Weights Class Reference

Represents a set of weights (double values and scaled with a certain precision their integer counterparts) with a quick access. More...

#include <OpenMS/CHEMISTRY/MASSDECOMPOSITION/IMS/Weights.h>

Public Types
typedef long unsigned int	weight_type
	Type of integer values to be used. More...
typedef double	alphabet_mass_type
	Type of double values to be used. More...
typedef std::vector< weight_type >	weights_type
	Type of container to store integer values. More...
typedef std::vector< alphabet_mass_type >	alphabet_masses_type
	Type of container to store double values. More...
typedef weights_type::size_type	size_type
	Type of container's size. More...

Public Member Functions
	Weights ()
	Empty constructor. More...
	Weights (const alphabet_masses_type &masses, alphabet_mass_type precision)
	Weights (const Weights &other)
Weights &	operator= (const Weights &other)
size_type	size () const
weight_type	getWeight (size_type i) const
void	setPrecision (alphabet_mass_type precision)
alphabet_mass_type	getPrecision () const
weight_type	operator[] (size_type i) const
weight_type	back () const
alphabet_mass_type	getAlphabetMass (size_type i) const
alphabet_mass_type	getParentMass (const std::vector< unsigned int > &decomposition) const
void	swap (size_type index1, size_type index2)
bool	divideByGCD ()
alphabet_mass_type	getMinRoundingError () const
alphabet_mass_type	getMaxRoundingError () const

Private Attributes
alphabet_masses_type	alphabet_masses_
alphabet_mass_type	precision_
weights_type	weights_

Detailed Description

Represents a set of weights (double values and scaled with a certain precision their integer counterparts) with a quick access.

Many algorithms can't work with real-valued alphabets and need integer weights. Those are usually obtained by dividing all alphabet masses by a "precision" parameter (0; 1) and rounding the result to integers. Class Weights allows access to the scaled masses (the weights) and to the original masses as well. Weights are cached and will not be recalculated on access.

Note

Words 'weights' and 'masses' were used deliberately for naming corresponding values to help users quickly understand how they can be used. Names were chosen due to similarity in 'weights' and 'masses' interconnection in this class with real life. In reality mass value is always the same, and weight value depends on circumstances. The same as here original double masses stay the same, and scaled integer weights depend on precision applied.

Author

Anton Pervukhin Anton.nosp@m..Per.nosp@m.vukhi.nosp@m.n@Ce.nosp@m.BiTec.nosp@m..Uni.nosp@m.-Biel.nosp@m.efel.nosp@m.d.DE

Member Typedef Documentation

alphabet_mass_type

typedef double alphabet_mass_type

Type of double values to be used.

alphabet_masses_type

typedef std::vector<alphabet_mass_type> alphabet_masses_type

Type of container to store double values.

size_type

typedef weights_type::size_type size_type

Type of container's size.

weight_type

typedef long unsigned int weight_type

Type of integer values to be used.

weights_type

typedef std::vector<weight_type> weights_type

Type of container to store integer values.

Constructor & Destructor Documentation

Weights() [1/3]

Weights ( )

inline

Empty constructor.

Weights() [2/3]

Weights ( const alphabet_masses_type &  masses, alphabet_mass_type  precision  )

inline

Constructor with double values and precision.

Parameters

masses	Original double values to be scaled.
precision	Precision to scale double values.

Weights() [3/3]

Weights ( const Weights &  other )

inline

Copy constructor.

Parameters

other

Weights to be copied.

Member Function Documentation

back()

weight_type back ( ) const

inline

Gets a last weight.

Returns

a last weight.

divideByGCD()

bool divideByGCD

(

)

Divides the integer weights by their gcd. The precision is also adjusted.

For example, given alphabet weights 3.0, 5.0, 8.0 with precision 0.1, the integer weights would be 30, 50, 80. After calling this method, the new weights are 3, 5, 8 with precision 1.0 (since the gcd of 30, 50, and 80 is 10).

Returns

true if anything was changed, that is, if the gcd was > 1. false if the gcd was already 1 or there are less than two weights.

getAlphabetMass()

alphabet_mass_type getAlphabetMass ( size_type  i ) const

inline

Gets an original (double) alphabet mass by index.

Parameters

i	An index to access alphabet masses.

Returns

A double alphabet mass.

getMaxRoundingError()

alphabet_mass_type getMaxRoundingError

(

)

const

getMinRoundingError()

alphabet_mass_type getMinRoundingError

(

)

const

getParentMass()

alphabet_mass_type getParentMass

(

const std::vector< unsigned int > &

decomposition

)

const

Returns a parent mass for a given decomposition

getPrecision()

alphabet_mass_type getPrecision ( ) const

inline

Gets precision.

Returns

Precision to scale double values to integer.

getWeight()

weight_type getWeight ( size_type  i ) const

inline

Gets a scaled integer weight by index.

Parameters

i	An index to access weights.

Returns

An integer weight.

Referenced by IntegerMassDecomposer< ValueType, DecompositionValueType >::fillExtendedResidueTable_(), and IntegerMassDecomposer< ValueType, DecompositionValueType >::IntegerMassDecomposer().

operator=()

Weights& operator=

(

const Weights &

other

)

Assignment operator.

Parameters

other

Weights to be assigned.

Returns

Reference to this object.

operator[]()

weight_type operator[] ( size_type  i ) const

inline

Operator to access weights by index.

Parameters

i	An index to access weights.

Returns

An integer weight.

See also

getWeight(size_type i)

setPrecision()

void setPrecision

(

alphabet_mass_type

precision

)

Sets a new precision to scale double values to integer.

Parameters

precision

A new precision.

size()

size_type size ( ) const

inline

Gets size of a set of weights.

Returns

Size of a set of weights.

Referenced by IntegerMassDecomposer< ValueType, DecompositionValueType >::fillExtendedResidueTable_(), and IntegerMassDecomposer< ValueType, DecompositionValueType >::IntegerMassDecomposer().

swap()

void swap	(	size_type	index1,
		size_type	index2
	)

Exchanges weight and mass at index1 with weight and mass at index2.

Parameters

index1	Index of weight and mass to be exchanged.
index2	Index of weight and mass to be exchanged.

Member Data Documentation

alphabet_masses_

alphabet_masses_type alphabet_masses_

private

Container to store original (double) alphabet masses.

precision_

alphabet_mass_type precision_

private

Precision which is used to scale double values to integer.

weights_

weights_type weights_

private

Container to store scaled integer weights.