ProfileHandle Class Reference

Provides a profile for a sequence. More...

#include <profile_handle.hh>

Public Member Functions

 ProfileHandle ()
const std::vector
< ProfileColumn > & 
GetColumns () const
const ProfileColumnGetNullModel () 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
ProfileColumnoperator[] (size_t index)
const ProfileColumnoperator[] (size_t index) const
ProfileColumnat (size_t index)
const ProfileColumnat (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)

Detailed Description

Provides a profile for a sequence.

Properties:

Definition at line 129 of file profile_handle.hh.


Constructor & Destructor Documentation

ProfileHandle (  )  [inline]

Constructs an empty profile handle (sequence = '', 0 columns).

Definition at line 132 of file profile_handle.hh.


Member Function Documentation

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 
)

Extract subset of profile for columns from until to-1 (0-indexing). Null model is copied from this profile.

Exceptions:
Error if to <= from or to > size().
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.


Friends And Related Function Documentation

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.


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