OpenMS
SpectrumAlignment Class Reference

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...
 
SpectrumAlignmentoperator= (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...
 
DefaultParamHandleroperator= (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 ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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< Stringsubsections_
 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:

NameTypeDefaultRestrictionsDescription
tolerance float0.3  Defines the absolute (in Da) or relative (in ppm) tolerance
is_relative_tolerance stringfalse true, falseIf 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()

~SpectrumAlignment ( )
override

destructor

Member Function Documentation

◆ getSpectrumAlignment()

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

◆ operator=()

SpectrumAlignment& operator= ( const SpectrumAlignment source)

assignment operator