Weight Class Reference

#include <weights.hpp>

Inheritance diagram for Weight:

List of all members.

Public Member Functions
	Weight (const Alphabet &a1, const Alphabet &a2, AlignmentType t, bool _allow_DI=true, bool _allow_ID=false)
virtual	~Weight ()
virtual void	StreamOut (std::ostream &ost)
const Alphabet &	GetAlphabet1 () const
const Alphabet &	GetAlphabet2 () const
virtual bool	IsBoltzmann () const
Public Attributes
Frequencies	freq1
Frequencies	freq2
double	scale
Align model specification.
AlignmentType	align_type
bool	allow_DI
bool	allow_ID
classical scoring parameters.
int	gap_open
int	gap_extension
transition weights
xdouble	tMM
xdouble	tMI
xdouble	tMD
xdouble	tIM
xdouble	tII
xdouble	tID
xdouble	tDM
xdouble	tDI
xdouble	tDD
start and end probabs
xdouble	tSM
xdouble	tSI
xdouble	tSD
xdouble	tME
xdouble	tIE
xdouble	tDE
Protected Member Functions
void	Normalize (bool setupUIPAC=false)
void	AverageUIPAC ()

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Detailed Description

A base class for different models.

Examples:

pairprobmap.cpp.

Definition at line 75 of file weights.hpp.

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Constructor & Destructor Documentation

Weight::Weight	(	const Alphabet &	a1,
		const Alphabet &	a2,
		AlignmentType	t,
		bool	_allow_DI = true,
		bool	_allow_ID = false
	)

Constructor.

Parameters:

	a1	alphabet of the first sequence
	a2	alphabet of the second sequence
	t	alignment model to be used
	_allow_DI	allow an insertion after a deletion.
	_allow_ID	allow a deletion after an insertion

virtual Weight::~Weight

(

)

[inline, virtual]

Virtual desctructor.

Definition at line 107 of file weights.hpp.

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Member Function Documentation

const Alphabet& Weight::GetAlphabet1

(

)

const [inline]

Returns:

Alphabet of the first sequence.

Definition at line 117 of file weights.hpp.

const Alphabet& Weight::GetAlphabet2

(

)

const [inline]

Returns:

Alphabet of the second sequence.

Definition at line 125 of file weights.hpp.

virtual bool Weight::IsBoltzmann

(

)

const [inline, virtual]

Returns:

true if the object is of type BoltzmannWeight

Reimplemented in BoltzmannWeight.

Definition at line 133 of file weights.hpp.

void Weight::Normalize

(

bool

setupUIPAC = false

)

[protected]

Normalize the pair frequencies such that they sum to one

Parameters:

setupUIPAC

if true only regular letters are normalized and the extended letters are set the the average value

virtual void Weight::StreamOut

(

std::ostream &

ost

)

[virtual]

Write out the data.

Parameters:

ost

ostream object

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Member Data Documentation

AlignmentType Weight::align_type

Align model.

Definition at line 150 of file weights.hpp.

bool Weight::allow_DI

allow an insertion after a deletion.

Definition at line 155 of file weights.hpp.

bool Weight::allow_ID

Parameters:

allow

a deletion after an insertion.

Definition at line 160 of file weights.hpp.

Frequencies Weight::freq1

Background frequencies for the first sequence.

Definition at line 84 of file weights.hpp.

Frequencies Weight::freq2

Background frequencies for the second sequence.

Definition at line 88 of file weights.hpp.

int Weight::gap_extension

Gap extension costs.

Definition at line 173 of file weights.hpp.

int Weight::gap_open

Gap open costs.

Definition at line 169 of file weights.hpp.

double Weight::scale

Scale of the corresponding score matrix. The relation between the score matrix and the log-odds is given by S(a,b) = scale * log(p(a,b)/q(a)/q(b))

Examples:

freescore.cpp.

Definition at line 143 of file weights.hpp.

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

• src/weights.hpp