bpp-seq
2.2.0
|
Miyata et al. (1979) Amino-Acid chemical distance. More...
#include <Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.h>
Public Member Functions | |
MiyataAAChemicalDistance () | |
MiyataAAChemicalDistance (const MiyataAAChemicalDistance &md) | |
MiyataAAChemicalDistance & | operator= (const MiyataAAChemicalDistance &md) |
virtual | ~MiyataAAChemicalDistance () |
MiyataAAChemicalDistance * | clone () 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 Alphabet * | getAlphabet () const |
Get the alphabet associated to this index. More... | |
Matrix< double > * | getIndexMatrix () const |
Private Attributes | |
LinearMatrix< double > | distanceMatrix_ |
const ProteicAlphabet * | alpha_ |
bool | sym_ |
Miyata et al. (1979) Amino-Acid chemical distance.
Two kinds of matrix can be built:
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.
MiyataAAChemicalDistance::MiyataAAChemicalDistance | ( | ) |
Definition at line 51 of file MiyataAAChemicalDistance.cpp.
Referenced by clone().
|
inline |
Definition at line 79 of file MiyataAAChemicalDistance.h.
|
inlinevirtual |
Definition at line 93 of file MiyataAAChemicalDistance.h.
|
inlinevirtual |
Implements bpp::AlphabetIndex2.
Definition at line 95 of file MiyataAAChemicalDistance.h.
References MiyataAAChemicalDistance().
|
inlinevirtual |
Get the alphabet associated to this index.
Implements bpp::AlphabetIndex2.
Definition at line 105 of file MiyataAAChemicalDistance.h.
References alpha_.
|
virtual |
Get the index associated to a pair of states.
state1 | First state to consider, as a int value. |
state2 | Second state to consider, as a int value. |
Implements bpp::AlphabetIndex2.
Definition at line 59 of file MiyataAAChemicalDistance.cpp.
|
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. |
Implements bpp::AlphabetIndex2.
Definition at line 68 of file MiyataAAChemicalDistance.cpp.
|
virtual |
Implements bpp::AlphabetIndex2.
Definition at line 77 of file MiyataAAChemicalDistance.cpp.
References distanceMatrix_, and sym_.
|
inlinevirtual |
Implements bpp::AlphabetIndex2.
Definition at line 111 of file MiyataAAChemicalDistance.h.
References sym_.
|
inline |
Definition at line 85 of file MiyataAAChemicalDistance.h.
References alpha_, distanceMatrix_, and sym_.
|
inline |
Definition at line 110 of file MiyataAAChemicalDistance.h.
References sym_.
Referenced by bpp::BppOAlphabetIndex2Format::read().
|
private |
Definition at line 73 of file MiyataAAChemicalDistance.h.
Referenced by getAlphabet(), and operator=().
|
private |
Definition at line 72 of file MiyataAAChemicalDistance.h.
Referenced by getIndexMatrix(), and operator=().
|
private |
Definition at line 74 of file MiyataAAChemicalDistance.h.
Referenced by getIndexMatrix(), isSymmetric(), operator=(), and setSymmetric().