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

Simple dissimilarity distance. More...

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

+ Inheritance diagram for bpp::SimpleIndexDistance:
+ Collaboration diagram for bpp::SimpleIndexDistance:

Public Member Functions

 SimpleIndexDistance (std::shared_ptr< AlphabetIndex1 > index)
 
 SimpleIndexDistance (const SimpleIndexDistance &sid)
 
SimpleIndexDistance & operator= (const SimpleIndexDistance &sid)
 
virtual ~SimpleIndexDistance ()
 
double getIndex (int state1, int state2) const override
 Get the index associated to a pair of states. More...
 
double getIndex (const std::string &state1, const std::string &state2) const override
 Get the index associated to a pair of states. More...
 
std::shared_ptr< const Alphabet > getAlphabet () const override
 Get the alphabet associated to this index. More...
 
const Alphabet & alphabet () const override
 Get the alphabet associated to this index. More...
 
SimpleIndexDistance * clone () const override
 
const Matrix< double > & getIndexMatrix () const override
 
void setSymmetric (bool yn)
 
bool isSymmetric () const override
 
std::shared_ptr< const AlphabetIndex1 > getAlphabetIndex1 () const
 

Protected Member Functions

void computeIndexMatrix_ ()
 

Private Attributes

std::shared_ptr< AlphabetIndex1 > index_
 
size_t size_
 
RowMatrix< double > indexMatrix_
 
bool sym_
 

Detailed Description

Simple dissimilarity distance.

Take a one-dimensional index and return the difference between the indexes of two states.

Definition at line 27 of file SimpleIndexDistance.h.

Constructor & Destructor Documentation

◆ SimpleIndexDistance() [1/2]

bpp::SimpleIndexDistance::SimpleIndexDistance ( std::shared_ptr< AlphabetIndex1 >  index)
inline

Definition at line 37 of file SimpleIndexDistance.h.

References computeIndexMatrix_().

Referenced by clone().

◆ SimpleIndexDistance() [2/2]

bpp::SimpleIndexDistance::SimpleIndexDistance ( const SimpleIndexDistance &  sid)
inline

Definition at line 46 of file SimpleIndexDistance.h.

◆ ~SimpleIndexDistance()

virtual bpp::SimpleIndexDistance::~SimpleIndexDistance ( )
inlinevirtual

Definition at line 62 of file SimpleIndexDistance.h.

Member Function Documentation

◆ alphabet()

const Alphabet& bpp::SimpleIndexDistance::alphabet ( ) const
inlineoverridevirtual

Get the alphabet associated to this index.

Returns
Alphabet The alphabet associated to this index.

Implements bpp::AlphabetIndex2.

Definition at line 77 of file SimpleIndexDistance.h.

References index_.

◆ clone()

SimpleIndexDistance* bpp::SimpleIndexDistance::clone ( ) const
inlineoverridevirtual

Implements bpp::AlphabetIndex2.

Definition at line 79 of file SimpleIndexDistance.h.

References SimpleIndexDistance().

◆ computeIndexMatrix_()

void bpp::SimpleIndexDistance::computeIndexMatrix_ ( )
inlineprotected

Definition at line 84 of file SimpleIndexDistance.h.

References getAlphabet(), index_, indexMatrix_, size_, and sym_.

Referenced by setSymmetric(), and SimpleIndexDistance().

◆ getAlphabet()

std::shared_ptr<const Alphabet> bpp::SimpleIndexDistance::getAlphabet ( ) const
inlineoverridevirtual

Get the alphabet associated to this index.

Returns
Alphabet The alphabet associated to this index.

Implements bpp::AlphabetIndex2.

Definition at line 75 of file SimpleIndexDistance.h.

References index_.

Referenced by computeIndexMatrix_(), and getIndex().

◆ getAlphabetIndex1()

std::shared_ptr<const AlphabetIndex1> bpp::SimpleIndexDistance::getAlphabetIndex1 ( ) const
inline
Returns
The AlphabetIndex1 object associated to this object.

Definition at line 109 of file SimpleIndexDistance.h.

References index_.

◆ getIndex() [1/2]

double bpp::SimpleIndexDistance::getIndex ( const std::string &  state1,
const std::string &  state2 
) const
inlineoverridevirtual

Get the index associated to a pair of states.

Parameters
state1First state to consider, as a string value.
state2Second state to consider, as a string value.
Returns
The index associated to the pair of states.

Implements bpp::AlphabetIndex2.

Definition at line 70 of file SimpleIndexDistance.h.

References getAlphabet(), and indexMatrix_.

◆ getIndex() [2/2]

double bpp::SimpleIndexDistance::getIndex ( int  state1,
int  state2 
) const
inlineoverridevirtual

Get the index associated to a pair of states.

Parameters
state1First state to consider, as a int value in the Alphabet
state2Second state to consider, as a int value in the Alphabet
Returns
The index associated to the pair of states.

Implements bpp::AlphabetIndex2.

Definition at line 65 of file SimpleIndexDistance.h.

References getAlphabet(), and indexMatrix_.

◆ getIndexMatrix()

const Matrix<double>& bpp::SimpleIndexDistance::getIndexMatrix ( ) const
inlineoverridevirtual
Returns
A matrix object with all indices.

Implements bpp::AlphabetIndex2.

Definition at line 81 of file SimpleIndexDistance.h.

References indexMatrix_.

◆ isSymmetric()

bool bpp::SimpleIndexDistance::isSymmetric ( ) const
inlineoverridevirtual
Returns
True if the index is symetric (that is, index(i,j) == index(j, i)).

Implements bpp::AlphabetIndex2.

Definition at line 104 of file SimpleIndexDistance.h.

References sym_.

◆ operator=()

SimpleIndexDistance& bpp::SimpleIndexDistance::operator= ( const SimpleIndexDistance &  sid)
inline

Definition at line 53 of file SimpleIndexDistance.h.

References index_, indexMatrix_, size_, and sym_.

◆ setSymmetric()

void bpp::SimpleIndexDistance::setSymmetric ( bool  yn)
inline

Definition at line 98 of file SimpleIndexDistance.h.

References computeIndexMatrix_(), and sym_.

Member Data Documentation

◆ index_

std::shared_ptr<AlphabetIndex1> bpp::SimpleIndexDistance::index_
private

Definition at line 31 of file SimpleIndexDistance.h.

Referenced by alphabet(), computeIndexMatrix_(), getAlphabet(), getAlphabetIndex1(), and operator=().

◆ indexMatrix_

RowMatrix<double> bpp::SimpleIndexDistance::indexMatrix_
private

Definition at line 33 of file SimpleIndexDistance.h.

Referenced by computeIndexMatrix_(), getIndex(), getIndexMatrix(), and operator=().

◆ size_

size_t bpp::SimpleIndexDistance::size_
private

Definition at line 32 of file SimpleIndexDistance.h.

Referenced by computeIndexMatrix_(), and operator=().

◆ sym_

bool bpp::SimpleIndexDistance::sym_
private

Definition at line 34 of file SimpleIndexDistance.h.

Referenced by computeIndexMatrix_(), isSymmetric(), operator=(), and setSymmetric().

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