bpp-seq  2.2.0
bpp::GranthamAAPolarityIndex Class Reference

Polarity index used in Grantham (1974). More...

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

+ Inheritance diagram for bpp::GranthamAAPolarityIndex:
+ Collaboration diagram for bpp::GranthamAAPolarityIndex:

Public Member Functions

 GranthamAAPolarityIndex ()
 
virtual ~GranthamAAPolarityIndex ()
 
GranthamAAPolarityIndexclone () const
 
double getIndex (int state) const throw (BadIntException)
 Get the index associated to a state. More...
 
double getIndex (const std::string &state) const throw (BadCharException)
 Get the index associated to a state. More...
 
std::vector< double > * getIndexVector () const
 
const AlphabetgetAlphabet () const
 Get the alphabet associated to this index. More...
 

Private Attributes

std::vector< double > polarity_
 

Detailed Description

Polarity index used in Grantham (1974).

Database: AAindex1
Entry: GRAR740102
H GRAR740102
D Polarity (Grantham, 1974)
R LIT:2004143b PMID:4843792
A Grantham, R.
T Amino acid difference formula to help explain protein evolution
J Science 185, 862-864 (1974)
I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
8.1 10.5 11.6 13.0 5.5 10.5 12.3 9.0 10.4 5.2
4.9 11.3 5.7 5.2 8.0 9.2 8.6 5.4 6.2 5.9
//

Definition at line 67 of file GranthamAAPolarityIndex.h.

Constructor & Destructor Documentation

◆ GranthamAAPolarityIndex()

bpp::GranthamAAPolarityIndex::GranthamAAPolarityIndex ( )
inline

Definition at line 74 of file GranthamAAPolarityIndex.h.

References polarity_.

Referenced by clone().

◆ ~GranthamAAPolarityIndex()

virtual bpp::GranthamAAPolarityIndex::~GranthamAAPolarityIndex ( )
inlinevirtual

Definition at line 100 of file GranthamAAPolarityIndex.h.

Member Function Documentation

◆ clone()

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

Implements bpp::AlphabetIndex1.

Definition at line 102 of file GranthamAAPolarityIndex.h.

References GranthamAAPolarityIndex().

◆ getAlphabet()

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

Get the alphabet associated to this index.

Returns
Alphabet The alphabet associated to this index.

Implements bpp::AlphabetIndex1.

Definition at line 118 of file GranthamAAPolarityIndex.h.

References bpp::AlphabetTools::PROTEIN_ALPHABET.

◆ getIndex() [1/2]

double bpp::GranthamAAPolarityIndex::getIndex ( int  state) const
throw (BadIntException
)
inlinevirtual

Get the index associated to a state.

Parameters
stateThe state to consider, as a int value.
Returns
The index associated to the state

Implements bpp::AlphabetIndex1.

Definition at line 105 of file GranthamAAPolarityIndex.h.

References polarity_, and bpp::AlphabetTools::PROTEIN_ALPHABET.

◆ getIndex() [2/2]

double bpp::GranthamAAPolarityIndex::getIndex ( const std::string &  state) const
throw (BadCharException
)
inlinevirtual

Get the index associated to a state.

Parameters
stateThe state to consider, as a string value.
Returns
The index associated to the state

Implements bpp::AlphabetIndex1.

Definition at line 111 of file GranthamAAPolarityIndex.h.

References bpp::LetterAlphabet::charToInt(), polarity_, and bpp::AlphabetTools::PROTEIN_ALPHABET.

◆ getIndexVector()

std::vector<double>* bpp::GranthamAAPolarityIndex::getIndexVector ( ) const
inlinevirtual
Returns
A vector object with all indices.

Implements bpp::AlphabetIndex1.

Definition at line 116 of file GranthamAAPolarityIndex.h.

References polarity_.

Member Data Documentation

◆ polarity_

std::vector<double> bpp::GranthamAAPolarityIndex::polarity_
private

Definition at line 71 of file GranthamAAPolarityIndex.h.

Referenced by getIndex(), getIndexVector(), and GranthamAAPolarityIndex().


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