bpp::UserAlphabetIndex1 Class Reference

Alphabet index given by user. More...

#include <Bpp/Seq/AlphabetIndex/UserAlphabetIndex1.h>

Inheritance diagram for bpp::UserAlphabetIndex1:

Collaboration diagram for bpp::UserAlphabetIndex1:

Public Member Functions
	UserAlphabetIndex1 (const Alphabet *alph)
	UserAlphabetIndex1 (const UserAlphabetIndex1 &uAlph)
UserAlphabetIndex1 &	operator= (const UserAlphabetIndex1 &uAlph)
virtual	~UserAlphabetIndex1 ()
UserAlphabetIndex1 *	clone () const
double	getIndex (int state) const
	Get the index associated to a state. More...
void	setIndex (int state, double val)
double	getIndex (const std::string &state) const
	Get the index associated to a state. More...
void	setIndex (const std::string &state, double val)
std::vector< double > *	getIndexVector () const
const Alphabet *	getAlphabet () const
	Get the alphabet associated to this index. More...

Private Attributes
const Alphabet *	alph_
std::vector< double >	index_

Detailed Description

Alphabet index given by user.

Definition at line 54 of file UserAlphabetIndex1.h.

Constructor & Destructor Documentation

UserAlphabetIndex1() [1/2]

bpp::UserAlphabetIndex1::UserAlphabetIndex1 ( const Alphabet *  alph )

inline

Definition at line 62 of file UserAlphabetIndex1.h.

Referenced by clone().

UserAlphabetIndex1() [2/2]

bpp::UserAlphabetIndex1::UserAlphabetIndex1 ( const UserAlphabetIndex1 &  uAlph )

inline

Definition at line 67 of file UserAlphabetIndex1.h.

~UserAlphabetIndex1()

virtual bpp::UserAlphabetIndex1::~UserAlphabetIndex1 ( )

inlinevirtual

Definition at line 79 of file UserAlphabetIndex1.h.

Member Function Documentation

clone()

UserAlphabetIndex1* bpp::UserAlphabetIndex1::clone ( ) const

inlinevirtual

Implements bpp::AlphabetIndex1.

Definition at line 81 of file UserAlphabetIndex1.h.

References UserAlphabetIndex1().

getAlphabet()

const Alphabet* bpp::UserAlphabetIndex1::getAlphabet ( ) const

inlinevirtual

Get the alphabet associated to this index.

Returns

Alphabet The alphabet associated to this index.

Implements bpp::AlphabetIndex1.

Definition at line 106 of file UserAlphabetIndex1.h.

References alph_.

getIndex() [1/2]

double bpp::UserAlphabetIndex1::getIndex ( int  state ) const

inlinevirtual

Get the index associated to a state.

Parameters

state

The state to consider, as a int value.

Returns

The index associated to the state

Implements bpp::AlphabetIndex1.

Definition at line 84 of file UserAlphabetIndex1.h.

References alph_, bpp::Alphabet::getStateIndex(), and index_.

getIndex() [2/2]

double bpp::UserAlphabetIndex1::getIndex ( const std::string &  state ) const

inlinevirtual

Get the index associated to a state.

Parameters

state

The state to consider, as a string value.

Returns

The index associated to the state

Implements bpp::AlphabetIndex1.

Definition at line 94 of file UserAlphabetIndex1.h.

References alph_, bpp::Alphabet::getStateIndex(), and index_.

getIndexVector()

std::vector<double>* bpp::UserAlphabetIndex1::getIndexVector ( ) const

inlinevirtual

Returns

A vector object with all indices.

Implements bpp::AlphabetIndex1.

Definition at line 104 of file UserAlphabetIndex1.h.

References index_.

operator=()

UserAlphabetIndex1& bpp::UserAlphabetIndex1::operator= ( const UserAlphabetIndex1 &  uAlph )

inline

Definition at line 72 of file UserAlphabetIndex1.h.

References alph_, and index_.

setIndex() [1/2]

void bpp::UserAlphabetIndex1::setIndex ( int  state, double  val  )

inline

Definition at line 89 of file UserAlphabetIndex1.h.

References alph_, bpp::Alphabet::getStateIndex(), and index_.

setIndex() [2/2]

void bpp::UserAlphabetIndex1::setIndex ( const std::string &  state, double  val  )

inline

Definition at line 99 of file UserAlphabetIndex1.h.

References alph_, bpp::Alphabet::getStateIndex(), and index_.

Member Data Documentation

alph_

const Alphabet* bpp::UserAlphabetIndex1::alph_

private

Definition at line 58 of file UserAlphabetIndex1.h.

Referenced by getAlphabet(), getIndex(), operator=(), and setIndex().

index_

std::vector<double> bpp::UserAlphabetIndex1::index_

private

Definition at line 59 of file UserAlphabetIndex1.h.

Referenced by getIndex(), getIndexVector(), operator=(), and setIndex().

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

• Bpp/Seq/AlphabetIndex/UserAlphabetIndex1.h