OpenStructure
|
#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) |
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.
|
inline |
Construct a profile with all frequencies set to 0.
Definition at line 172 of file profile_handle.hh.
|
inline |
Definition at line 176 of file profile_handle.hh.
|
static |
|
inline |
Definition at line 227 of file profile_handle.hh.
|
inline |
Definition at line 229 of file profile_handle.hh.
|
inline |
Definition at line 228 of file profile_handle.hh.
|
inline |
Definition at line 230 of file profile_handle.hh.
Real GetEntropy | ( | ) | const |
Get entropy for this column.
Real GetFreq | ( | char | ch | ) | const |
|
inline |
Definition at line 201 of file profile_handle.hh.
|
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.
|
inline |
Definition at line 208 of file profile_handle.hh.
|
static |
|
inline |
Definition at line 225 of file profile_handle.hh.
|
inline |
Definition at line 183 of file profile_handle.hh.
|
inline |
Definition at line 222 of file profile_handle.hh.
void SetFreq | ( | char | ch, |
Real | freq | ||
) |
|
inline |
Definition at line 197 of file profile_handle.hh.
|
friend |
Definition at line 242 of file profile_handle.hh.
|
friend |
Definition at line 262 of file profile_handle.hh.