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Public Member Functions | Static Public Member Functions | Friends
ProfileColumn Class Reference

#include <profile_handle.hh>

Public Member Functions

 ProfileColumn ()
 
 ProfileColumn (const ProfileColumn &rhs)
 
ProfileColumnoperator= (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
 
Realfreqs_begin ()
 
Realfreqs_end ()
 
const Realfreqs_begin () const
 
const Realfreqs_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 ( )
inline

Construct a profile with all frequencies set to 0.

Definition at line 172 of file profile_handle.hh.

ProfileColumn ( const ProfileColumn rhs)
inline

Definition at line 176 of file profile_handle.hh.

Member Function Documentation

static ProfileColumn BLOSUMNullModel ( )
static
Real* freqs_begin ( )
inline

Definition at line 227 of file profile_handle.hh.

const Real* freqs_begin ( ) const
inline

Definition at line 229 of file profile_handle.hh.

Real* freqs_end ( )
inline

Definition at line 228 of file profile_handle.hh.

const Real* freqs_end ( ) const
inline

Definition at line 230 of file profile_handle.hh.

Real GetEntropy ( ) const

Get entropy for this column.

Real GetFreq ( char  ch) const
HMMDataPtr GetHMMData ( ) const
inline

Definition at line 201 of file profile_handle.hh.

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.

Real GetTransProb ( HMMTransition  transition) const
inline

Definition at line 208 of file profile_handle.hh.

static ProfileColumn HHblitsNullModel ( )
static
bool operator!= ( const ProfileColumn rhs) const
inline

Definition at line 225 of file profile_handle.hh.

ProfileColumn& operator= ( const ProfileColumn rhs)
inline

Definition at line 183 of file profile_handle.hh.

bool operator== ( const ProfileColumn rhs) const
inline

Definition at line 222 of file profile_handle.hh.

void SetFreq ( char  ch,
Real  freq 
)
void SetHMMData ( HMMDataPtr  p)
inline

Definition at line 197 of file profile_handle.hh.

Friends And Related Function Documentation

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

Definition at line 242 of file profile_handle.hh.

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

Definition at line 262 of file profile_handle.hh.


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