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
void	clear ()
size_t	size () const
bool	empty () const
void	push_back (const ProfileColumn &c)
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::const_iterator	columns_end () const
ProfileColumnList::iterator	columns_end ()
ProfileColumnList::const_iterator	columns_begin () const
ProfileColumnList::iterator	columns_begin ()
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 123 of file profile_handle.hh.

---

Constructor & Destructor Documentation

ProfileHandle

(

)

[inline]

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

Definition at line 126 of file profile_handle.hh.

---

Member Function Documentation

const ProfileColumn& at

(

size_t

index

)

const [inline]

Definition at line 164 of file profile_handle.hh.

ProfileColumn& at

(

size_t

index

)

[inline]

Definition at line 162 of file profile_handle.hh.

void clear

(

)

[inline]

Definition at line 150 of file profile_handle.hh.

ProfileColumnList::iterator columns_begin

(

)

[inline]

Definition at line 177 of file profile_handle.hh.

ProfileColumnList::const_iterator columns_begin

(

)

const [inline]

Definition at line 176 of file profile_handle.hh.

ProfileColumnList::iterator columns_end

(

)

[inline]

Definition at line 175 of file profile_handle.hh.

ProfileColumnList::const_iterator columns_end

(

)

const [inline]

Definition at line 174 of file profile_handle.hh.

bool empty

(

)

const [inline]

Definition at line 154 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.

const std::vector<ProfileColumn>& GetColumns

(

)

const [inline]

Definition at line 130 of file profile_handle.hh.

const ProfileColumn& GetNullModel

(

)

const [inline]

Definition at line 132 of file profile_handle.hh.

String GetSequence

(

)

const [inline]

Definition at line 136 of file profile_handle.hh.

bool operator!=

(

const ProfileHandle &

other

)

const [inline]

Definition at line 172 of file profile_handle.hh.

bool operator==

(

const ProfileHandle &

other

)

const [inline]

Definition at line 166 of file profile_handle.hh.

const ProfileColumn& operator[]

(

size_t

index

)

const [inline]

Definition at line 160 of file profile_handle.hh.

ProfileColumn& operator[]

(

size_t

index

)

[inline]

Definition at line 158 of file profile_handle.hh.

void push_back

(

const ProfileColumn &

c

)

[inline]

Definition at line 156 of file profile_handle.hh.

void SetNullModel

(

const ProfileColumn &

null_model

)

[inline]

Definition at line 134 of file profile_handle.hh.

void SetSequence

(

const String &

seq

)

[inline]

Definition at line 138 of file profile_handle.hh.

size_t size

(

)

const [inline]

Definition at line 152 of file profile_handle.hh.

---

Friends And Related Function Documentation

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

Definition at line 182 of file profile_handle.hh.

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

Definition at line 202 of file profile_handle.hh.

---

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

• stage/include/ost/seq/profile_handle.hh