ProfileColumn Class Reference

Defines profile of 20 frequencies for one residue. More...

#include <profile_handle.hh>

Public Member Functions
	ProfileColumn ()
	ProfileColumn (const ProfileColumn &rhs)
ProfileColumn &	operator= (const ProfileColumn &rhs)
Real	GetFreq (char ch) const
void	SetFreq (char ch, Real freq)
bool	operator== (const ProfileColumn &rhs) const
bool	operator!= (const ProfileColumn &rhs) const
Real *	freqs_begin ()
Real *	freqs_end ()
const Real *	freqs_begin () const
const Real *	freqs_end () const
Real	GetEntropy () const
Real	GetScore (const ProfileColumn &other, const ProfileColumn &null_model) const
Static Public Member Functions
static ProfileColumn	BLOSUMNullModel ()
static ProfileColumn	HHblitsNullModel ()
static int	GetIndex (char ch)
Friends
std::ofstream &	operator<< (std::ofstream &os, ProfileColumn &col)
std::ifstream &	operator>> (std::ifstream &is, ProfileColumn &col)

---

Detailed Description

Defines profile of 20 frequencies for one residue.

Frequencies are identified by the one-letter-code for that amino acid. (possible codes: ACDEFGHIKLMNPQRSTVWY)

Definition at line 52 of file profile_handle.hh.

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Constructor & Destructor Documentation

ProfileColumn

(

)

[inline]

Construct a profile with all frequencies set to 0.

Definition at line 56 of file profile_handle.hh.

ProfileColumn

(

const ProfileColumn &

rhs

)

[inline]

Definition at line 60 of file profile_handle.hh.

---

Member Function Documentation

static ProfileColumn BLOSUMNullModel

(

)

[static]

const Real* freqs_begin

(

)

const [inline]

Definition at line 85 of file profile_handle.hh.

Real* freqs_begin

(

)

[inline]

Definition at line 83 of file profile_handle.hh.

const Real* freqs_end

(

)

const [inline]

Definition at line 86 of file profile_handle.hh.

Real* freqs_end

(

)

[inline]

Definition at line 84 of file profile_handle.hh.

Real GetEntropy

(

)

const

Get entropy for this column.

Real GetFreq

(

char

ch

)

const

static int GetIndex

(

char

ch

)

[static]

Translate one-letter-code to index (0-indexing).

Real GetScore	(	const ProfileColumn &	other,
		const ProfileColumn &	null_model
	)			const

Get column score as in Soeding-2005.

static ProfileColumn HHblitsNullModel

(

)

[static]

bool operator!=

(

const ProfileColumn &

rhs

)

const [inline]

Definition at line 81 of file profile_handle.hh.

ProfileColumn& operator=

(

const ProfileColumn &

rhs

)

[inline]

Definition at line 63 of file profile_handle.hh.

bool operator==

(

const ProfileColumn &

rhs

)

const [inline]

Definition at line 78 of file profile_handle.hh.

void SetFreq	(	char	ch,
		Real	freq
	)

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Friends And Related Function Documentation

std::ofstream& operator<<	(	std::ofstream &	os,
		ProfileColumn &	col
	)			[friend]

Definition at line 98 of file profile_handle.hh.

std::ifstream& operator>>	(	std::ifstream &	is,
		ProfileColumn &	col
	)			[friend]

Definition at line 108 of file profile_handle.hh.

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

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