| OpenMS 2.5.0

Private Member Functions | Private Attributes | Static Private Attributes | List of all members
SpectrumCheapDPCorr Class Reference
Spectrum Comparison

SpectrumCheapDPCorr calculates an optimal alignment on stick spectra. More...

`#include <OpenMS/COMPARISON/SPECTRA/SpectrumCheapDPCorr.h>`

Inheritance diagram for SpectrumCheapDPCorr:

## Public Member Functions

| SpectrumCheapDPCorr ()
| default constructor More...
| SpectrumCheapDPCorr (const SpectrumCheapDPCorr &source)
| copy constructor More...
| ~SpectrumCheapDPCorr () override
| destructor More...
SpectrumCheapDPCorr & | operator= (const SpectrumCheapDPCorr &source)
| assignment operator More...
double | operator() (const PeakSpectrum &a, const PeakSpectrum &b) const override
| function call operator, calculates the similarity More...
double | operator() (const PeakSpectrum &a) const override
| calculates self similarity More...
Public Member Functions inherited from PeakSpectrumCompareFunctor
| PeakSpectrumCompareFunctor ()
| default constructor More...
| PeakSpectrumCompareFunctor (const PeakSpectrumCompareFunctor &source)
| copy constructor More...
| ~PeakSpectrumCompareFunctor () override
| destructor More...
PeakSpectrumCompareFunctor & | operator= (const PeakSpectrumCompareFunctor &source)
| assignment operator More...
Public Member Functions inherited from DefaultParamHandler
| DefaultParamHandler (const String &name)
| Constructor with name that is displayed in error messages. More...
| DefaultParamHandler (const DefaultParamHandler &rhs)
| Copy constructor. More...
virtual | ~DefaultParamHandler ()
| Destructor. More...
virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs)
| Assignment operator. More...
virtual bool | operator== (const DefaultParamHandler &rhs) const
| Equality operator. More...
void | setParameters (const Param &param)
| Sets the parameters. More...
const Param & | getParameters () const
| Non-mutable access to the parameters. More...
const Param & | getDefaults () const
| Non-mutable access to the default parameters. More...
const String & | getName () const
| Non-mutable access to the name. More...
void | setName (const String &name)
| Mutable access to the name. More...
const std::vector< String > & | getSubsections () const
| Non-mutable access to the registered subsections. More...

## Private Member Functions

double | dynprog_ (const PeakSpectrum &, const PeakSpectrum &, int, int, int, int) const
| O(n^2) dynamical programming. More...
double | comparepeaks_ (double posa, double posb, double inta, double intb) const
| similarity of two peaks More...

## Private Attributes

PeakSpectrum | lastconsensus_
| consensus spectrum of the last comparison More...
bool | keeppeaks_
| should peaks with no alignment partner be kept in the consensus? More...
double | factor_
| weighting factor for the next consensus spectrum More...
Map< UInt, UInt > | peak_map_
| last peak map More...

## Static Private Attributes

static const String | info_
const PeakSpectrum & | lastconsensus () const
| return consensus spectrum from last function call operator More...
Map< UInt, UInt > | getPeakMap () const
void | setFactor (double f)
| set weighting of the second spectrum for consensus from next function call operator More...
static PeakSpectrumCompareFunctor * | create ()
static const String | getProductName ()

## Additional Inherited Members

Static Public Member Functions inherited from PeakSpectrumCompareFunctor
static void | registerChildren ()
| registers all derived products More...
static const String | getProductName ()
Protected Member Functions inherited from DefaultParamHandler
virtual void | updateMembers_ ()
| This method is used to update extra member variables at the end of the setParameters() method. More...
void | defaultsToParam_ ()
| Updates the parameters after the defaults have been set in the constructor. More...
Protected Attributes inherited from DefaultParamHandler
Param | param_
| Container for current parameters. More...
Param | defaults_
| Container for default parameters. This member should be filled in the constructor of derived classes! More...
std::vector< String > | subsections_
| Container for registered subsections. This member should be filled in the constructor of derived classes! More...
String | error_name_
| Name that is displayed in error messages during the parameter checking. More...
bool | check_defaults_
| If this member is set to false no checking if parameters in done;. More...
bool | warn_empty_defaults_
| If this member is set to false no warning is emitted when defaults are empty;. More...

## Detailed Description

SpectrumCheapDPCorr calculates an optimal alignment on stick spectra.

to save computing time only Peak Pairs that could get a score > 0 are considered which Peak Pairs could get scores > 0 ?
Peaks get a score depending on the difference in position and the heights of the peaks
pairs with positions that differ more than some limit get score 0

Parameters of this class are:

Name | Type | Default | Restrictions | Description
--- | --- | --- | --- | ---
variation | float | 0.001 |  | Maximum difference in position (in percent of the current m/z). Note that big values of variation ( 1 being the maximum ) result in consideration of all possible pairings which has a running time of O(n*n)
int_cnt | int | 0 |  | How the peak heights are used in the score. 0 = product 1 = sqrt(product) 2 = sum 3 = agreeing intensity
keeppeaks | int | 0 |  | Flag that states if peaks without alignment partner are kept in the consensus spectrum.

Note:

- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.

## Constructor & Destructor Documentation

## ◆ SpectrumCheapDPCorr() [1/2]

SpectrumCheapDPCorr | ( |  | ) |

default constructor

## ◆ SpectrumCheapDPCorr() [2/2]

SpectrumCheapDPCorr | ( | const SpectrumCheapDPCorr & | source | ) |

copy constructor

## ◆ ~SpectrumCheapDPCorr()

~SpectrumCheapDPCorr | ( |  | ) |

override

destructor

## Member Function Documentation

## ◆ comparepeaks_()

double comparepeaks_ | ( | double | posa,
|  | double | posb,
|  | double | inta,
|  | double | intb
| ) |  | const

private

similarity of two peaks

## ◆ create()

static PeakSpectrumCompareFunctor* create | ( |  | ) |

inline static

## ◆ dynprog_()

double dynprog_ | ( | const PeakSpectrum & | ,
|  | const PeakSpectrum & | ,
|  | int | ,
|  | int | ,
|  | int | ,
|  | int |
| ) |  | const

private

O(n^2) dynamical programming.

## ◆ getPeakMap()

Map<UInt, UInt> getPeakMap | ( |  | ) | const

## ◆ getProductName()

static const String getProductName | ( |  | ) |

inline static

## ◆ lastconsensus()

const PeakSpectrum& lastconsensus | ( |  | ) | const

return consensus spectrum from last function call operator

## ◆ operator()() [1/2]

double operator() | ( | const PeakSpectrum & | a,
|  | const PeakSpectrum & | b
| ) |  | const

override virtual

function call operator, calculates the similarity

Implements PeakSpectrumCompareFunctor.

## ◆ operator()() [2/2]

double operator() | ( | const PeakSpectrum & | a | ) | const

override virtual

calculates self similarity

Implements PeakSpectrumCompareFunctor.

## ◆ operator=()

SpectrumCheapDPCorr& operator= | ( | const SpectrumCheapDPCorr & | source | ) |

assignment operator

## ◆ setFactor()

void setFactor | ( | double | f | ) |

set weighting of the second spectrum for consensus from next function call operator

## Member Data Documentation

## ◆ factor_

double factor_

mutable private

weighting factor for the next consensus spectrum

## ◆ info_

const String info_

static private

## ◆ keeppeaks_

bool keeppeaks_

private

should peaks with no alignment partner be kept in the consensus?

## ◆ lastconsensus_

PeakSpectrum lastconsensus_

mutable private

consensus spectrum of the last comparison

## ◆ peak_map_

Map<UInt, UInt> peak_map_

mutable private

last peak map