MDA
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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... | |
Class to represent a domain.
The class is mainly designed for Pfam domains. It can store all the necessary values.
MDAT::Domain::Domain | ( | const std::string & | name, |
const std::string & | accession, | ||
size_t | seq_start, | ||
size_t | seq_end | ||
) |
Constructor with minimal Domain information.
name | Name of the domain. |
accession | The accession number. |
seq_start | First position of the domain. |
seq_end | Last 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 |
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) |
Complete Domain constructor.
name | Name of the domain. |
accession | The accession number. |
seq_start | First position of the domain. |
seq_end | Last position of the domain. |
env_start | First position of the envelope. |
env_end | Last position of the envelope. |
hmm_start | First position of the HMM match. |
hmm_end | Last position of hte HMM match. |
evalue | The evalue of the the domain. |
id | The id of the domain. |
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Returns the accesion number of the domain.
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Returns the accesion number of the domain.
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Returns the last position of the envelope.
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Sets the last position of the envelope.
val | The new value. |
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Returns the length of the evelope.
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Returns the first position of the envelope.
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Sets the first position of the envelope.
val | The new value. |
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Returns the evalue of the domain.
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Returns the last position of the HMM match.
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Sets the last position of the HMM match.
val | The new value. |
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Returns the first position of the HMM match.
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Sets the first position of the HMM match.
val | The new value. |
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Returns the id of the domain.
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Sets the id of the domain.
val | The id of the domain. |
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Returns the name of the domain.
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The original position of the domain in a domain architecture.
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Sets the original position of the domain in a domain architecture.
pos | The position. |
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Sets how often the domain is repeated.
val | The number of repeates. |
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Returns how often the domain is repeated.
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Returns the the last position of the domain.
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Sets the last position of the domain.
val | The new value. |
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Returns the length of the domain.
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Returns the first position of the domain.
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Sets the first position of the domain.
val | The new value. |