yat  0.20.3pre
Public Member Functions | Protected Member Functions | Friends | Related Functions | List of all members
theplu::yat::omic::GFF Class Referenceabstract

#include <yat/omic/GFF.h>

Inheritance diagram for theplu::yat::omic::GFF:
theplu::yat::omic::GFF2 theplu::yat::omic::GFF3

Public Member Functions

 GFF (void)
 Default Constructor. More...
 
virtual ~GFF (void)
 Destructor.
 
const std::string & attribute (const std::string &key) const
 
const std::map< std::string, std::string > & attributes (void) const
 
const std::string & end (void) const
 
const std::string & phase (void) const
 
const std::string & score (void) const
 
const std::string & seqid (void) const
 
const std::string & source (void) const
 
const std::string & start (void) const
 
const std::string & strand (void) const
 
const std::string & type (void) const
 

Protected Member Functions

const std::vector< std::string > & vec (void) const
 

Friends

std::ostream & operator<< (std::ostream &, const GFF &)
 protected friend
 
bool getline (std::istream &, GFF &)
 

Related Functions

(Note that these are not member functions.)

bool getline (std::istream &is, GFF &gff)
 
std::ostream & operator<< (std::ostream &os, const GFF &gff)
 output operator for GFF More...
 

Detailed Description

Abstract class for GFF2 and GFF3

Since
New in yat 0.8

Constructor & Destructor Documentation

◆ GFF()

theplu::yat::omic::GFF::GFF ( void  )

Default Constructor.

Constructs an empty GFF. Class need to be loaded with function getline before calling any other functions.

See also
getline(std::istream& is, GFF& gff);

Member Function Documentation

◆ attribute()

const std::string& theplu::yat::omic::GFF::attribute ( const std::string &  key) const
Returns
attribute value for attribute key

If attribute with key key has several values, the values are given appended together comma-separated as it appears in file.

◆ attributes()

const std::map<std::string, std::string>& theplu::yat::omic::GFF::attributes ( void  ) const
Returns
map containing all attributes
See also
attribute(const std::string& key) const

◆ end()

const std::string& theplu::yat::omic::GFF::end ( void  ) const
Returns
end string

◆ phase()

const std::string& theplu::yat::omic::GFF::phase ( void  ) const
Returns
phase string

◆ score()

const std::string& theplu::yat::omic::GFF::score ( void  ) const
Returns
score string

◆ seqid()

const std::string& theplu::yat::omic::GFF::seqid ( void  ) const
Returns
seqid string

◆ source()

const std::string& theplu::yat::omic::GFF::source ( void  ) const
Returns
source string

◆ start()

const std::string& theplu::yat::omic::GFF::start ( void  ) const
Returns
start string

◆ strand()

const std::string& theplu::yat::omic::GFF::strand ( void  ) const
Returns
strand string

◆ type()

const std::string& theplu::yat::omic::GFF::type ( void  ) const
Returns
type string

◆ vec()

const std::vector<std::string>& theplu::yat::omic::GFF::vec ( void  ) const
protected
Returns
vector with the 9 elements

Friends And Related Function Documentation

◆ getline()

bool getline ( std::istream &  is,
GFF gff 
)
related
Returns
true iff a GFF object was loaded successfully

Empty lines and lines starting with '#' are ignored.

Since
New in yat 0.8

◆ operator<<()

std::ostream & operator<< ( std::ostream &  os,
const GFF gff 
)
related

output operator for GFF

Since
New in yat 0.8

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

Generated on Sat Feb 18 2023 03:31:44 for yat by  doxygen 1.8.14