#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/IsotopeDistribution.h>

Collaboration diagram for IsotopeDistribution:

Public Types
typedefs
enum	Sorted { INTENSITY , MASS , UNDEFINED }

typedef Peak1D	MassAbundance
	container type, first holds the weight of the isotope, second the probability More...

typedef std::vector< MassAbundance >	ContainerType

typedef ContainerType::iterator	iterator

typedef ContainerType::iterator	Iterator

typedef ContainerType::const_iterator	const_iterator

typedef ContainerType::const_iterator	ConstIterator

typedef ContainerType::reverse_iterator	reverse_iterator

typedef ContainerType::reverse_iterator	ReverseIterator

typedef ContainerType::const_reverse_iterator	const_reverse_iterator

typedef ContainerType::const_reverse_iterator	ConstReverseIterator

Public Member Functions
Constructors and Destructors
	IsotopeDistribution ()

	IsotopeDistribution (const IsotopeDistribution &)=default
	Copy constructor. More...

	IsotopeDistribution (IsotopeDistribution &&) noexcept=default
	Move constructor. More...

virtual	~IsotopeDistribution ()=default
	Destructor. More...

Accessors
void	set (const ContainerType &distribution)
	overwrites the container which holds the distribution using `distribution` More...

void	set (ContainerType &&distribution)
	overwrites the container which holds the distribution using `distribution` More...

const ContainerType &	getContainer () const
	returns the container which holds the distribution More...

Peak1D::CoordinateType	getMax () const
	returns the isotope with the largest m/z More...

Peak1D::CoordinateType	getMin () const
	returns the isotope with the smallest m/z More...

Peak1D	getMostAbundant () const
	returns the most abundant isotope which is stored in the distribution More...

Size	size () const
	returns the size of the distribution which is the number of isotopes in the distribution More...

void	clear ()
	clears the distribution More...

void	resize (UInt size)

void	trimIntensities (double cutoff)
	remove intensities below the cutoff More...

void	sortByIntensity ()
	sort isotope distribution by intensity More...

void	sortByMass ()
	sort isotope distribution by mass More...

void	renormalize ()
	Re-normalizes the sum of the probabilities of all the isotopes to 1. More...

void	merge (double resolution, double min_prob)
	Merges distributions of arbitrary data points with constant defined resolution. More...

void	trimRight (double cutoff)
	Trims the right side of the isotope distribution to isotopes with a significant contribution. More...

void	trimLeft (double cutoff)
	Trims the left side of the isotope distribution to isotopes with a significant contribution. More...

double	averageMass () const
	Compute average mass of isotope distribution (weighted average of all isotopes) More...

Operators
IsotopeDistribution &	operator= (const IsotopeDistribution &isotope_distribution)
	Assignment operator. More...

bool	operator== (const IsotopeDistribution &isotope_distribution) const
	equality operator, returns true if the `isotope_distribution` is identical to this, false else More...

bool	operator!= (const IsotopeDistribution &isotope_distribution) const
	inequality operator, returns true if the `isotope_distribution` differs from this, false else More...

bool	operator< (const IsotopeDistribution &isotope_distribution) const
	less operator More...

Iterators
Iterator	begin ()

Iterator	end ()

ConstIterator	begin () const

ConstIterator	end () const

ReverseIterator	rbegin ()

ReverseIterator	rend ()

ConstReverseIterator	rbegin () const

ConstReverseIterator	rend () const

void	insert (const Peak1D::CoordinateType &mass, const Peak1D::IntensityType &intensity)

Data Access Operators
ContainerType	distribution_
	stores the isotope distribution More...

Peak1D &	operator[] (const Size &index)
	operator to access a cell of the distribution and wraps it in SpectrumFragment struct More...

const Peak1D &	operator[] (const Size &index) const
	const operator to access a cell of the distribution and wraps it in SpectrumFragment struct More...

void	sort_ (std::function< bool(const MassAbundance &p1, const MassAbundance &p2)> sorter)
	sort wrapper of the distribution More...

void	transform_ (std::function< void(MassAbundance &)> lambda)
	takes a function as a parameter to transform the distribution More...

Member Typedef Documentation

◆ const_iterator

typedef ContainerType::const_iterator const_iterator

◆ const_reverse_iterator

typedef ContainerType::const_reverse_iterator const_reverse_iterator

◆ ConstIterator

typedef ContainerType::const_iterator ConstIterator

◆ ConstReverseIterator

typedef ContainerType::const_reverse_iterator ConstReverseIterator

◆ ContainerType

typedef std::vector<MassAbundance> ContainerType

◆ iterator

typedef ContainerType::iterator iterator

◆ Iterator

typedef ContainerType::iterator Iterator

◆ MassAbundance

typedef Peak1D MassAbundance

container type, first holds the weight of the isotope, second the probability

◆ reverse_iterator

typedef ContainerType::reverse_iterator reverse_iterator

◆ ReverseIterator

typedef ContainerType::reverse_iterator ReverseIterator

Member Enumeration Documentation

◆ Sorted

enum Sorted

Enumerator
INTENSITY
MASS
UNDEFINED

Constructor & Destructor Documentation

◆ IsotopeDistribution() [1/3]

IsotopeDistribution ( )

Default constructor

◆ IsotopeDistribution() [2/3]

IsotopeDistribution ( const IsotopeDistribution & )

default

Copy constructor.

◆ IsotopeDistribution() [3/3]

IsotopeDistribution ( IsotopeDistribution && )

defaultnoexcept

Move constructor.

◆ ~IsotopeDistribution()

virtual ~IsotopeDistribution ( )

virtualdefault

Destructor.

Member Function Documentation

◆ averageMass()

double averageMass ( ) const

Compute average mass of isotope distribution (weighted average of all isotopes)

◆ begin() [1/2]

Iterator begin ( )

inline

◆ begin() [2/2]

ConstIterator begin ( ) const

inline

◆ clear()

void clear ( )

clears the distribution

◆ end() [1/2]

Iterator end ( )

inline

◆ end() [2/2]

ConstIterator end ( ) const

inline

◆ getContainer()

const ContainerType& getContainer ( ) const

returns the container which holds the distribution

◆ getMax()

Peak1D::CoordinateType getMax ( ) const

returns the isotope with the largest m/z

◆ getMin()

Peak1D::CoordinateType getMin ( ) const

returns the isotope with the smallest m/z

◆ getMostAbundant()

Peak1D getMostAbundant ( ) const

returns the most abundant isotope which is stored in the distribution

◆ insert()

void insert	(	const Peak1D::CoordinateType &	mass,
		const Peak1D::IntensityType &	intensity
	)

inline

◆ merge()

void merge	(	double	resolution,
		double	min_prob
	)

Merges distributions of arbitrary data points with constant defined resolution.

It creates a new IsotopeDistribution Container and assigns each isotope to the nearest bin. This function should be used to downsample the existing distribution. If the size of the new Container is larger this function throws an IllegalArgument Exception.

◆ operator!=()

bool operator!= ( const IsotopeDistribution & isotope_distribution ) const

inequality operator, returns true if the isotope_distribution differs from this, false else

◆ operator<()

bool operator< ( const IsotopeDistribution & isotope_distribution ) const

less operator

◆ operator=()

IsotopeDistribution& operator= ( const IsotopeDistribution & isotope_distribution )

Assignment operator.

◆ operator==()

bool operator== ( const IsotopeDistribution & isotope_distribution ) const

equality operator, returns true if the isotope_distribution is identical to this, false else

◆ operator[]() [1/2]

Peak1D& operator[] ( const Size & index )

inline

operator to access a cell of the distribution and wraps it in SpectrumFragment struct

◆ operator[]() [2/2]

const Peak1D& operator[] ( const Size & index ) const

inline

const operator to access a cell of the distribution and wraps it in SpectrumFragment struct

◆ rbegin() [1/2]

ReverseIterator rbegin ( )

inline

◆ rbegin() [2/2]

ConstReverseIterator rbegin ( ) const

inline

◆ rend() [1/2]

ReverseIterator rend ( )

inline

◆ rend() [2/2]

ConstReverseIterator rend ( ) const

inline

◆ renormalize()

void renormalize ( )

Re-normalizes the sum of the probabilities of all the isotopes to 1.

The re-normalisation may be needed as in some distributions with a lot of isotopes the calculations tend to be inexact.

◆ resize()

void resize ( UInt size )

◆ set() [1/2]

void set ( const ContainerType & distribution )

overwrites the container which holds the distribution using distribution

◆ set() [2/2]

void set ( ContainerType && distribution )

overwrites the container which holds the distribution using distribution

◆ size()

Size size ( ) const

returns the size of the distribution which is the number of isotopes in the distribution

◆ sort_()

void sort_ ( std::function< bool(const MassAbundance &p1, const MassAbundance &p2)> sorter )

protected

sort wrapper of the distribution

◆ sortByIntensity()

void sortByIntensity ( )

sort isotope distribution by intensity

◆ sortByMass()

void sortByMass ( )

sort isotope distribution by mass

◆ transform_()

void transform_ ( std::function< void(MassAbundance &)> lambda )

protected

takes a function as a parameter to transform the distribution

◆ trimIntensities()

void trimIntensities ( double cutoff )

remove intensities below the cutoff

◆ trimLeft()

void trimLeft ( double cutoff )

Trims the left side of the isotope distribution to isotopes with a significant contribution.

If the isotope distribution is calculated for large masses, it might happen that many entries contain only small numbers. This function can be used to remove these entries.

Note: Consider normalising the distribution afterwards.

◆ trimRight()

void trimRight ( double cutoff )

Trims the right side of the isotope distribution to isotopes with a significant contribution.

If the isotope distribution is calculated for large masses, it might happen that many entries contain only small numbers. This function can be used to remove these entries.

Note: Consider normalising the distribution afterwards.

Member Data Documentation

◆ distribution_

ContainerType distribution_

protected

stores the isotope distribution

Public Types

Public Member Functions

Data Access Operators

Member Typedef Documentation

◆ const_iterator

◆ const_reverse_iterator

◆ ConstIterator

◆ ConstReverseIterator

◆ ContainerType

◆ iterator

◆ Iterator

◆ MassAbundance

◆ reverse_iterator

◆ ReverseIterator

Member Enumeration Documentation

◆ Sorted

Constructor & Destructor Documentation

◆ IsotopeDistribution() [1/3]

◆ IsotopeDistribution() [2/3]

◆ IsotopeDistribution() [3/3]

◆ ~IsotopeDistribution()

Member Function Documentation

◆ averageMass()

◆ begin() [1/2]

◆ begin() [2/2]

◆ clear()

◆ end() [1/2]

◆ end() [2/2]

◆ getContainer()

◆ getMax()

◆ getMin()

◆ getMostAbundant()

◆ insert()

◆ merge()

◆ operator!=()

◆ operator<()

◆ operator=()

◆ operator==()

◆ operator[]() [1/2]

◆ operator[]() [2/2]

◆ rbegin() [1/2]

◆ rbegin() [2/2]

◆ rend() [1/2]

◆ rend() [2/2]

◆ renormalize()

◆ resize()

◆ set() [1/2]

◆ set() [2/2]

◆ size()

◆ sort_()

◆ sortByIntensity()

◆ sortByMass()

◆ transform_()

◆ trimIntensities()

◆ trimLeft()

◆ trimRight()

Member Data Documentation

◆ distribution_