OpenMS  2.8.0
Public Types | Public Member Functions | Private Attributes | List of all members
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>

Collaboration diagram for Weights:
[legend]

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_typeweights_type
 Type of container to store integer values. More...
 
typedef std::vector< alphabet_mass_typealphabet_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)
 
Weightsoperator= (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

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
massesOriginal double values to be scaled.
precisionPrecision to scale double values.

◆ Weights() [3/3]

Weights ( const Weights other)
inline

Copy constructor.

Parameters
otherWeights 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
iAn 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
iAn 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
otherWeights to be assigned.
Returns
Reference to this object.

◆ operator[]()

weight_type operator[] ( size_type  i) const
inline

Operator to access weights by index.

Parameters
iAn 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
precisionA new precision.

◆ size()

size_type size ( ) const
inline

◆ swap()

void swap ( size_type  index1,
size_type  index2 
)

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

Parameters
index1Index of weight and mass to be exchanged.
index2Index 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.