bpp::AAIndex1Entry Class Reference

Create a AlphabetIndex1 object from an AAIndex2 entry. More...

#include <Bpp/Seq/AlphabetIndex/AAIndex1Entry.h>

Inheritance diagram for bpp::AAIndex1Entry:

Collaboration diagram for bpp::AAIndex1Entry:

Public Member Functions
	AAIndex1Entry (std::istream &input) throw (IOException)
	Create a new AAIndex1Entry from an input stream. More...
	AAIndex1Entry (const AAIndex1Entry &index)
AAIndex1Entry &	operator= (const AAIndex1Entry &index)
virtual	~AAIndex1Entry ()
AAIndex1Entry *	clone () 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 Alphabet *	getAlphabet () const
	Get the alphabet associated to this index. More...

Private Attributes
std::vector< double >	property_
const ProteicAlphabet *	alpha_

Detailed Description

Create a AlphabetIndex1 object from an AAIndex2 entry.

Definition at line 51 of file AAIndex1Entry.h.

Constructor & Destructor Documentation

AAIndex1Entry() [1/2]

AAIndex1Entry::AAIndex1Entry	(	std::istream &	input	)
throw	(	IOException
	)

Create a new AAIndex1Entry from an input stream.

Parameters

input

The input stream to use.

Exceptions

IOException

if the stream content does not follow the AAIndex1 database entry format.

Definition at line 49 of file AAIndex1Entry.cpp.

Referenced by clone().

AAIndex1Entry() [2/2]

bpp::AAIndex1Entry::AAIndex1Entry ( const AAIndex1Entry &  index )

inline

Definition at line 67 of file AAIndex1Entry.h.

~AAIndex1Entry()

virtual bpp::AAIndex1Entry::~AAIndex1Entry ( )

inlinevirtual

Definition at line 79 of file AAIndex1Entry.h.

Member Function Documentation

clone()

AAIndex1Entry* bpp::AAIndex1Entry::clone ( ) const

inlinevirtual

Implements bpp::AlphabetIndex1.

Definition at line 81 of file AAIndex1Entry.h.

References AAIndex1Entry().

getAlphabet()

const Alphabet* bpp::AAIndex1Entry::getAlphabet ( ) const

inlinevirtual

Get the alphabet associated to this index.

Returns

Alphabet The alphabet associated to this index.

Implements bpp::AlphabetIndex1.

Definition at line 97 of file AAIndex1Entry.h.

References alpha_.

getIndex() [1/2]

double bpp::AAIndex1Entry::getIndex ( int  state ) const throw ( BadIntException )

inlinevirtual

Get the index associated to a state.

Parameters

state

The state to consider, as a int value.

Returns

The index associated to the state

Implements bpp::AlphabetIndex1.

Definition at line 84 of file AAIndex1Entry.h.

References alpha_, and property_.

getIndex() [2/2]

double bpp::AAIndex1Entry::getIndex ( const std::string &  state ) const throw ( BadCharException )

inlinevirtual

Get the index associated to a state.

Parameters

state

The state to consider, as a string value.

Returns

The index associated to the state

Implements bpp::AlphabetIndex1.

Definition at line 90 of file AAIndex1Entry.h.

References alpha_, bpp::LetterAlphabet::charToInt(), and property_.

getIndexVector()

std::vector<double>* bpp::AAIndex1Entry::getIndexVector ( ) const

inlinevirtual

Returns

A vector object with all indices.

Implements bpp::AlphabetIndex1.

Definition at line 95 of file AAIndex1Entry.h.

References property_.

operator=()

AAIndex1Entry& bpp::AAIndex1Entry::operator= ( const AAIndex1Entry &  index )

inline

Definition at line 72 of file AAIndex1Entry.h.

References alpha_, and property_.

Member Data Documentation

alpha_

const ProteicAlphabet* bpp::AAIndex1Entry::alpha_

private

Definition at line 56 of file AAIndex1Entry.h.

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

property_

std::vector<double> bpp::AAIndex1Entry::property_

private

Definition at line 55 of file AAIndex1Entry.h.

Referenced by getIndex(), getIndexVector(), and operator=().

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

• Bpp/Seq/AlphabetIndex/AAIndex1Entry.h
• Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp