scores a fragment based on sum of secondary structure identity and sequence identity More...

#include <IdentityEval.hh>

Inheritance diagram for core::fragment::picking_old::vall::eval::IdentityEval:

Collaboration diagram for core::fragment::picking_old::vall::eval::IdentityEval:

Public Types
typedef Super::VallFragmentScore	VallFragmentScore

typedef std::string	String

typedef core::Real	Real

typedef Super::PageConstIterator	PageConstIterator
	typedef for ExtentEvaluator concept More...

typedef Super::Extent	Extent
	typedef for ExtentEvaluator concept More...

typedef PageConstIterator	VallResidueConstIterator

Public Types inherited from core::fragment::picking_old::vall::eval::VallFragmentEval
typedef core::fragment::picking_old::vall::scores::VallFragmentScore	VallFragmentScore

typedef VallFragmentScore::PageConstIterator	PageConstIterator
	typedef for ExtentEvaluator concept More...

typedef core::fragment::picking_old::concepts::Extent < VallSection::PageConstIterator >	Extent
	typedef for ExtentEvaluator concept More...

typedef PageConstIterator	VallResidueConstIterator

Public Member Functions
	IdentityEval ()
	default constructor More...

	IdentityEval (String const &ss, String const &aa, Real const ss_penalty=1.0, Real const aa_penalty=1.0, bool const randomize=true)
	full values constructor More...

	IdentityEval (String const &ss, Real const ss_penalty=1.0, bool const randomize=true)
	secondary structure constructor More...

	IdentityEval (IdentityEval const &rval)
	default copy constructor More...

virtual	~IdentityEval ()
	default destructor More...

IdentityEval &	operator= (IdentityEval const &rval)
	copy assignment More...

virtual VallFragmentEvalOP	clone () const
	clone this object More...

virtual bool	eval_impl (Extent const &extent, VallFragmentScore &fs)
	for a fragment extent, evaluate and store results in a VallFragmentScore More...

String const &	ss_str () const
	get secondary structure string More...

void	ss_str (String const &ss)
	set secondary structure string More...

String const &	aa_str () const
	get amino acid string More...

void	aa_str (String const &aa)
	set amino acid string More...

Real	ss_penalty () const
	get secondary structure penalty More...

void	ss_penalty (Real const penalty)
	set secondary structure penalty More...

Real	aa_penalty () const
	get amino acid penalty More...

void	aa_penalty (Real const penalty)
	set amino acid penalty More...

bool	randomize () const
	adding random noise to score? More...

void	randomize (bool const flag)
	set flag to add random noise between [0, 0.001) to score More...

virtual void	pre_catalog_op (VallLibrary const &)
	operation to be perform before catalog() starts More...

Public Member Functions inherited from core::fragment::picking_old::vall::eval::VallFragmentEval
	VallFragmentEval ()
	default constructor More...

	VallFragmentEval (VallFragmentEval const &rval)
	default copy constructor More...

virtual	~VallFragmentEval ()
	default destructor More...

VallFragmentEval &	operator= (VallFragmentEval const &rval)
	copy assignment More...

bool	operator() (Extent const &extent, VallFragmentScore &fs)
	called by VallLibrarian: for a fragment extent, evaluate and store results in a VallFragmentScore More...

virtual void	post_catalog_op (VallLibrary const &)
	operation to be performed after catalog() finished More...

Private Types
typedef VallFragmentEval	Super

Private Attributes
String	ss_
	secondary structure string to match against More...

String	aa_
	amino acid string to match against More...

Real	ss_penalty_
	secondary structure penalty if non-matching More...

Real	aa_penalty_
	amino acid penalty if non-matching More...

bool	randomize_
	flag to add random noise between [0, 0.001) into score More...

Detailed Description

scores a fragment based on sum of secondary structure identity and sequence identity

Definition at line 42 of file IdentityEval.hh.

Member Typedef Documentation

typedef Super::Extent core::fragment::picking_old::vall::eval::IdentityEval::Extent

typedef for ExtentEvaluator concept

Definition at line 68 of file IdentityEval.hh.

typedef Super::PageConstIterator core::fragment::picking_old::vall::eval::IdentityEval::PageConstIterator

typedef for ExtentEvaluator concept

Definition at line 64 of file IdentityEval.hh.

typedef core::Real core::fragment::picking_old::vall::eval::IdentityEval::Real

Definition at line 57 of file IdentityEval.hh.

typedef std::string core::fragment::picking_old::vall::eval::IdentityEval::String

Definition at line 56 of file IdentityEval.hh.

typedef VallFragmentEval core::fragment::picking_old::vall::eval::IdentityEval::Super

private

Definition at line 48 of file IdentityEval.hh.

typedef Super::VallFragmentScore core::fragment::picking_old::vall::eval::IdentityEval::VallFragmentScore

Definition at line 54 of file IdentityEval.hh.

typedef PageConstIterator core::fragment::picking_old::vall::eval::IdentityEval::VallResidueConstIterator

Definition at line 74 of file IdentityEval.hh.

Constructor & Destructor Documentation

core::fragment::picking_old::vall::eval::IdentityEval::IdentityEval ( )

default constructor

Definition at line 45 of file IdentityEval.cc.

Referenced by clone().

core::fragment::picking_old::vall::eval::IdentityEval::IdentityEval	(	String const &	ss,
		String const &	aa,
		Real const	ss_penalty = `1.0`,
		Real const	aa_penalty = `1.0`,
		bool const	randomize = `true`
	)

full values constructor

Parameters

ss	secondary structure string to match against
aa	amino acid structure string to match against

Definition at line 56 of file IdentityEval.cc.

References aa_, and ss_.

core::fragment::picking_old::vall::eval::IdentityEval::IdentityEval	(	String const &	ss,
		Real const	ss_penalty = `1.0`,
		bool const	randomize = `true`
	)

secondary structure constructor

Definition at line 75 of file IdentityEval.cc.

References aa_, and ss_.

core::fragment::picking_old::vall::eval::IdentityEval::IdentityEval ( IdentityEval const & rval)

default copy constructor

Definition at line 92 of file IdentityEval.cc.

core::fragment::picking_old::vall::eval::IdentityEval::~IdentityEval ( )

virtual

default destructor

Definition at line 103 of file IdentityEval.cc.

Member Function Documentation

Real core::fragment::picking_old::vall::eval::IdentityEval::aa_penalty ( ) const

inline

get amino acid penalty

Definition at line 187 of file IdentityEval.hh.

References aa_penalty_.

void core::fragment::picking_old::vall::eval::IdentityEval::aa_penalty ( Real const penalty)

inline

set amino acid penalty

Definition at line 194 of file IdentityEval.hh.

References aa_penalty_.

String const& core::fragment::picking_old::vall::eval::IdentityEval::aa_str ( ) const

inline

get amino acid string

Definition at line 159 of file IdentityEval.hh.

References aa_.

void core::fragment::picking_old::vall::eval::IdentityEval::aa_str ( String const & aa)

inline

set amino acid string

Definition at line 166 of file IdentityEval.hh.

References aa_.

VallFragmentEvalOP core::fragment::picking_old::vall::eval::IdentityEval::clone ( ) const

virtual

clone this object

Implements core::fragment::picking_old::vall::eval::VallFragmentEval.

Definition at line 121 of file IdentityEval.cc.

References IdentityEval().

bool core::fragment::picking_old::vall::eval::IdentityEval::eval_impl	(	Extent const &	extent,
		VallFragmentScore &	fs
	)

virtual

for a fragment extent, evaluate and store results in a VallFragmentScore

Returns: true, so score is always stored during VallLibrarian::catalog()

Implements core::fragment::picking_old::vall::eval::VallFragmentEval.

Definition at line 128 of file IdentityEval.cc.

References aa_, aa_penalty_, core::fragment::picking_old::concepts::Extent< PageIterator >::begin, core::fragment::picking_old::concepts::Extent< PageIterator >::distance(), core::fragment::picking_old::concepts::Extent< PageIterator >::end, randomize_, core::fragment::picking_old::vall::eval::RG(), core::fragment::picking_old::vall::scores::VallFragmentScore::score, ss_, and ss_penalty_.

IdentityEval & core::fragment::picking_old::vall::eval::IdentityEval::operator= ( IdentityEval const & rval)

copy assignment

Definition at line 107 of file IdentityEval.cc.

References aa_, aa_penalty_, core::fragment::picking_old::vall::eval::VallFragmentEval::operator=(), randomize_, ss_, and ss_penalty_.

void core::fragment::picking_old::vall::eval::IdentityEval::pre_catalog_op ( VallLibrary const & )

virtual

operation to be perform before catalog() starts

Reimplemented from core::fragment::picking_old::vall::eval::VallFragmentEval.

Definition at line 178 of file IdentityEval.cc.

References aa_, ss_, and core::fragment::picking_old::vall::eval::TR().

bool core::fragment::picking_old::vall::eval::IdentityEval::randomize ( ) const

inline

adding random noise to score?

Definition at line 201 of file IdentityEval.hh.

References randomize_.

void core::fragment::picking_old::vall::eval::IdentityEval::randomize ( bool const flag)

inline

set flag to add random noise between [0, 0.001) to score

Definition at line 208 of file IdentityEval.hh.

References randomize_.

Real core::fragment::picking_old::vall::eval::IdentityEval::ss_penalty ( ) const

inline

get secondary structure penalty

Definition at line 173 of file IdentityEval.hh.

References ss_penalty_.

void core::fragment::picking_old::vall::eval::IdentityEval::ss_penalty ( Real const penalty)

inline

set secondary structure penalty

Definition at line 180 of file IdentityEval.hh.

References ss_penalty_.

String const& core::fragment::picking_old::vall::eval::IdentityEval::ss_str ( ) const

inline

get secondary structure string

Definition at line 145 of file IdentityEval.hh.

References ss_.

void core::fragment::picking_old::vall::eval::IdentityEval::ss_str ( String const & ss)

inline

set secondary structure string

Definition at line 152 of file IdentityEval.hh.

References ss_.

Member Data Documentation

String core::fragment::picking_old::vall::eval::IdentityEval::aa_

private

amino acid string to match against

Definition at line 229 of file IdentityEval.hh.

Referenced by aa_str(), eval_impl(), IdentityEval(), operator=(), and pre_catalog_op().

Real core::fragment::picking_old::vall::eval::IdentityEval::aa_penalty_

private

amino acid penalty if non-matching

Definition at line 237 of file IdentityEval.hh.

Referenced by aa_penalty(), eval_impl(), and operator=().

bool core::fragment::picking_old::vall::eval::IdentityEval::randomize_

private

flag to add random noise between [0, 0.001) into score

Definition at line 241 of file IdentityEval.hh.

Referenced by eval_impl(), operator=(), and randomize().

String core::fragment::picking_old::vall::eval::IdentityEval::ss_

private

secondary structure string to match against

Definition at line 225 of file IdentityEval.hh.

Referenced by eval_impl(), IdentityEval(), operator=(), pre_catalog_op(), and ss_str().

Real core::fragment::picking_old::vall::eval::IdentityEval::ss_penalty_

private

secondary structure penalty if non-matching

Definition at line 233 of file IdentityEval.hh.

Referenced by eval_impl(), operator=(), and ss_penalty().

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

src/core/fragment/picking_old/vall/eval/IdentityEval.hh
src/core/fragment/picking_old/vall/eval/IdentityEval.cc

Public Types

Public Member Functions

Private Types

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation