OpenMS
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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/SpectrumAlignment.h>
Public Member Functions | |
SpectrumAlignment () | |
default constructor More... | |
SpectrumAlignment (const SpectrumAlignment &source) | |
copy constructor More... | |
~SpectrumAlignment () override | |
destructor More... | |
SpectrumAlignment & | operator= (const SpectrumAlignment &source) |
assignment operator More... | |
template<typename SpectrumType1 , typename SpectrumType2 > | |
void | getSpectrumAlignment (std::vector< std::pair< Size, Size > > &alignment, const SpectrumType1 &s1, const SpectrumType2 &s2) const |
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... | |
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
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 |
default constructor
SpectrumAlignment | ( | const SpectrumAlignment & | source | ) |
copy constructor
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override |
destructor
SpectrumAlignment& operator= | ( | const SpectrumAlignment & | source | ) |
assignment operator