bpp::DefaultNucleotideScore Class Reference

Default Substitution Matrix for nucleotide alignments. More...

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

Inheritance diagram for bpp::DefaultNucleotideScore:

Collaboration diagram for bpp::DefaultNucleotideScore:

Public Member Functions
	DefaultNucleotideScore (const NucleicAlphabet *alphabet)
	Build a new DefaultNucleotideScore object. More...
	DefaultNucleotideScore (const DefaultNucleotideScore &dns)
DefaultNucleotideScore &	operator= (const DefaultNucleotideScore &dns)
virtual	~DefaultNucleotideScore ()
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 Alphabet *	getAlphabet () const
	Get the alphabet associated to this index. More...
DefaultNucleotideScore *	clone () const
LinearMatrix< double > *	getIndexMatrix () const
bool	isSymmetric () const

Private Attributes
LinearMatrix< double >	distanceMatrix_
const NucleicAlphabet *	alpha_

Detailed Description

Default Substitution Matrix for nucleotide alignments.

Definition at line 57 of file DefaultNucleotideScore.h.

Constructor & Destructor Documentation

DefaultNucleotideScore() [1/2]

DefaultNucleotideScore::DefaultNucleotideScore

(

const NucleicAlphabet *

alphabet

)

Build a new DefaultNucleotideScore object.

Parameters

alphabet

The alphabet to use.

Definition at line 48 of file DefaultNucleotideScore.cpp.

References distanceMatrix_.

Referenced by clone().

DefaultNucleotideScore() [2/2]

bpp::DefaultNucleotideScore::DefaultNucleotideScore ( const DefaultNucleotideScore &  dns )

inline

Definition at line 72 of file DefaultNucleotideScore.h.

~DefaultNucleotideScore()

virtual bpp::DefaultNucleotideScore::~DefaultNucleotideScore ( )

inlinevirtual

Definition at line 83 of file DefaultNucleotideScore.h.

Member Function Documentation

clone()

DefaultNucleotideScore* bpp::DefaultNucleotideScore::clone ( ) const

inlinevirtual

Implements bpp::AlphabetIndex2.

Definition at line 101 of file DefaultNucleotideScore.h.

References DefaultNucleotideScore().

getAlphabet()

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

inlinevirtual

Get the alphabet associated to this index.

Returns

Alphabet The alphabet associated to this index.

Implements bpp::AlphabetIndex2.

Definition at line 100 of file DefaultNucleotideScore.h.

References alpha_.

getIndex() [1/2]

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

virtual

Get the index associated to a pair of states.

Parameters

state1	First state to consider, as a int value.
state2	Second state to consider, as a int value.

Returns

The index associated to the pair of states.

If states are unresolved, takes the best score of all possible matches and divides it by the number of different states.

Author

Sylvain Gaillard

Implements bpp::AlphabetIndex2.

Definition at line 74 of file DefaultNucleotideScore.cpp.

getIndex() [2/2]

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

virtual

Get the index associated to a pair of states.

Parameters

state1	First state to consider, as a string value.
state2	Second state to consider, as a string value.

Returns

The index associated to the pair of states.

Implements bpp::AlphabetIndex2.

Definition at line 101 of file DefaultNucleotideScore.cpp.

getIndexMatrix()

LinearMatrix< double > * DefaultNucleotideScore::getIndexMatrix ( ) const

virtual

Returns

A matrix object with all indices.

Implements bpp::AlphabetIndex2.

Definition at line 109 of file DefaultNucleotideScore.cpp.

References distanceMatrix_.

isSymmetric()

bool bpp::DefaultNucleotideScore::isSymmetric ( ) const

inlinevirtual

Returns

True if the index is symatric (that is, index(i,j) == index(j, i)).

Implements bpp::AlphabetIndex2.

Definition at line 103 of file DefaultNucleotideScore.h.

operator=()

DefaultNucleotideScore& bpp::DefaultNucleotideScore::operator= ( const DefaultNucleotideScore &  dns )

inline

Definition at line 76 of file DefaultNucleotideScore.h.

References alpha_, and distanceMatrix_.

Member Data Documentation

alpha_

const NucleicAlphabet* bpp::DefaultNucleotideScore::alpha_

private

Definition at line 62 of file DefaultNucleotideScore.h.

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

distanceMatrix_

LinearMatrix<double> bpp::DefaultNucleotideScore::distanceMatrix_

private

Definition at line 61 of file DefaultNucleotideScore.h.

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

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

• Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.h
• Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp