Aligns the peaks of two sorted spectra Method 1: Using a banded (width via 'tolerance' parameter) alignment if absolute tolerances are given. Scoring function is the m/z distance between peaks. Intensity does not play a role! More...
#include <OpenMS/COMPARISON/SPECTRA/SpectrumAlignment.h>
Inheritance diagram for SpectrumAlignment:
Public Member Functions | |
| template<typename SpectrumType1 , typename SpectrumType2 > | |
| void | getSpectrumAlignment (std::vector< std::pair< Size, Size > > &alignment, const SpectrumType1 &s1, const SpectrumType2 &s2) const |
| SpectrumAlignment () | |
| default constructor More... | |
| SpectrumAlignment (const SpectrumAlignment &source) | |
| copy constructor More... | |
| virtual | ~SpectrumAlignment () |
| destructor More... | |
| SpectrumAlignment & | operator= (const SpectrumAlignment &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... | |
Additional Inherited Members | |
| 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
Aligns the peaks of two sorted spectra Method 1: Using a banded (width via 'tolerance' parameter) alignment if absolute tolerances are given. Scoring function is the m/z distance between peaks. Intensity does not play a role!
Method 2: If relative tolerance (ppm) is specified a simple matching of peaks is performed: Peaks from s1 (usually the theoretical spectrum) are assigned to the closest peak in s2 if it lies in the tolerance window
- Note
- : a peak in s2 can be matched to none, one or multiple peaks in s1. Peaks in s1 may be matched to none or one peak in s2.
- : intensity is ignored TODO: improve time complexity, currently O(|s1|*log(|s2|))
| 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' is interpreted as ppm-value |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
Constructor & Destructor Documentation
◆ SpectrumAlignment() [1/2]
default constructor
◆ SpectrumAlignment() [2/2]
| SpectrumAlignment | ( | const SpectrumAlignment & | source | ) |
copy constructor
◆ ~SpectrumAlignment()
|
virtual |
destructor
Member Function Documentation
◆ getSpectrumAlignment()
|
inline |
Referenced by SpectraMerger::mergeSpectra_(), and RNPxlSearch::postScoreHits_().
◆ operator=()
| SpectrumAlignment& operator= | ( | const SpectrumAlignment & | source | ) |
assignment operator