ProfileHandle Class Reference

Provides a profile for a sequence. More...

#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.

const ProfileColumn& at

(

size_t

index

)

const [inline]

Definition at line 187 of file profile_handle.hh.

ProfileColumn& at

(

size_t

index

)

[inline]

Definition at line 185 of file profile_handle.hh.

void clear

(

)

[inline]

Definition at line 175 of file profile_handle.hh.

ProfileColumnList::const_iterator columns_begin

(

)

const [inline]

Definition at line 201 of file profile_handle.hh.

ProfileColumnList::iterator columns_begin

(

)

[inline]

Definition at line 199 of file profile_handle.hh.

ProfileColumnList::const_iterator columns_end

(

)

const [inline]

Definition at line 204 of file profile_handle.hh.

ProfileColumnList::iterator columns_end

(

)

[inline]

Definition at line 200 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.

const ProfileColumn& operator[]

(

size_t

index

)

const [inline]

Definition at line 183 of file profile_handle.hh.

ProfileColumn& operator[]

(

size_t

index

)

[inline]

Definition at line 181 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