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>

Inheritance diagram for SpectrumAlignment:

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Collaboration diagram for SpectrumAlignment:

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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 &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...

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...

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|))

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' 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]

SpectrumAlignment ( )

default constructor

◆ SpectrumAlignment() [2/2]

SpectrumAlignment ( const SpectrumAlignment & source )

copy constructor

◆ ~SpectrumAlignment()

~SpectrumAlignment ( )

override

destructor

Member Function Documentation

◆ getSpectrumAlignment()

void getSpectrumAlignment	(	std::vector< std::pair< Size, Size > > &	alignment,
		const SpectrumType1 &	s1,
		const SpectrumType2 &	s2
	)		const

inline

References MatchedIterator< CONT_T, TRAIT, CONST_T >::end(), MatchedIterator< CONT_T, TRAIT, CONST_T >::refIdx(), OpenMS::StringUtils::reverse(), and MatchedIterator< CONT_T, TRAIT, CONST_T >::tgtIdx().

Referenced by SpectraMerger::mergeSpectra_().

◆ operator=()

SpectrumAlignment& operator= ( const SpectrumAlignment & source )

assignment operator

Public Member Functions

Additional Inherited Members