ProfileColumn Class Reference

#include <profile_handle.hh>

Public Member Functions
	ProfileColumn ()
	ProfileColumn (const ProfileColumn &rhs)
ProfileColumn &	operator= (const ProfileColumn &rhs)
void	SetHMMData (HMMDataPtr p)
HMMDataPtr	GetHMMData () const
Real	GetTransProb (HMMTransition transition) const
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 168 of file profile_handle.hh.

Constructor & Destructor Documentation

ProfileColumn() [1/2]

ProfileColumn ( )

inline

Construct a profile with all frequencies set to 0.

Definition at line 172 of file profile_handle.hh.

ProfileColumn() [2/2]

ProfileColumn ( const ProfileColumn &  rhs )

inline

Definition at line 176 of file profile_handle.hh.

Member Function Documentation

BLOSUMNullModel()

static ProfileColumn BLOSUMNullModel ( )

static

freqs_begin() [1/2]

Real* freqs_begin ( )

inline

Definition at line 227 of file profile_handle.hh.

freqs_begin() [2/2]

const Real* freqs_begin ( ) const

inline

Definition at line 229 of file profile_handle.hh.

freqs_end() [1/2]

Real* freqs_end ( )

inline

Definition at line 228 of file profile_handle.hh.

freqs_end() [2/2]

const Real* freqs_end ( ) const

inline

Definition at line 230 of file profile_handle.hh.

GetEntropy()

Real GetEntropy

(

)

const

Get entropy for this column.

GetFreq()

Real GetFreq

(

char

ch

)

const

GetHMMData()

HMMDataPtr GetHMMData ( ) const

inline

Definition at line 201 of file profile_handle.hh.

GetIndex()

static int GetIndex ( char  ch )

static

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

GetScore()

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

Get column score as in Soeding-2005.

GetTransProb()

Real GetTransProb ( HMMTransition  transition ) const

inline

Definition at line 208 of file profile_handle.hh.

HHblitsNullModel()

static ProfileColumn HHblitsNullModel ( )

static

operator!=()

bool operator!= ( const ProfileColumn &  rhs ) const

inline

Definition at line 225 of file profile_handle.hh.

operator=()

ProfileColumn& operator= ( const ProfileColumn &  rhs )

inline

Definition at line 183 of file profile_handle.hh.

operator==()

bool operator== ( const ProfileColumn &  rhs ) const

inline

Definition at line 222 of file profile_handle.hh.

SetFreq()

void SetFreq	(	char	ch,
		Real	freq
	)

SetHMMData()

void SetHMMData ( HMMDataPtr  p )

inline

Definition at line 197 of file profile_handle.hh.

Friends And Related Function Documentation

operator<<

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

friend

Definition at line 242 of file profile_handle.hh.

operator>>

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

friend

Definition at line 262 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