IsotopeDistribution Class Reference

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

Public Types
enum	Sorted { INTENSITY, MASS, UNDEFINED }
typedefs
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 &isotope_distribution)
	Copy constructor. More...
virtual	~IsotopeDistribution ()
	Destructor. More...
Accessors
void	set (const 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 maximal weight isotope which is stored in the distribution More...
Peak1D::CoordinateType	getMin () const
	returns the minimal weight isotope which is stored in the distribution 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 and resets max isotope to 0 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 the isotopes to 1 More...
void	merge (double resolution, double min_prob)
	Merges distributions 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...
bool	isNormalized () const
double	averageMass () const
bool	isConvolutionUnit () const
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
Peak1D &	operator[] (const Size &index)
	operator which access a cell of the distribution and wraps it in SpectrumFragment struct More...

Protected Member Functions
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...

Protected Attributes
ContainerType	distribution_
	stores the isotope 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() [1/2]

IsotopeDistribution

(

)

Default constructor, note max_isotope must be set later

IsotopeDistribution() [2/2]

IsotopeDistribution

(

const IsotopeDistribution &

isotope_distribution

)

Copy constructor.

~IsotopeDistribution()

virtual ~IsotopeDistribution ( )

virtual

Destructor.

Member Function Documentation

averageMass()

double averageMass

(

)

const

begin() [1/2]

Iterator begin ( )

inline

begin() [2/2]

ConstIterator begin ( ) const

inline

clear()

void clear

(

)

clears the distribution and resets max isotope to 0

Referenced by MetaProSIPDecomposition::calculateIsotopePatternsFor13CRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor13CRangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor15NRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor15NRangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor18ORange(), MetaProSIPDecomposition::calculateIsotopePatternsFor18ORangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor2HRange(), and MetaProSIPDecomposition::calculateIsotopePatternsFor2HRangeOfAveraginePeptide().

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

Referenced by TOPPMetaProSIP::calculateCorrelation(), MetaProSIPDecomposition::calculateIsotopePatternsFor13CRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor13CRangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor15NRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor15NRangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor18ORange(), MetaProSIPDecomposition::calculateIsotopePatternsFor18ORangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor2HRange(), and MetaProSIPDecomposition::calculateIsotopePatternsFor2HRangeOfAveraginePeptide().

getMax()

Peak1D::CoordinateType getMax

(

)

const

returns the maximal weight isotope which is stored in the distribution

getMin()

Peak1D::CoordinateType getMin

(

)

const

returns the minimal weight isotope which is stored in the distribution

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

Referenced by MetaProSIPDecomposition::calculateIsotopePatternsFor13CRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor13CRangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor15NRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor15NRangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor18ORange(), MetaProSIPDecomposition::calculateIsotopePatternsFor18ORangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor2HRange(), and MetaProSIPDecomposition::calculateIsotopePatternsFor2HRangeOfAveraginePeptide().

isConvolutionUnit()

bool isConvolutionUnit

(

)

const

isNormalized()

bool isNormalized

(

)

const

merge()

void merge	(	double	resolution,
		double	min_prob
	)

Merges distributions 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[]()

Peak1D& operator[] ( const Size &  index )

inline

operator which 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 the isotopes to 1

The re-normalisation is needed as in distributions with a lot of isotopes (and with high max isotope) the calculations tend to be inexact.

resize()

void resize

(

UInt

size

)

set()

void set

(

const ContainerType &

distribution

)

overwrites the container which holds the distribution using distribution

Referenced by MetaProSIPDecomposition::calculateIsotopePatternsFor13CRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor15NRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor18ORange(), and MetaProSIPDecomposition::calculateIsotopePatternsFor2HRange().

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 (and with high max isotope) it might happen that many entries contain only small numbers. This function can be used to remove these entries.

Do 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 (and with high max isotope) it might happen that many entries contain only small numbers. This function can be used to remove these entries.

Do consider normalising the distribution afterwards.

Member Data Documentation

distribution_

ContainerType distribution_

protected

stores the isotope distribution