OpenMS
2.6.0
|
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/IsotopeDistribution.h>
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... | |
typedef ContainerType::const_iterator const_iterator |
typedef ContainerType::const_reverse_iterator const_reverse_iterator |
typedef ContainerType::const_iterator ConstIterator |
typedef ContainerType::const_reverse_iterator ConstReverseIterator |
typedef std::vector<MassAbundance> ContainerType |
typedef ContainerType::iterator iterator |
typedef ContainerType::iterator Iterator |
typedef Peak1D MassAbundance |
container type, first holds the weight of the isotope, second the probability
typedef ContainerType::reverse_iterator reverse_iterator |
typedef ContainerType::reverse_iterator ReverseIterator |
enum Sorted |
Default constructor
|
default |
Copy constructor.
|
defaultnoexcept |
Move constructor.
|
virtualdefault |
Destructor.
double averageMass | ( | ) | const |
Compute average mass of isotope distribution (weighted average of all isotopes)
|
inline |
References IsotopeDistribution::begin().
Referenced by IsotopeDistribution::begin().
|
inline |
void clear | ( | ) |
clears the distribution
|
inline |
|
inline |
const ContainerType& getContainer | ( | ) | const |
returns the container which holds the distribution
Peak1D::CoordinateType getMax | ( | ) | const |
returns the isotope with the largest m/z
Peak1D::CoordinateType getMin | ( | ) | const |
returns the isotope with the smallest m/z
Peak1D getMostAbundant | ( | ) | const |
returns the most abundant isotope which is stored in the distribution
|
inline |
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.
bool operator!= | ( | const IsotopeDistribution & | isotope_distribution | ) | const |
inequality operator, returns true if the isotope_distribution
differs from this, false else
bool operator< | ( | const IsotopeDistribution & | isotope_distribution | ) | const |
less operator
IsotopeDistribution& operator= | ( | const IsotopeDistribution & | isotope_distribution | ) |
Assignment operator.
bool operator== | ( | const IsotopeDistribution & | isotope_distribution | ) | const |
equality operator, returns true if the isotope_distribution
is identical to this, false else
operator to access a cell of the distribution and wraps it in SpectrumFragment struct
const operator to access a cell of the distribution and wraps it in SpectrumFragment struct
|
inline |
|
inline |
|
inline |
|
inline |
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.
void resize | ( | UInt | size | ) |
void set | ( | const ContainerType & | distribution | ) |
overwrites the container which holds the distribution using distribution
void set | ( | ContainerType && | distribution | ) |
overwrites the container which holds the distribution using distribution
Size size | ( | ) | const |
returns the size of the distribution which is the number of isotopes in the distribution
|
protected |
sort wrapper of the distribution
void sortByIntensity | ( | ) |
sort isotope distribution by intensity
void sortByMass | ( | ) |
sort isotope distribution by mass
|
protected |
takes a function as a parameter to transform the distribution
void trimIntensities | ( | double | cutoff | ) |
remove intensities below the cutoff
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.
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.
|
protected |
stores the isotope distribution