| OpenMS 2.5.0

Public Member Functions | List of all members
SpectrumAlignment Class Reference
Spectrum Comparison

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...
| ~SpectrumAlignment () override
| 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 &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

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(), and MatchedIterator< CONT_T, TRAIT, CONST_T >::tgtIdx().

Referenced by SpectraMerger::mergeSpectra_().

## ◆ operator=()

SpectrumAlignment& operator= | ( | const SpectrumAlignment & | source | ) |

assignment operator