ProfileHandle Class Reference

#include <profile_handle.hh>

Public Member Functions
	ProfileHandle ()
const std::vector< ProfileColumn > &	GetColumns () const
const ProfileColumn &	GetNullModel () const
void	SetNullModel (const ProfileColumn &null_model)
String	GetSequence () const
void	SetSequence (const String &seq)
Real	GetNeff () const
void	SetNeff (Real neff)
ProfileHandlePtr	Extract (uint from, uint to) const
Real	GetAverageEntropy () const
Real	GetAverageScore (const ProfileHandle &other, uint offset=0) const
void	AddColumn (const ProfileColumn &c, char olc='X')
void	clear ()
size_t	size () const
bool	empty () const
ProfileColumn &	operator[] (size_t index)
const ProfileColumn &	operator[] (size_t index) const
ProfileColumn &	at (size_t index)
const ProfileColumn &	at (size_t index) const
ProfileColumn &	back ()
const ProfileColumn &	back () const
bool	operator== (const ProfileHandle &other) const
bool	operator!= (const ProfileHandle &other) const
ProfileColumnList::iterator	columns_begin ()
ProfileColumnList::iterator	columns_end ()
ProfileColumnList::const_iterator	columns_begin () const
ProfileColumnList::const_iterator	columns_end () const

Friends
std::ofstream &	operator<< (std::ofstream &os, ProfileHandle &prof)
std::ifstream &	operator>> (std::ifstream &is, ProfileHandle &prof)

Detailed Description

Provides a profile for a sequence.

Properties:

• consists of N ProfileColumn (N = #residues in sequence)
• contains sequence (String) of length N
• user must enforce consistency between sequence length and #columns
• contains a null_model to use for this sequence

Definition at line 291 of file profile_handle.hh.

Constructor & Destructor Documentation

ProfileHandle()

ProfileHandle ( )

inline

Constructs an empty profile handle (sequence = '', 0 columns).

Definition at line 294 of file profile_handle.hh.

Member Function Documentation

AddColumn()

void AddColumn ( const ProfileColumn &  c, char  olc = 'X'  )

inline

Definition at line 334 of file profile_handle.hh.

at() [1/2]

ProfileColumn& at ( size_t  index )

inline

Definition at line 351 of file profile_handle.hh.

at() [2/2]

const ProfileColumn& at ( size_t  index ) const

inline

Definition at line 353 of file profile_handle.hh.

back() [1/2]

ProfileColumn& back ( )

inline

Definition at line 355 of file profile_handle.hh.

back() [2/2]

const ProfileColumn& back ( ) const

inline

Definition at line 357 of file profile_handle.hh.

clear()

void clear ( )

inline

Definition at line 341 of file profile_handle.hh.

columns_begin() [1/2]

ProfileColumnList::iterator columns_begin ( )

inline

Definition at line 369 of file profile_handle.hh.

columns_begin() [2/2]

ProfileColumnList::const_iterator columns_begin ( ) const

inline

Definition at line 371 of file profile_handle.hh.

columns_end() [1/2]

ProfileColumnList::iterator columns_end ( )

inline

Definition at line 370 of file profile_handle.hh.

columns_end() [2/2]

ProfileColumnList::const_iterator columns_end ( ) const

inline

Definition at line 374 of file profile_handle.hh.

empty()

bool empty ( ) const

inline

Definition at line 345 of file profile_handle.hh.

Extract()

ProfileHandlePtr Extract	(	uint	from,
		uint	to
	)		const

Extract subset of profile for columns from until to-1 (0-indexing). Null model is copied from this profile.

Exceptions

Error

if to <= from or to > size().

GetAverageEntropy()

Real GetAverageEntropy

(

)

const

Compute average entropy over all columns.

GetAverageScore()

Real GetAverageScore	(	const ProfileHandle &	other,
		uint	offset = 0
	)		const

Compute score comparing columns other[i] and this->at(i+offset) Column score as in Soeding-2005, null model of this object used, result normalized by other.size()

GetColumns()

const std::vector<ProfileColumn>& GetColumns ( ) const

inline

Definition at line 298 of file profile_handle.hh.

GetNeff()

Real GetNeff ( ) const

inline

Definition at line 316 of file profile_handle.hh.

GetNullModel()

const ProfileColumn& GetNullModel ( ) const

inline

Definition at line 300 of file profile_handle.hh.

GetSequence()

String GetSequence ( ) const

inline

Definition at line 306 of file profile_handle.hh.

operator!=()

bool operator!= ( const ProfileHandle &  other ) const

inline

Definition at line 365 of file profile_handle.hh.

operator==()

bool operator== ( const ProfileHandle &  other ) const

inline

Definition at line 359 of file profile_handle.hh.

operator[]() [1/2]

ProfileColumn& operator[] ( size_t  index )

inline

Definition at line 347 of file profile_handle.hh.

operator[]() [2/2]

const ProfileColumn& operator[] ( size_t  index ) const

inline

Definition at line 349 of file profile_handle.hh.

SetNeff()

void SetNeff ( Real  neff )

inline

Definition at line 318 of file profile_handle.hh.

SetNullModel()

void SetNullModel ( const ProfileColumn &  null_model )

inline

Definition at line 302 of file profile_handle.hh.

SetSequence()

void SetSequence ( const String &  seq )

inline

Definition at line 308 of file profile_handle.hh.

size()

size_t size ( ) const

inline

Definition at line 343 of file profile_handle.hh.

Friends And Related Function Documentation

operator<<

std::ofstream& operator<< ( std::ofstream &  os, ProfileHandle &  prof  )

friend

Definition at line 381 of file profile_handle.hh.

operator>>

std::ifstream& operator>> ( std::ifstream &  is, ProfileHandle &  prof  )

friend

Definition at line 401 of file profile_handle.hh.

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

• build-dev-doc/stage/include/ost/seq/profile_handle.hh