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MDAT::Domain Class Reference

Class to represent a domain. More...

#include <Domain.hpp>

Public Member Functions

Constructores & Destructors
 Domain ()
 Standard domain constructor.
 
 Domain (const std::string &name, const std::string &accession, size_t seq_start, size_t seq_end)
 Constructor with minimal Domain information. More...
 
 Domain (const std::string &name, const std::string &accession, size_t seq_start, size_t seq_end, size_t env_start, size_t env_end, size_t hmm_start, size_t hmm_end, double evalue, int id=-1)
 Complete Domain constructor. More...
 
virtual ~Domain ()
 Destructor.
 
Basic functions
std::string name () const
 Returns the name of the domain. More...
 
std::string accession () const
 Returns the accesion number of the domain. More...
 
void accession (const std::string &accession)
 Returns the accesion number of the domain. More...
 
size_t seq_start () const
 Returns the first position of the domain. More...
 
size_t seq_end () const
 Returns the the last position of the domain. More...
 
size_t env_start () const
 Returns the first position of the envelope. More...
 
size_t env_end () const
 Returns the last position of the envelope. More...
 
void seq_start (size_t val)
 Sets the first position of the domain. More...
 
void seq_end (size_t val)
 Sets the last position of the domain. More...
 
void env_start (size_t val)
 Sets the first position of the envelope. More...
 
void env_end (size_t val)
 Sets the last position of the envelope. More...
 
size_t hmm_start () const
 Returns the first position of the HMM match. More...
 
size_t hmm_end () const
 Returns the last position of the HMM match. More...
 
void hmm_start (size_t val)
 Sets the first position of the HMM match. More...
 
void hmm_end (size_t val)
 Sets the last position of the HMM match. More...
 
void repeated (int val)
 Sets how often the domain is repeated. More...
 
int repeated () const
 Returns how often the domain is repeated. More...
 
double evalue () const
 Returns the evalue of the domain. More...
 
int id () const
 Returns the id of the domain. More...
 
void id (int val)
 Sets the id of the domain. More...
 
size_t seq_length () const
 Returns the length of the domain. More...
 
void seq_length (size_t length)
 
size_t env_length () const
 Returns the length of the evelope. More...
 
size_t hmm_length () const
 Returns the length of the HMM match. More...
 
int ori_pos () const
 The original position of the domain in a domain architecture. More...
 
void ori_pos (int pos)
 Sets the original position of the domain in a domain architecture. More...
 

Detailed Description

Class to represent a domain.

The class is mainly designed for Pfam domains. It can store all the necessary values.

Constructor & Destructor Documentation

MDAT::Domain::Domain ( const std::string &  name,
const std::string &  accession,
size_t  seq_start,
size_t  seq_end 
)

Constructor with minimal Domain information.

Parameters
nameName of the domain.
accessionThe accession number.
seq_startFirst position of the domain.
seq_endLast position of the domain.
MDAT::Domain::Domain ( const std::string &  name,
const std::string &  accession,
size_t  seq_start,
size_t  seq_end,
size_t  env_start,
size_t  env_end,
size_t  hmm_start,
size_t  hmm_end,
double  evalue,
int  id = -1 
)

Complete Domain constructor.

Parameters
nameName of the domain.
accessionThe accession number.
seq_startFirst position of the domain.
seq_endLast position of the domain.
env_startFirst position of the envelope.
env_endLast position of the envelope.
hmm_startFirst position of the HMM match.
hmm_endLast position of hte HMM match.
evalueThe evalue of the the domain.
idThe id of the domain.

Member Function Documentation

std::string MDAT::Domain::accession ( ) const
inline

Returns the accesion number of the domain.

Returns
The accession number.
void MDAT::Domain::accession ( const std::string &  accession)
inline

Returns the accesion number of the domain.

Returns
The accession number.
size_t MDAT::Domain::env_end ( ) const
inline

Returns the last position of the envelope.

Returns
The last position of the envelope.
void MDAT::Domain::env_end ( size_t  val)
inline

Sets the last position of the envelope.

Parameters
valThe new value.
size_t MDAT::Domain::env_length ( ) const
inline

Returns the length of the evelope.

Returns
The envelope length.
size_t MDAT::Domain::env_start ( ) const
inline

Returns the first position of the envelope.

Returns
The first position of the envelope.
void MDAT::Domain::env_start ( size_t  val)
inline

Sets the first position of the envelope.

Parameters
valThe new value.
double MDAT::Domain::evalue ( ) const
inline

Returns the evalue of the domain.

Returns
The evalue.
size_t MDAT::Domain::hmm_end ( ) const
inline

Returns the last position of the HMM match.

Returns
The the last position.
void MDAT::Domain::hmm_end ( size_t  val)
inline

Sets the last position of the HMM match.

Parameters
valThe new value.
size_t MDAT::Domain::hmm_length ( ) const
inline

Returns the length of the HMM match.

Returns
Length of the HMM match.
size_t MDAT::Domain::hmm_start ( ) const
inline

Returns the first position of the HMM match.

Returns
The first position.
void MDAT::Domain::hmm_start ( size_t  val)
inline

Sets the first position of the HMM match.

Parameters
valThe new value.
int MDAT::Domain::id ( ) const
inline

Returns the id of the domain.

Returns
The id of the domain.
void MDAT::Domain::id ( int  val)
inline

Sets the id of the domain.

Parameters
valThe id of the domain.
std::string MDAT::Domain::name ( ) const
inline

Returns the name of the domain.

Returns
The name.
int MDAT::Domain::ori_pos ( ) const
inline

The original position of the domain in a domain architecture.

Returns
The original position.
void MDAT::Domain::ori_pos ( int  pos)
inline

Sets the original position of the domain in a domain architecture.

Parameters
posThe position.
void MDAT::Domain::repeated ( int  val)
inline

Sets how often the domain is repeated.

Parameters
valThe number of repeates.
int MDAT::Domain::repeated ( ) const
inline

Returns how often the domain is repeated.

Returns
The number of repeats.
size_t MDAT::Domain::seq_end ( ) const
inline

Returns the the last position of the domain.

Returns
The last position of the domain.
void MDAT::Domain::seq_end ( size_t  val)
inline

Sets the last position of the domain.

Parameters
valThe new value.
size_t MDAT::Domain::seq_length ( ) const
inline

Returns the length of the domain.

Returns
Domain length.
size_t MDAT::Domain::seq_start ( ) const
inline

Returns the first position of the domain.

Returns
The first position of the domain.
void MDAT::Domain::seq_start ( size_t  val)
inline

Sets the first position of the domain.

Parameters
valThe new value.