bpp-seq3
3.0.0
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Two dimensionnal alphabet index interface. More...
#include <Bpp/Seq/AlphabetIndex/AlphabetIndex2.h>
Public Member Functions | |
AlphabetIndex2 () | |
virtual | ~AlphabetIndex2 () |
virtual AlphabetIndex2 * | clone () const =0 |
virtual double | getIndex (int state1, int state2) const =0 |
Get the index associated to a pair of states. More... | |
virtual double | getIndex (const std::string &state1, const std::string &state2) const =0 |
Get the index associated to a pair of states. More... | |
virtual std::shared_ptr< const Alphabet > | getAlphabet () const =0 |
Get the alphabet associated to this index. More... | |
virtual const Alphabet & | alphabet () const =0 |
Get the alphabet associated to this index. More... | |
virtual const Matrix< double > & | getIndexMatrix () const =0 |
virtual bool | isSymmetric () const =0 |
Two dimensionnal alphabet index interface.
Derivatives of this interface implement distances between two states.
Definition at line 25 of file AlphabetIndex2.h.
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inline |
Definition at line 28 of file AlphabetIndex2.h.
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inlinevirtual |
Definition at line 29 of file AlphabetIndex2.h.
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pure virtual |
Get the alphabet associated to this index.
Implemented in bpp::SimpleScore, bpp::SimpleIndexDistance, bpp::DefaultNucleotideScore, bpp::CodonFromProteicAlphabetIndex2, bpp::ProteicAlphabetIndex2, and bpp::UserAlphabetIndex2.
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pure virtual |
Implements bpp::Clonable.
Implemented in bpp::ProteicAlphabetIndex2, bpp::SimpleScore, bpp::SimpleIndexDistance, bpp::MiyataAAChemicalDistance, bpp::GranthamAAChemicalDistance, bpp::DefaultNucleotideScore, bpp::CodonFromProteicAlphabetIndex2, bpp::BLOSUM50, bpp::AAIndex2Entry, and bpp::UserAlphabetIndex2.
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pure virtual |
Get the alphabet associated to this index.
Implemented in bpp::SimpleScore, bpp::SimpleIndexDistance, bpp::DefaultNucleotideScore, bpp::CodonFromProteicAlphabetIndex2, bpp::ProteicAlphabetIndex2, and bpp::UserAlphabetIndex2.
Referenced by bpp::SiteContainerTools::alignNW().
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pure virtual |
Get the index associated to a pair of states.
state1 | First state to consider, as a string value. |
state2 | Second state to consider, as a string value. |
Implemented in bpp::SimpleScore, bpp::SimpleIndexDistance, bpp::MiyataAAChemicalDistance, bpp::GranthamAAChemicalDistance, bpp::DefaultNucleotideScore, bpp::CodonFromProteicAlphabetIndex2, bpp::BLOSUM50, bpp::AAIndex2Entry, and bpp::UserAlphabetIndex2.
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pure virtual |
Get the index associated to a pair of states.
state1 | First state to consider, as a int value in the Alphabet |
state2 | Second state to consider, as a int value in the Alphabet |
Implemented in bpp::SimpleScore, bpp::SimpleIndexDistance, bpp::MiyataAAChemicalDistance, bpp::GranthamAAChemicalDistance, bpp::DefaultNucleotideScore, bpp::CodonFromProteicAlphabetIndex2, bpp::BLOSUM50, bpp::AAIndex2Entry, and bpp::UserAlphabetIndex2.
Referenced by bpp::SiteContainerTools::alignNW().
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pure virtual |
Implemented in bpp::SimpleScore, bpp::SimpleIndexDistance, bpp::MiyataAAChemicalDistance, bpp::GranthamAAChemicalDistance, bpp::DefaultNucleotideScore, bpp::CodonFromProteicAlphabetIndex2, bpp::BLOSUM50, bpp::AAIndex2Entry, and bpp::UserAlphabetIndex2.
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pure virtual |
Implemented in bpp::SimpleScore, bpp::SimpleIndexDistance, bpp::MiyataAAChemicalDistance, bpp::GranthamAAChemicalDistance, bpp::DefaultNucleotideScore, bpp::CodonFromProteicAlphabetIndex2, bpp::BLOSUM50, bpp::AAIndex2Entry, and bpp::UserAlphabetIndex2.