bpp-seq3  3.0.0
Public Member Functions | Private Attributes | List of all members
bpp::AlphabetNumericState Class Reference

States that do have a double value. More...

#include <Bpp/Seq/Alphabet/AlphabetNumericState.h>

+ Inheritance diagram for bpp::AlphabetNumericState:
+ Collaboration diagram for bpp::AlphabetNumericState:

Public Member Functions

 AlphabetNumericState (int num, double value, const std::string &letter, const std::string &name)
 
virtual ~AlphabetNumericState ()
 
double getValue () const
 Get the state value. More...
 
void setValue (double value)
 Set the state value. More...
 
int getNum () const
 Get the state's number. More...
 
void setNum (int num)
 Set the state's number. More...
 
const std::string & getLetter () const
 Get the letter(s) corresponding to the state. More...
 
void setLetter (const std::string &letter)
 Set the letter(s) of the state. More...
 
const std::string & getName () const
 Get the name of the state. More...
 
void setName (const std::string &name)
 Set the name of the state. More...
 
bool operator== (AlphabetState &l2)
 operator == More...
 
The Clonable interface.
AlphabetNumericState * clone () const
 

Private Attributes

double value_
 
int num_
 
std::string letter_
 
std::string name_
 

Detailed Description

States that do have a double value.

Author
Laurent Guéguen

Definition at line 26 of file AlphabetNumericState.h.

Constructor & Destructor Documentation

◆ AlphabetNumericState()

bpp::AlphabetNumericState::AlphabetNumericState ( int  num,
double  value,
const std::string &  letter,
const std::string &  name 
)
inline

Definition at line 32 of file AlphabetNumericState.h.

Referenced by clone().

◆ ~AlphabetNumericState()

virtual bpp::AlphabetNumericState::~AlphabetNumericState ( )
inlinevirtual

Definition at line 35 of file AlphabetNumericState.h.

Member Function Documentation

◆ clone()

AlphabetNumericState* bpp::AlphabetNumericState::clone ( ) const
inlinevirtual

Implements bpp::Clonable.

Definition at line 42 of file AlphabetNumericState.h.

References AlphabetNumericState().

◆ getLetter()

const std::string& bpp::AlphabetState::getLetter ( ) const
inlineinherited

Get the letter(s) corresponding to the state.

The letter is a string because it may more than one char (for instance: codon).

Returns
The state's letter.

Definition at line 63 of file AlphabetState.h.

References bpp::AlphabetState::letter_.

Referenced by bpp::CaseMaskedAlphabet::CaseMaskedAlphabet(), bpp::LexicalAlphabet::getAlphabetType(), bpp::AbstractAlphabet::getCharCodeAt(), bpp::RNY::intToChar(), bpp::LetterAlphabet::registerState(), bpp::LetterAlphabet::setState(), and bpp::AbstractAlphabet::updateMaps_().

◆ getName()

const std::string& bpp::AlphabetState::getName ( ) const
inlineinherited

Get the name of the state.

Returns
The full name of the state (i.e. Adenine).

Definition at line 76 of file AlphabetState.h.

References bpp::AlphabetState::name_.

Referenced by bpp::CaseMaskedAlphabet::CaseMaskedAlphabet(), and bpp::WordAlphabet::getName().

◆ getNum()

int bpp::AlphabetState::getNum ( ) const
inlineinherited

Get the state's number.

Returns
The state's number (i.e. -1 for gap (-)).

Definition at line 47 of file AlphabetState.h.

References bpp::AlphabetState::num_.

Referenced by bpp::CaseMaskedAlphabet::CaseMaskedAlphabet(), bpp::AlphabetTools::checkAlphabetCodingSize(), bpp::AbstractAlphabet::getIntCodeAt(), bpp::NucleicAlphabet::getOverlap(), bpp::AlphabetState::operator==(), bpp::LetterAlphabet::registerState(), bpp::LetterAlphabet::setState(), bpp::NucleicAlphabet::subtract(), and bpp::AbstractAlphabet::updateMaps_().

◆ getValue()

double bpp::AlphabetNumericState::getValue ( ) const
inline

Get the state value.

Returns
The state value

Definition at line 50 of file AlphabetNumericState.h.

References value_.

Referenced by bpp::NumericAlphabet::remap().

◆ operator==()

bool bpp::AlphabetState::operator== ( AlphabetState &  l2)
inlineinherited

operator ==

Comparison is done on state num

Definition at line 89 of file AlphabetState.h.

References bpp::AlphabetState::getNum().

◆ setLetter()

void bpp::AlphabetState::setLetter ( const std::string &  letter)
inlineinherited

Set the letter(s) of the state.

Parameters
letterThe state's letter.

Definition at line 69 of file AlphabetState.h.

References bpp::AlphabetState::letter_.

◆ setName()

void bpp::AlphabetState::setName ( const std::string &  name)
inlineinherited

Set the name of the state.

Parameters
nameThe state's name

Definition at line 82 of file AlphabetState.h.

References bpp::AlphabetState::name_.

◆ setNum()

void bpp::AlphabetState::setNum ( int  num)
inlineinherited

Set the state's number.

Parameters
numThe state's number.

Definition at line 53 of file AlphabetState.h.

References bpp::AlphabetState::num_.

◆ setValue()

void bpp::AlphabetNumericState::setValue ( double  value)
inline

Set the state value.

Parameters
valueThe given state value.

Definition at line 56 of file AlphabetNumericState.h.

References value_.

Member Data Documentation

◆ letter_

std::string bpp::AlphabetState::letter_
privateinherited

Definition at line 25 of file AlphabetState.h.

Referenced by bpp::AlphabetState::getLetter(), and bpp::AlphabetState::setLetter().

◆ name_

std::string bpp::AlphabetState::name_
privateinherited

Definition at line 26 of file AlphabetState.h.

Referenced by bpp::AlphabetState::getName(), and bpp::AlphabetState::setName().

◆ num_

int bpp::AlphabetState::num_
privateinherited

Definition at line 24 of file AlphabetState.h.

Referenced by bpp::AlphabetState::getNum(), and bpp::AlphabetState::setNum().

◆ value_

double bpp::AlphabetNumericState::value_
private

Definition at line 29 of file AlphabetNumericState.h.

Referenced by getValue(), and setValue().

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