For each element in the reference container the closest peak in the target will be searched. If no match is found within the tolerance window, the peak will be skipped over. More...

#include <OpenMS/DATASTRUCTURES/MatchedIterator.h>

Collaboration diagram for MatchedIterator< CONT_T, TRAIT, CONST_T >:

[legend]

Public Types
using	iterator_category = std::forward_iterator_tag

using	value_type = typename CONT_T::value_type

using	difference_type = std::ptrdiff_t

using	pointer = typename std::conditional< CONST_T, typename CONT_T::value_type const , typename CONT_T::value_type >::type

using	reference = typename std::conditional< CONST_T, typename CONT_T::value_type const &, typename CONT_T::value_type & >::type

using	CONT_IT = typename std::conditional< CONST_T, typename CONT_T::const_iterator, typename CONT_T::iterator >::type

using	CONST_CONT_IT = typename CONT_T::const_iterator

Public Member Functions
	MatchedIterator (const CONT_T &ref, const CONT_T &target, float tolerance)
	Constructs a MatchedIterator on two containers. The way a match is found, depends on the TRAIT type (ppm or Da tolerance)

	MatchedIterator (const CONST_CONT_IT ref_begin, const CONST_CONT_IT ref_end, const CONST_CONT_IT tgt_begin, const CONST_CONT_IT tgt_end, float tolerance)
	Constructs a MatchedIterator on two containers. The way a match is found, depends on the TRAIT type (ppm or Da tolerance)

	MatchedIterator ()
	Default CTor; do not use this for anything other than assigning to it;.

	MatchedIterator (const MatchedIterator &rhs)=default
	Copy CTor (default)

MatchedIterator &	operator= (const MatchedIterator &rhs)=default
	Assignment operator (default)

bool	operator== (const MatchedIterator &rhs) const

bool	operator!= (const MatchedIterator &rhs) const

template<bool _CONST = CONST_T>
std::enable_if< _CONST, reference >::type	operator* () const
	dereference current target element

template<bool _CONST = CONST_T>
std::enable_if<!_CONST, reference >::type	operator* ()

template<bool _CONST = CONST_T>
std::enable_if< _CONST, pointer >::type	operator-> () const
	pointer to current target element

template<bool _CONST = CONST_T>
std::enable_if<!_CONST, pointer >::type	operator-> ()

const value_type &	ref () const
	current element in reference container

size_t	refIdx () const
	index into reference container

size_t	tgtIdx () const
	index into target container

MatchedIterator &	operator++ ()
	Advances to the next valid pair.

MatchedIterator	operator++ (int)
	post-increment

Static Public Member Functions
static MatchedIterator	end ()
	the end iterator

Protected Member Functions
	MatchedIterator (bool)

void	setToEnd_ ()

bool	isEnd_ () const

void	advanceTarget_ ()

Protected Attributes
CONST_CONT_IT	ref_begin_

CONST_CONT_IT	ref_end_

CONST_CONT_IT	tgt_begin_

CONST_CONT_IT	tgt_end_

CONT_IT	it_ref_

CONT_IT	it_tgt_

float	tol_

bool	is_end_ = false

Detailed Description

template<typename CONT_T, typename TRAIT, bool CONST_T = true>
class OpenMS::MatchedIterator< CONT_T, TRAIT, CONST_T >

For each element in the reference container the closest peak in the target will be searched. If no match is found within the tolerance window, the peak will be skipped over.

This class can be used for example to iterate through the matching peaks in two spectra (e.g. experimental spectrum and reference spectrum) that are within a given tolerance (in m/z, RT, or something user-defined).

The iterator always chooses the closest matching peak in the target container, if more than one candidate is found in the match-window. If two peaks have equal distance, the smaller value is preferred. If no peak is found within the given tolerance (distance), the reference peak does not yield a result and the next reference peak is tested. This means the operator++ can be called at most(!) ref.size()-1 times before it == is.end().

The TRAIT template argument (e.g., ValueTrait, DaTrait or PpmTrait) encodes the distance metric (on the value directly, or a member of the value_type, e.g. ppm or Da for m/z, or RT or any other metric you like). The simplest use case would be a vector<float> or similar. The TRAIT struct just defines two functions which return some distance metrics and accept elements of the container CONT_T as arguments. Both containers must be sorted with respect to the comparator used in TRAIT.

The CONST_T template argument switches between a 'const_iterator' and an 'iterator'.

This iterator is much more efficient than iterating over the reference container and calling findNearest(), i.e. binary search on the target container, i.e. O(n+m) vs. O(n*log(m)). Since this container is much more cache-friendly, the actual speedups are even larger.

Member Typedef Documentation

◆ CONST_CONT_IT

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

using CONST_CONT_IT = typename CONT_T::const_iterator

◆ CONT_IT

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

using CONT_IT = typename std::conditional<CONST_T, typename CONT_T::const_iterator, typename CONT_T::iterator>::type

◆ difference_type

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

using difference_type = std::ptrdiff_t

◆ iterator_category

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

using iterator_category = std::forward_iterator_tag

◆ pointer

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

using pointer = typename std::conditional<CONST_T, typename CONT_T::value_type const*, typename CONT_T::value_type*>::type

◆ reference

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

using reference = typename std::conditional<CONST_T, typename CONT_T::value_type const&, typename CONT_T::value_type&>::type

◆ value_type

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

using value_type = typename CONT_T::value_type

Constructor & Destructor Documentation

◆ MatchedIterator() [1/5]

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

MatchedIterator	(	const CONT_T &	ref,
		const CONT_T &	target,
		float	tolerance
	)

inlineexplicit

Constructs a MatchedIterator on two containers. The way a match is found, depends on the TRAIT type (ppm or Da tolerance)

For each element in the reference container the closest peak in the target will be searched. If no match is found within the tolerance window, the peak will be skipped over.

Parameters

[in]	ref	For each element in this reference container the closest peak in the target will be searched
[in]	target	Target container
[in]	tolerance	Maximal distance between a valid matching pair in reference and target (unit is according to TRAIT::getDiffAbsolute(), i.e. could be ppm, Da, seconds, ...)

◆ MatchedIterator() [2/5]

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

MatchedIterator	(	const CONST_CONT_IT	ref_begin,
		const CONST_CONT_IT	ref_end,
		const CONST_CONT_IT	tgt_begin,
		const CONST_CONT_IT	tgt_end,
		float	tolerance
	)

inlineexplicit

Constructs a MatchedIterator on two containers. The way a match is found, depends on the TRAIT type (ppm or Da tolerance)

For each element in the reference container the closest peak in the target will be searched. If no match is found within the tolerance window, the peak will be skipped over.

Parameters

[in]	ref_begin	Begin range of reference container
[in]	ref_end	End range of reference container
[in]	tgt_begin	Begin range of reference container
[in]	tgt_end	End range of reference container
[in]	tolerance	Maximal distance between a valid matching pair in reference and target (unit is according to TRAIT::getDiffAbsolute(), i.e. could be ppm, Da, seconds, ...)

References MatchedIterator< CONT_T, TRAIT, CONST_T >::advanceTarget_(), MatchedIterator< CONT_T, TRAIT, CONST_T >::setToEnd_(), MatchedIterator< CONT_T, TRAIT, CONST_T >::tgt_begin_, and MatchedIterator< CONT_T, TRAIT, CONST_T >::tgt_end_.

◆ MatchedIterator() [3/5]

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

MatchedIterator ( )

inlineexplicit

Default CTor; do not use this for anything other than assigning to it;.

Referenced by MatchedIterator< CONT_T, TRAIT, CONST_T >::end().

◆ MatchedIterator() [4/5]

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

MatchedIterator ( const MatchedIterator< CONT_T, TRAIT, CONST_T > & rhs )

default

Copy CTor (default)

◆ MatchedIterator() [5/5]

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

MatchedIterator ( bool )

inlineprotected

protected Ctor which creates and end() iterator the bool argument is only used to call the correct target (its value is ignored)

Member Function Documentation

◆ advanceTarget_()

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

void advanceTarget_ ( )

inlineprotected

References MatchedIterator< CONT_T, TRAIT, CONST_T >::it_ref_, MatchedIterator< CONT_T, TRAIT, CONST_T >::it_tgt_, MatchedIterator< CONT_T, TRAIT, CONST_T >::ref_end_, MatchedIterator< CONT_T, TRAIT, CONST_T >::setToEnd_(), MatchedIterator< CONT_T, TRAIT, CONST_T >::tgt_end_, and MatchedIterator< CONT_T, TRAIT, CONST_T >::tol_.

Referenced by MatchedIterator< CONT_T, TRAIT, CONST_T >::MatchedIterator(), and MatchedIterator< CONT_T, TRAIT, CONST_T >::operator++().

◆ end()

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

static MatchedIterator end ( )

inlinestatic

the end iterator

References MatchedIterator< CONT_T, TRAIT, CONST_T >::MatchedIterator().

Referenced by SpectrumAlignment::getSpectrumAlignment().

◆ isEnd_()

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

bool isEnd_ ( ) const

inlineprotected

References MatchedIterator< CONT_T, TRAIT, CONST_T >::is_end_.

Referenced by MatchedIterator< CONT_T, TRAIT, CONST_T >::operator++(), and MatchedIterator< CONT_T, TRAIT, CONST_T >::operator==().

◆ operator!=()

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

bool operator!= ( const MatchedIterator< CONT_T, TRAIT, CONST_T > & rhs ) const

inline

◆ operator*() [1/2]

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

template<bool _CONST = CONST_T>

std::enable_if<!_CONST, reference >::type operator* ( )

inline

References MatchedIterator< CONT_T, TRAIT, CONST_T >::it_tgt_.

◆ operator*() [2/2]

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

template<bool _CONST = CONST_T>

std::enable_if< _CONST, reference >::type operator* ( ) const

inline

dereference current target element

References MatchedIterator< CONT_T, TRAIT, CONST_T >::it_tgt_.

◆ operator++() [1/2]

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

MatchedIterator & operator++ ( )

inline

Advances to the next valid pair.

Exceptions

Exception::InvalidIterator If iterator is already at end

References MatchedIterator< CONT_T, TRAIT, CONST_T >::advanceTarget_(), MatchedIterator< CONT_T, TRAIT, CONST_T >::isEnd_(), MatchedIterator< CONT_T, TRAIT, CONST_T >::it_ref_, and OPENMS_PRECONDITION.

◆ operator++() [2/2]

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

MatchedIterator operator++ ( int )

inline

post-increment

◆ operator->() [1/2]

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

template<bool _CONST = CONST_T>

std::enable_if<!_CONST, pointer >::type operator-> ( )

inline

◆ operator->() [2/2]

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

template<bool _CONST = CONST_T>

std::enable_if< _CONST, pointer >::type operator-> ( ) const

inline

pointer to current target element

◆ operator=()

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

MatchedIterator & operator= ( const MatchedIterator< CONT_T, TRAIT, CONST_T > & rhs )

default

Assignment operator (default)

◆ operator==()

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

bool operator== ( const MatchedIterator< CONT_T, TRAIT, CONST_T > & rhs ) const

inline

References MatchedIterator< CONT_T, TRAIT, CONST_T >::isEnd_(), MatchedIterator< CONT_T, TRAIT, CONST_T >::it_ref_, MatchedIterator< CONT_T, TRAIT, CONST_T >::it_tgt_, MatchedIterator< CONT_T, TRAIT, CONST_T >::ref_begin_, MatchedIterator< CONT_T, TRAIT, CONST_T >::ref_end_, MatchedIterator< CONT_T, TRAIT, CONST_T >::tgt_begin_, and MatchedIterator< CONT_T, TRAIT, CONST_T >::tgt_end_.

◆ ref()

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

const value_type & ref ( ) const

inline

current element in reference container

References MatchedIterator< CONT_T, TRAIT, CONST_T >::it_ref_.

◆ refIdx()

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

size_t refIdx ( ) const

inline

index into reference container

References MatchedIterator< CONT_T, TRAIT, CONST_T >::it_ref_, and MatchedIterator< CONT_T, TRAIT, CONST_T >::ref_begin_.

Referenced by SpectrumAlignment::getSpectrumAlignment().

◆ setToEnd_()

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

void setToEnd_ ( )

inlineprotected

References MatchedIterator< CONT_T, TRAIT, CONST_T >::is_end_.

Referenced by MatchedIterator< CONT_T, TRAIT, CONST_T >::advanceTarget_(), and MatchedIterator< CONT_T, TRAIT, CONST_T >::MatchedIterator().

◆ tgtIdx()

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

size_t tgtIdx ( ) const

inline

index into target container

References MatchedIterator< CONT_T, TRAIT, CONST_T >::it_tgt_, and MatchedIterator< CONT_T, TRAIT, CONST_T >::tgt_begin_.

Referenced by SpectrumAlignment::getSpectrumAlignment().

Member Data Documentation

◆ is_end_

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

bool is_end_ = false

protected

Referenced by MatchedIterator< CONT_T, TRAIT, CONST_T >::isEnd_(), and MatchedIterator< CONT_T, TRAIT, CONST_T >::setToEnd_().

◆ it_ref_

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

CONT_IT it_ref_

protected

Referenced by MatchedIterator< CONT_T, TRAIT, CONST_T >::advanceTarget_(), MatchedIterator< CONT_T, TRAIT, CONST_T >::operator++(), MatchedIterator< CONT_T, TRAIT, CONST_T >::operator==(), MatchedIterator< CONT_T, TRAIT, CONST_T >::ref(), and MatchedIterator< CONT_T, TRAIT, CONST_T >::refIdx().

◆ it_tgt_

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

CONT_IT it_tgt_

protected

Referenced by MatchedIterator< CONT_T, TRAIT, CONST_T >::advanceTarget_(), MatchedIterator< CONT_T, TRAIT, CONST_T >::operator*(), MatchedIterator< CONT_T, TRAIT, CONST_T >::operator*(), MatchedIterator< CONT_T, TRAIT, CONST_T >::operator==(), and MatchedIterator< CONT_T, TRAIT, CONST_T >::tgtIdx().

◆ ref_begin_

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

CONST_CONT_IT ref_begin_

protected

Referenced by MatchedIterator< CONT_T, TRAIT, CONST_T >::operator==(), and MatchedIterator< CONT_T, TRAIT, CONST_T >::refIdx().

◆ ref_end_

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

CONST_CONT_IT ref_end_

protected

Referenced by MatchedIterator< CONT_T, TRAIT, CONST_T >::advanceTarget_(), and MatchedIterator< CONT_T, TRAIT, CONST_T >::operator==().

◆ tgt_begin_

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

CONST_CONT_IT tgt_begin_

protected

Referenced by MatchedIterator< CONT_T, TRAIT, CONST_T >::MatchedIterator(), MatchedIterator< CONT_T, TRAIT, CONST_T >::operator==(), and MatchedIterator< CONT_T, TRAIT, CONST_T >::tgtIdx().

◆ tgt_end_

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

CONST_CONT_IT tgt_end_

protected

Referenced by MatchedIterator< CONT_T, TRAIT, CONST_T >::advanceTarget_(), MatchedIterator< CONT_T, TRAIT, CONST_T >::MatchedIterator(), and MatchedIterator< CONT_T, TRAIT, CONST_T >::operator==().

◆ tol_

template<typename CONT_T , typename TRAIT , bool CONST_T = true>

float tol_

protected

Referenced by MatchedIterator< CONT_T, TRAIT, CONST_T >::advanceTarget_().

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

◆ CONST_CONT_IT

◆ CONT_IT

◆ difference_type

◆ iterator_category

◆ pointer

◆ reference

◆ value_type

Constructor & Destructor Documentation

◆ MatchedIterator() [1/5]

◆ MatchedIterator() [2/5]

◆ MatchedIterator() [3/5]

◆ MatchedIterator() [4/5]

◆ MatchedIterator() [5/5]

Member Function Documentation

◆ advanceTarget_()

◆ end()

◆ isEnd_()

◆ operator!=()

◆ operator*() [1/2]

◆ operator*() [2/2]

◆ operator++() [1/2]

◆ operator++() [2/2]

◆ operator->() [1/2]

◆ operator->() [2/2]

◆ operator=()

◆ operator==()

◆ ref()

◆ refIdx()

◆ setToEnd_()

◆ tgtIdx()

Member Data Documentation

◆ is_end_

◆ it_ref_

◆ it_tgt_

◆ ref_begin_

◆ ref_end_

◆ tgt_begin_

◆ tgt_end_

◆ tol_