OpenMS
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Similarity score via spectra alignment. More...
#include <OpenMS/COMPARISON/SpectrumAlignmentScore.h>
Public Member Functions | |
SpectrumAlignmentScore () | |
default constructor More... | |
SpectrumAlignmentScore (const SpectrumAlignmentScore &source) | |
copy constructor More... | |
~SpectrumAlignmentScore () override | |
destructor More... | |
SpectrumAlignmentScore & | operator= (const SpectrumAlignmentScore &source) |
assignment operator More... | |
double | operator() (const PeakSpectrum &spec1, const PeakSpectrum &spec2) const override |
function call operator, calculates the similarity More... | |
double | operator() (const PeakSpectrum &spec) 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... | |
DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
Assignment operator. More... | |
virtual bool | operator== (const DefaultParamHandler &rhs) const |
Equality operator. More... | |
void | setParameters (const Param ¶m) |
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... | |
Additional Inherited Members | |
Static Public Member Functions inherited from DefaultParamHandler | |
static void | writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="") |
Writes all parameters to meta values. More... | |
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... | |
Similarity score via spectra alignment.
This class implements a simple scoring based on the alignment of spectra. This alignment is implemented in the SpectrumAlignment class and performs a dynamic programming alignment of the peaks, minimizing the distances between the aligned peaks and maximizing the number of peak pairs.
The scoring is done via the simple formula score = sum / (sqrt(sum1 * sum2)). sum is the product of the intensities of the aligned peaks, with the given exponent (default is 2). sum1 and sum2 are the sum of the intensities squared for each peak of both spectra respectively.
A binned version of this scoring is implemented in the ZhangSimilarityScoring class.
Parameters of this class are:Name | Type | Default | Restrictions | Description |
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tolerance | float | 0.3 | Defines the absolute (in Da) or relative (in ppm) tolerance | |
is_relative_tolerance | string | false | true, false | if true, the tolerance value is interpreted as ppm |
use_linear_factor | string | false | true, false | if true, the intensities are weighted with the relative m/z difference |
use_gaussian_factor | string | false | true, false | if true, the intensities are weighted with the relative m/z difference using a gaussian |
default constructor
SpectrumAlignmentScore | ( | const SpectrumAlignmentScore & | source | ) |
copy constructor
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override |
destructor
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overridevirtual |
calculates self similarity
Implements PeakSpectrumCompareFunctor.
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overridevirtual |
function call operator, calculates the similarity
Implements PeakSpectrumCompareFunctor.
SpectrumAlignmentScore& operator= | ( | const SpectrumAlignmentScore & | source | ) |
assignment operator