Similarity score via spectra alignment. More...
#include <OpenMS/COMPARISON/SPECTRA/SpectrumAlignmentScore.h>
Inheritance diagram for SpectrumAlignmentScore:
Public Member Functions | |
| SpectrumAlignmentScore () | |
| default constructor More... | |
| SpectrumAlignmentScore (const SpectrumAlignmentScore &source) | |
| copy constructor More... | |
| virtual | ~SpectrumAlignmentScore () |
| destructor More... | |
| SpectrumAlignmentScore & | operator= (const SpectrumAlignmentScore &source) |
| assignment operator More... | |
| double | operator() (const PeakSpectrum &spec1, const PeakSpectrum &spec2) const |
| function call operator, calculates the similarity More... | |
| double | operator() (const PeakSpectrum &spec) const |
| calculates self similarity More... | |
 Public Member Functions inherited from PeakSpectrumCompareFunctor | |
| PeakSpectrumCompareFunctor () | |
| default constructor More... | |
| PeakSpectrumCompareFunctor (const PeakSpectrumCompareFunctor &source) | |
| copy constructor More... | |
| virtual | ~PeakSpectrumCompareFunctor () |
| 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 ¶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... | |
Static Public Member Functions | |
| static PeakSpectrumCompareFunctor * | create () |
| static const String | getProductName () |
| Static Public Member Functions inherited from PeakSpectrumCompareFunctor | |
| static void | registerChildren () |
| registers all derived products More... | |
| static const String | getProductName () |
Protected Member Functions | |
| double | getFactor_ (double mz_tolerance, double mz_difference, bool is_gaussian=false) const |
| returns the factor associated with the m/z tolerance and m/z difference of the peaks 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... | |
Additional Inherited Members | |
| 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
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 |
|---|---|---|---|---|
| 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 |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
Constructor & Destructor Documentation
◆ SpectrumAlignmentScore() [1/2]
default constructor
◆ SpectrumAlignmentScore() [2/2]
| SpectrumAlignmentScore | ( | const SpectrumAlignmentScore & | source | ) |
copy constructor
◆ ~SpectrumAlignmentScore()
|
virtual |
destructor
Member Function Documentation
◆ create()
|
inlinestatic |
◆ getFactor_()
|
protected |
returns the factor associated with the m/z tolerance and m/z difference of the peaks
◆ getProductName()
|
inlinestatic |
◆ operator()() [1/2]
|
virtual |
function call operator, calculates the similarity
Implements PeakSpectrumCompareFunctor.
◆ operator()() [2/2]
|
virtual |
calculates self similarity
Implements PeakSpectrumCompareFunctor.
◆ operator=()
| SpectrumAlignmentScore& operator= | ( | const SpectrumAlignmentScore & | source | ) |
assignment operator