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 |
Real | GetAverageScore (const ProfileHandle &other, uint offset=0) const |
void | AddColumn (const ProfileColumn &c, char olc='X') |
void | clear () |
size_t | size () const |
bool | empty () const |
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::iterator | columns_begin () |
ProfileColumnList::iterator | columns_end () |
ProfileColumnList::const_iterator | columns_begin () const |
ProfileColumnList::const_iterator | columns_end () const |
Friends | |
std::ofstream & | operator<< (std::ofstream &os, ProfileHandle &prof) |
std::ifstream & | operator>> (std::ifstream &is, ProfileHandle &prof) |
Provides a profile for a sequence.
Properties:
Definition at line 129 of file profile_handle.hh.
ProfileHandle | ( | ) | [inline] |
Constructs an empty profile handle (sequence = '', 0 columns).
Definition at line 132 of file profile_handle.hh.
void AddColumn | ( | const ProfileColumn & | c, | |
char | olc = 'X' | |||
) | [inline] |
Definition at line 168 of file profile_handle.hh.
const ProfileColumn& at | ( | size_t | index | ) | const [inline] |
Definition at line 187 of file profile_handle.hh.
ProfileColumn& at | ( | size_t | index | ) | [inline] |
Definition at line 185 of file profile_handle.hh.
void clear | ( | ) | [inline] |
Definition at line 175 of file profile_handle.hh.
ProfileColumnList::const_iterator columns_begin | ( | ) | const [inline] |
Definition at line 201 of file profile_handle.hh.
ProfileColumnList::iterator columns_begin | ( | ) | [inline] |
Definition at line 199 of file profile_handle.hh.
ProfileColumnList::const_iterator columns_end | ( | ) | const [inline] |
Definition at line 204 of file profile_handle.hh.
ProfileColumnList::iterator columns_end | ( | ) | [inline] |
Definition at line 200 of file profile_handle.hh.
bool empty | ( | ) | const [inline] |
Definition at line 179 of file profile_handle.hh.
ProfileHandlePtr Extract | ( | uint | from, | |
uint | to | |||
) |
Real GetAverageEntropy | ( | ) | const |
Compute average entropy over all columns.
Real GetAverageScore | ( | const ProfileHandle & | other, | |
uint | offset = 0 | |||
) | const |
Compute score comparing columns other[i] and this->at(i+offset) Column score as in Soeding-2005, null model of this object used, result normalized by other.size().
const std::vector<ProfileColumn>& GetColumns | ( | ) | const [inline] |
Definition at line 136 of file profile_handle.hh.
const ProfileColumn& GetNullModel | ( | ) | const [inline] |
Definition at line 138 of file profile_handle.hh.
String GetSequence | ( | ) | const [inline] |
Definition at line 144 of file profile_handle.hh.
bool operator!= | ( | const ProfileHandle & | other | ) | const [inline] |
Definition at line 195 of file profile_handle.hh.
bool operator== | ( | const ProfileHandle & | other | ) | const [inline] |
Definition at line 189 of file profile_handle.hh.
const ProfileColumn& operator[] | ( | size_t | index | ) | const [inline] |
Definition at line 183 of file profile_handle.hh.
ProfileColumn& operator[] | ( | size_t | index | ) | [inline] |
Definition at line 181 of file profile_handle.hh.
void SetNullModel | ( | const ProfileColumn & | null_model | ) | [inline] |
Definition at line 140 of file profile_handle.hh.
void SetSequence | ( | const String & | seq | ) | [inline] |
Definition at line 146 of file profile_handle.hh.
size_t size | ( | ) | const [inline] |
Definition at line 177 of file profile_handle.hh.
std::ofstream& operator<< | ( | std::ofstream & | os, | |
ProfileHandle & | prof | |||
) | [friend] |
Definition at line 211 of file profile_handle.hh.
std::ifstream& operator>> | ( | std::ifstream & | is, | |
ProfileHandle & | prof | |||
) | [friend] |
Definition at line 231 of file profile_handle.hh.