protocols::frag_picker::scores::SequenceIdentity Class Reference

SequenceIdentity score counts identical residues. More...

#include <SequenceIdentity.hh>

Inheritance diagram for protocols::frag_picker::scores::SequenceIdentity:

Collaboration diagram for protocols::frag_picker::scores::SequenceIdentity:

Public Member Functions
	SequenceIdentity (Size priority, Real lowest_acceptable_value, bool use_lowest, std::string &fastaQuerySequence)
bool	score (FragmentCandidateOP f, FragmentScoreMapOP empty_map)
bool	describe_score (FragmentCandidateOP f, FragmentScoreMapOP empty_map, std::ostream &out)
	prints a detailed explanation how a fragment score has been computed More...
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...

Static Public Attributes
static const int	REWARD = 0
	will be added if the two residues are identical More...
static const int	PENALTY = 1
	will be added if the two residues are NOT identical More...

Private Attributes
Real	minScoreAllowed_
std::string &	query_

Additional Inherited Members
Protected Attributes inherited from protocols::frag_picker::scores::FragmentScoringMethod
Size	id_
Size	priority_
std::string	name_
Real	lowest_acceptable_value_
bool	use_lowest_

Detailed Description

SequenceIdentity score counts identical residues.

Detailed: Resulting score is the number of identical residues

on corresponding positions in a vall fragment and a query sequence

Constructor & Destructor Documentation

protocols::frag_picker::scores::SequenceIdentity::SequenceIdentity ( Size  priority, Real  lowest_acceptable_value, bool  use_lowest, std::string &  fastaQuerySequence  )

inline

Member Function Documentation

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

prints a detailed explanation how a fragment score has been computed

Detailed: besides extensive output, the method should return the same result as score()

References protocols::frag_picker::scores::FragmentScoringMethod::id_, protocols::frag_picker::scores::FragmentScoringMethod::lowest_acceptable_value_, PENALTY, query_, REWARD, and protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_.

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

virtual

Implements protocols::frag_picker::scores::FragmentScoringMethod.

References protocols::frag_picker::scores::FragmentScoringMethod::id_, protocols::frag_picker::scores::FragmentScoringMethod::lowest_acceptable_value_, PENALTY, query_, REWARD, and protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_.

Member Data Documentation

Real protocols::frag_picker::scores::SequenceIdentity::minScoreAllowed_

private

const int protocols::frag_picker::scores::SequenceIdentity::PENALTY = 1

static

will be added if the two residues are NOT identical

Referenced by describe_score(), and score().

std::string& protocols::frag_picker::scores::SequenceIdentity::query_

private

Referenced by describe_score(), and score().

const int protocols::frag_picker::scores::SequenceIdentity::REWARD = 0

static

will be added if the two residues are identical

Referenced by describe_score(), and score().

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

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