Rosetta: protocols::frag_picker::scores::ProfileScoreStructL1 Class Reference

a fragment candidate More...

#include <ProfileScoreStructL1.hh>

Inheritance diagram for protocols::frag_picker::scores::ProfileScoreStructL1:

Inheritance graph

Public Member Functions
	ProfileScoreStructL1 (core::Size, core::Real, bool, core::sequence::SequenceProfileOP, utility::vector1< core::Size > &, core::Size)

	~ProfileScoreStructL1 () override

void	do_caching_simple (VallChunkOP)

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_

utility::vector1< Matrix >	cache_

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_

std::string	cached_scores_id_

Detailed Description

a fragment candidate

Constructor & Destructor Documentation

protocols::frag_picker::scores::ProfileScoreStructL1::ProfileScoreStructL1	(	core::Size	priority,
		core::Real	lowest_acceptable_value,
		bool	use_lowest,
		core::sequence::SequenceProfileOP	query_profile,
		utility::vector1< core::Size > &	frag_sizes,
		core::Size	longest_vall_chunk
	)

References cache_, protocols::frag_picker::scores::create_cache(), query_profile_, scores_, and protocols::frag_picker::scores::trProfScoreL1().

protocols::frag_picker::scores::ProfileScoreStructL1::~ProfileScoreStructL1 ( )

overridedefault

Member Function Documentation

bool protocols::frag_picker::scores::ProfileScoreStructL1::cached_score	(	FragmentCandidateOP	f,
		FragmentScoreMapOP	empty_map
	)

overridevirtual

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

References cache_, cached_scores_id_, do_caching(), protocols::frag_picker::scores::FragmentScoringMethod::id_, protocols::frag_picker::scores::FragmentScoringMethod::lowest_acceptable_value_, and protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_.

void protocols::frag_picker::scores::ProfileScoreStructL1::clean_up ( )

inlineoverridevirtual

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

void protocols::frag_picker::scores::ProfileScoreStructL1::clear ( )

private

void protocols::frag_picker::scores::ProfileScoreStructL1::do_caching ( VallChunkOP chunk )

overridevirtual

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

References cache_, cached_scores_id_, do_caching_simple(), protocols::frag_picker::scores::rolling_score(), scores_, and protocols::frag_picker::scores::trProfScoreL1().

Referenced by cached_score().

void protocols::frag_picker::scores::ProfileScoreStructL1::do_caching_simple ( VallChunkOP chunk )

References query_profile_, score(), scores_, and protocols::frag_picker::scores::trProfScoreL1().

Referenced by do_caching().

bool protocols::frag_picker::scores::ProfileScoreStructL1::score	(	FragmentCandidateOP	f,
		FragmentScoreMapOP	empty_map
	)

overridevirtual

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

References protocols::frag_picker::scores::FragmentScoringMethod::id_, protocols::frag_picker::scores::FragmentScoringMethod::lowest_acceptable_value_, query_profile_, and protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_.

Referenced by do_caching_simple().

Member Data Documentation

utility::vector1< Matrix > protocols::frag_picker::scores::ProfileScoreStructL1::cache_

protected

Referenced by cached_score(), do_caching(), and ProfileScoreStructL1().

std::string protocols::frag_picker::scores::ProfileScoreStructL1::cached_scores_id_

private

Referenced by cached_score(), and do_caching().

core::sequence::SequenceProfileOP protocols::frag_picker::scores::ProfileScoreStructL1::query_profile_

private

Referenced by do_caching_simple(), ProfileScoreStructL1(), and score().

Matrix protocols::frag_picker::scores::ProfileScoreStructL1::scores_

protected

Referenced by do_caching(), do_caching_simple(), and ProfileScoreStructL1().

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

src/protocols/frag_picker/scores/ProfileScoreStructL1.hh
src/protocols/frag_picker/scores/ProfileScoreStructL1.cc