bpp-seq  2.2.0
bpp::MiyataAAChemicalDistance Class Reference

Miyata et al. (1979) Amino-Acid chemical distance. More...

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

+ Inheritance diagram for bpp::MiyataAAChemicalDistance:
+ Collaboration diagram for bpp::MiyataAAChemicalDistance:

Public Member Functions

 MiyataAAChemicalDistance ()
 
 MiyataAAChemicalDistance (const MiyataAAChemicalDistance &md)
 
MiyataAAChemicalDistanceoperator= (const MiyataAAChemicalDistance &md)
 
virtual ~MiyataAAChemicalDistance ()
 
MiyataAAChemicalDistanceclone () const
 
void setSymmetric (bool yn)
 
bool isSymmetric () const
 
Methods from the AlphabetIndex2 interface.
double getIndex (int state1, int state2) const throw (BadIntException)
 Get the index associated to a pair of states. More...
 
double getIndex (const std::string &state1, const std::string &state2) const throw (BadCharException)
 Get the index associated to a pair of states. More...
 
const AlphabetgetAlphabet () const
 Get the alphabet associated to this index. More...
 
Matrix< double > * getIndexMatrix () const
 

Private Attributes

LinearMatrix< double > distanceMatrix_
 
const ProteicAlphabetalpha_
 
bool sym_
 

Detailed Description

Miyata et al. (1979) Amino-Acid chemical distance.

Two kinds of matrix can be built:

  • a symmetric one, with $I_{i,j} = I_{i,j}$,
  • or a non-symmetric one, with $I_{i,j} = -I_{i,j}$.

Reference: Miyata, T., Miyazawa, S. and Yasunaga, T. Two types of amino acid substitutions in protein evolution J. Mol. Evol. 12, 219-236 (1979)

Data from AAIndex2 database, Accession Number MIYT790101.

Definition at line 68 of file MiyataAAChemicalDistance.h.

Constructor & Destructor Documentation

◆ MiyataAAChemicalDistance() [1/2]

MiyataAAChemicalDistance::MiyataAAChemicalDistance ( )

Definition at line 51 of file MiyataAAChemicalDistance.cpp.

Referenced by clone().

◆ MiyataAAChemicalDistance() [2/2]

bpp::MiyataAAChemicalDistance::MiyataAAChemicalDistance ( const MiyataAAChemicalDistance md)
inline

Definition at line 79 of file MiyataAAChemicalDistance.h.

◆ ~MiyataAAChemicalDistance()

virtual bpp::MiyataAAChemicalDistance::~MiyataAAChemicalDistance ( )
inlinevirtual

Definition at line 93 of file MiyataAAChemicalDistance.h.

Member Function Documentation

◆ clone()

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

Implements bpp::AlphabetIndex2.

Definition at line 95 of file MiyataAAChemicalDistance.h.

References MiyataAAChemicalDistance().

◆ getAlphabet()

const Alphabet* bpp::MiyataAAChemicalDistance::getAlphabet ( ) const
inlinevirtual

Get the alphabet associated to this index.

Returns
Alphabet The alphabet associated to this index.

Implements bpp::AlphabetIndex2.

Definition at line 105 of file MiyataAAChemicalDistance.h.

References alpha_.

◆ getIndex() [1/2]

double MiyataAAChemicalDistance::getIndex ( int  state1,
int  state2 
) const
throw (BadIntException
)
virtual

Get the index associated to a pair of states.

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

Implements bpp::AlphabetIndex2.

Definition at line 59 of file MiyataAAChemicalDistance.cpp.

◆ getIndex() [2/2]

double MiyataAAChemicalDistance::getIndex ( const std::string &  state1,
const std::string &  state2 
) const
throw (BadCharException
)
virtual

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 68 of file MiyataAAChemicalDistance.cpp.

◆ getIndexMatrix()

Matrix< double > * MiyataAAChemicalDistance::getIndexMatrix ( ) const
virtual
Returns
A matrix object with all indices.

Implements bpp::AlphabetIndex2.

Definition at line 77 of file MiyataAAChemicalDistance.cpp.

References distanceMatrix_, and sym_.

◆ isSymmetric()

bool bpp::MiyataAAChemicalDistance::isSymmetric ( ) const
inlinevirtual
Returns
True if the index is symatric (that is, index(i,j) == index(j, i)).

Implements bpp::AlphabetIndex2.

Definition at line 111 of file MiyataAAChemicalDistance.h.

References sym_.

◆ operator=()

MiyataAAChemicalDistance& bpp::MiyataAAChemicalDistance::operator= ( const MiyataAAChemicalDistance md)
inline

Definition at line 85 of file MiyataAAChemicalDistance.h.

References alpha_, distanceMatrix_, and sym_.

◆ setSymmetric()

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

Definition at line 110 of file MiyataAAChemicalDistance.h.

References sym_.

Referenced by bpp::BppOAlphabetIndex2Format::read().

Member Data Documentation

◆ alpha_

const ProteicAlphabet* bpp::MiyataAAChemicalDistance::alpha_
private

Definition at line 73 of file MiyataAAChemicalDistance.h.

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

◆ distanceMatrix_

LinearMatrix<double> bpp::MiyataAAChemicalDistance::distanceMatrix_
private

Definition at line 72 of file MiyataAAChemicalDistance.h.

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

◆ sym_

bool bpp::MiyataAAChemicalDistance::sym_
private

Definition at line 74 of file MiyataAAChemicalDistance.h.

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


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