f,
FragmentScoreMapOP  empty_map 
)
virtual

Member Data Documentation

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

Referenced by cached_score(), and do_caching().

Matrix protocols::frag_picker::scores::ProfileScoreSubMatrix::scores_
protected
std::string protocols::frag_picker::scores::ProfileScoreSubMatrix::sequence_
private
utility::vector1< utility::vector1< Real > > protocols::frag_picker::scores::ProfileScoreSubMatrix::sub_matrix_
private
std::string protocols::frag_picker::scores::ProfileScoreSubMatrix::subMatrixFile_
private

Referenced by ProfileScoreSubMatrix().


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