#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)

ProfileHandlePtr	Extract (uint from, uint to)

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

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 129 of file profile_handle.hh.

Constructor & Destructor Documentation

ProfileHandle ( )

inline

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

Definition at line 132 of file profile_handle.hh.

Member Function Documentation

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

inline

Definition at line 168 of file profile_handle.hh.

ProfileColumn& at ( size_t index )

inline

Definition at line 185 of file profile_handle.hh.

const ProfileColumn& at ( size_t index ) const

inline

Definition at line 187 of file profile_handle.hh.

void clear ( )

inline

Definition at line 175 of file profile_handle.hh.

ProfileColumnList::iterator columns_begin ( )

inline

Definition at line 199 of file profile_handle.hh.

ProfileColumnList::const_iterator columns_begin ( ) const

inline

Definition at line 201 of file profile_handle.hh.

ProfileColumnList::iterator columns_end ( )

inline

Definition at line 200 of file profile_handle.hh.

ProfileColumnList::const_iterator columns_end ( ) const

inline

Definition at line 204 of file profile_handle.hh.

bool empty ( ) const

inline

Definition at line 179 of file profile_handle.hh.

ProfileHandlePtr Extract	(	uint	from,
		uint	to
	)

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().

Real GetAverageEntropy ( ) const

Compute average entropy over all columns.

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()

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

inline

Definition at line 136 of file profile_handle.hh.

const ProfileColumn& GetNullModel ( ) const

inline

Definition at line 138 of file profile_handle.hh.

String GetSequence ( ) const

inline

Definition at line 144 of file profile_handle.hh.

bool operator!= ( const ProfileHandle & other ) const

inline

Definition at line 195 of file profile_handle.hh.

bool operator== ( const ProfileHandle & other ) const

inline

Definition at line 189 of file profile_handle.hh.

ProfileColumn& operator[] ( size_t index )

inline

Definition at line 181 of file profile_handle.hh.

const ProfileColumn& operator[] ( size_t index ) const

inline

Definition at line 183 of file profile_handle.hh.

void SetNullModel ( const ProfileColumn & null_model )

inline

Definition at line 140 of file profile_handle.hh.

void SetSequence ( const String & seq )

inline

Definition at line 146 of file profile_handle.hh.

size_t size ( ) const

inline

Definition at line 177 of file profile_handle.hh.

Friends And Related Function Documentation

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

friend

Definition at line 211 of file profile_handle.hh.

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

friend

Definition at line 231 of file profile_handle.hh.

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

stage/include/ost/seq/profile_handle.hh

Public Member Functions

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation