Pairs an alphabet of double-valued masses with the scaled integer weights derived from them. More...

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

Collaboration diagram for Weights:

Public Types
typedef long unsigned int	weight_type
	Type of integer values to be used.

typedef double	alphabet_mass_type
	Type of double values to be used.

typedef std::vector< weight_type >	weights_type
	Type of container to store integer values.

typedef std::vector< alphabet_mass_type >	alphabet_masses_type
	Type of container to store double values.

typedef weights_type::size_type	size_type
	Type of container's size.

Public Member Functions
	Weights ()
	Default constructor.

	Weights (const alphabet_masses_type &masses, alphabet_mass_type precision)
	Construct from a set of masses and a 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)
	Replace the precision and recompute the integer weights from the stored alphabet masses.

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
	Reconstruct a parent mass from a decomposition expressed as multiplicities of the alphabet.

void	swap (size_type index1, size_type index2)
	Exchange the alphabet mass and the integer weight at `index1` with those at `index2`.

bool	divideByGCD ()
	Divide every integer weight by the greatest common divisor of all weights and scale the precision accordingly.

alphabet_mass_type	getMinRoundingError () const
	Largest negative relative rounding error introduced by the current precision.

alphabet_mass_type	getMaxRoundingError () const
	Largest positive relative rounding error introduced by the current precision.

Private Attributes
alphabet_masses_type	alphabet_masses_

alphabet_mass_type	precision_

weights_type	weights_

Detailed Description

Pairs an alphabet of double-valued masses with the scaled integer weights derived from them.

Many mass-decomposition algorithms only operate on integer weights; this class provides those integers alongside the original double-valued masses, derived once at construction (or on the next setPrecision call) by computing round(mass / precision) per entry. Subsequent access is plain vector lookup – no recomputation happens on read.

Typical precision values are in (0, 1] (smaller values mean a finer-grained integer grid); the cpp itself does not enforce a range.

Note: The terms "weights" (the scaled integers) and "masses" (the original doubles) are intentionally kept distinct: the masses are invariants of the alphabet, while the weights depend on the chosen precision.

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

Default constructor.

Produces an empty instance; size returns 0 until masses and a precision have been supplied.

◆ Weights() [2/3]

Weights	(	const alphabet_masses_type &	masses,
		alphabet_mass_type	precision
	)

inline

Construct from a set of masses and a precision.

Stores masses as the alphabet masses and computes the integer weights via round(mass / precision) for each entry (so the size of both the alphabet-mass and the weight container is masses.size() after the call).

Parameters

[in]	masses	Original double-valued alphabet masses.
[in]	precision	Precision used to scale the masses; smaller values yield finer-grained integer weights.

◆ Weights() [3/3]

Weights ( const Weights & other )

inline

Copy constructor.

Parameters

[in] 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 ( )

Divide every integer weight by the greatest common divisor of all weights and scale the precision accordingly.

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 integer weights become 3, 5, 8 and the precision becomes 1.0 (since the gcd of 30, 50, 80 is 10).

Returns: true when the integer weights and the precision were changed (gcd > 1); false when the gcd was already 1 or fewer than two weights are stored.

◆ getAlphabetMass()

alphabet_mass_type getAlphabetMass ( size_type i ) const

inline

Gets an original (double) alphabet mass by index.

Parameters

[in] i An index to access alphabet masses.

Returns: A double alphabet mass.

◆ getMaxRoundingError()

alphabet_mass_type getMaxRoundingError ( ) const

Largest positive relative rounding error introduced by the current precision.

Returns: The maximum of (precision * weight[i] - mass[i]) / mass[i] over all entries with a positive value, or 0 if no entry's scaled weight over-estimates its mass.

◆ getMinRoundingError()

alphabet_mass_type getMinRoundingError ( ) const

Largest negative relative rounding error introduced by the current precision.

Returns: The minimum of (precision * weight[i] - mass[i]) / mass[i] over all entries with a negative value, or 0 if no entry's scaled weight under-estimates its mass.

◆ getParentMass()

alphabet_mass_type getParentMass ( const std::vector< unsigned int > & decomposition ) const

Reconstruct a parent mass from a decomposition expressed as multiplicities of the alphabet.

Parameters

[in] decomposition Per-alphabet-entry multiplicities; must have the same length as the alphabet.

Returns: sum(alphabet_mass[i] * decomposition[i]) using the stored original (double) masses.

Exceptions

Exception::InvalidParameter when decomposition.size() does not equal size.

◆ 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

[in] 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

[in] 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

[in] i An index to access weights.

Returns: An integer weight.

See also: getWeight(size_type i)

◆ setPrecision()

void setPrecision ( alphabet_mass_type precision )

Replace the precision and recompute the integer weights from the stored alphabet masses.

Parameters

[in] precision New precision; the integer weights are refreshed as round(mass / precision) for every stored alphabet mass.

◆ 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
	)

Exchange the alphabet mass and the integer weight at index1 with those at index2.

Both the alphabet_mass entry and its corresponding integer weight at the two indices are swapped, so the mass / weight pairing is preserved.

Parameters

[in]	index1	First index to swap.
[in]	index2	Second index to swap.

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.

Public Types

Public Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ alphabet_mass_type

◆ alphabet_masses_type

◆ size_type

◆ weight_type

◆ weights_type

Constructor & Destructor Documentation

◆ Weights() [1/3]

◆ Weights() [2/3]

◆ Weights() [3/3]

Member Function Documentation

◆ back()

◆ divideByGCD()

◆ getAlphabetMass()

◆ getMaxRoundingError()

◆ getMinRoundingError()

◆ getParentMass()

◆ getPrecision()

◆ getWeight()

◆ operator=()

◆ operator[]()

◆ setPrecision()

◆ size()

◆ swap()

Member Data Documentation

◆ alphabet_masses_

◆ precision_

◆ weights_