protocols::frag_picker::scores::ProfileScore Class Reference

a fragment candidate More...

#include <ProfileScore.hh>

Public Member Functions
	ProfileScore (Size priority, Real lowest_acceptable_value, bool use_lowest, sequence::SequenceProfileOP query_profile, sequence::ScoringSchemeOP profile_scoring, Size longest_vall_chunk)
	~ProfileScore ()
void	do_caching (VallChunkOP)
void	clean_up ()
bool	cached_score (FragmentCandidateOP, FragmentScoreMapOP)
bool	describe_score (FragmentCandidateOP f, FragmentScoreMapOP empty_map, std::ostream &out)
Public Member Functions inherited from protocols::frag_picker::scores::CachingScoringMethod
	CachingScoringMethod (Size priority, Real lowest_acceptable_value, bool use_lowest, std::string name)
virtual bool	score (FragmentCandidateOP fragment, FragmentScoreMapOP scores)
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_
Protected Attributes inherited from protocols::frag_picker::scores::FragmentScoringMethod
Size	id_
Size	priority_
std::string	name_
Real	lowest_acceptable_value_
bool	use_lowest_

Private Member Functions
void	clear ()

Private Attributes
sequence::SequenceProfileOP	query_profile_
sequence::ScoringSchemeOP	profile_scoring_
std::string	cached_scores_id_

Detailed Description

a fragment candidate

Constructor & Destructor Documentation

protocols::frag_picker::scores::ProfileScore::ProfileScore ( Size  priority, Real  lowest_acceptable_value, bool  use_lowest, sequence::SequenceProfileOP  query_profile, sequence::ScoringSchemeOP  profile_scoring, Size  longest_vall_chunk  )

inline

References profile_scoring_, query_profile_, scores_, and utility_exit_with_message.

protocols::frag_picker::scores::ProfileScore::~ProfileScore

(

)

Member Function Documentation

bool protocols::frag_picker::scores::ProfileScore::cached_score ( FragmentCandidateOP  f, FragmentScoreMapOP  empty_map  )

virtual

Reimplemented from protocols::frag_picker::scores::CachingScoringMethod.

void protocols::frag_picker::scores::ProfileScore::clean_up ( )

inlinevirtual

Implements protocols::frag_picker::scores::CachingScoringMethod.

Reimplemented in protocols::frag_picker::scores::ScoreEValuator.

Referenced by protocols::frag_picker::scores::ScoreEValuator::clean_up().

void protocols::frag_picker::scores::ProfileScore::clear ( )

private

bool protocols::frag_picker::scores::ProfileScore::describe_score	(	FragmentCandidateOP	f,
		FragmentScoreMapOP	empty_map,
		std::ostream &	out
	)

References F, and I.

void protocols::frag_picker::scores::ProfileScore::do_caching ( VallChunkOP  chunk )

virtual

Implements protocols::frag_picker::scores::CachingScoringMethod.

Reimplemented in protocols::frag_picker::scores::ScoreEValuator.

References protocols::frag_picker::VallChunk::chunk_key(), protocols::frag_picker::VallChunk::get_pdb_id(), protocols::frag_picker::VallChunk::get_profile(), protocols::frag_picker::VallChunk::size(), and protocols::frag_picker::scores::trProfScore.

Referenced by protocols::frag_picker::scores::ScoreEValuator::do_caching().

Member Data Documentation

std::string protocols::frag_picker::scores::ProfileScore::cached_scores_id_

private

sequence::ScoringSchemeOP protocols::frag_picker::scores::ProfileScore::profile_scoring_

private

Referenced by ProfileScore().

sequence::SequenceProfileOP protocols::frag_picker::scores::ProfileScore::query_profile_

private

Referenced by ProfileScore().

Matrix protocols::frag_picker::scores::ProfileScore::scores_

protected

Referenced by ProfileScore().

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

• src/protocols/frag_picker/scores/ProfileScore.hh
• src/protocols/frag_picker/scores/ProfileScore.cc