PeptideIdentificationList Class Reference

Container for peptide identifications from multiple spectra. More...

#include <OpenMS/METADATA/PeptideIdentificationList.h>

Inheritance diagram for PeptideIdentificationList:

Collaboration diagram for PeptideIdentificationList:

Public Member Functions
Additional constructors for std::vector compatibility
	PeptideIdentificationList (const std::vector< PeptideIdentification > &vec)
	Constructor from std::vector. More...
	PeptideIdentificationList (std::vector< PeptideIdentification > &&vec)
	Move constructor from std::vector. More...
	PeptideIdentificationList (std::initializer_list< PeptideIdentification > init)
	Constructor from initializer list. More...
Assignment operators for std::vector compatibility
PeptideIdentificationList &	operator= (const std::vector< PeptideIdentification > &vec)
	Assignment from std::vector. More...
PeptideIdentificationList &	operator= (std::vector< PeptideIdentification > &&vec)
	Move assignment from std::vector. More...
PeptideIdentificationList &	operator= (std::initializer_list< PeptideIdentification > init)
	Assignment from initializer list. More...
Public Member Functions inherited from ExposedVector< PeptideIdentification >
	ExposedVector ()=default
	ExposedVector (const size_t n)
	ExposedVector (const size_t n, const PeptideIdentification &val)
	ExposedVector (Iter begin, Iter end)
	ExposedVector (const ExposedVector &rhs)=default
	Copy C'tor. More...
	ExposedVector (ExposedVector &&rhs) noexcept=default
	Move C'tor. More...
ExposedVector &	operator= (const ExposedVector &rhs)=default
	Assignment. More...
ExposedVector &	operator= (ExposedVector &&rhs) noexcept=default
	Move Assignment. More...
iterator	begin () noexcept
const_iterator	begin () const noexcept
iterator	end () noexcept
const_iterator	end () const noexcept
const_iterator	cbegin () const noexcept
const_iterator	cend () const noexcept
size_t	size () const noexcept
void	resize (const size_t new_size)
void	reserve (const size_t new_size)
bool	empty () const noexcept
PeptideIdentification &	operator[] (size_t i) noexcept
const PeptideIdentification &	operator[] (size_t i) const noexcept
PeptideIdentification &	at (size_t i)
const PeptideIdentification &	at (size_t i) const
PeptideIdentification &	back () noexcept
const PeptideIdentification &	back () const noexcept
void	push_back (const PeptideIdentification &f)
void	push_back (PeptideIdentification &&f)
decltype(auto)	emplace_back (Args &&... args)
void	pop_back () noexcept
iterator	erase (const_iterator where) noexcept
iterator	erase (const_iterator from, const_iterator to) noexcept
iterator	insert (const_iterator where, T from, T to)
iterator	insert (const_iterator pos, const PeptideIdentification &value)
	Insert single element. More...
iterator	insert (const_iterator pos, PeptideIdentification &&value)
	Insert single element (move) More...
iterator	insert (const_iterator pos, size_type count, const PeptideIdentification &value)
	Insert n copies of value. More...
iterator	insert (const_iterator pos, std::initializer_list< PeptideIdentification > init)
	Insert from initializer list. More...
void	clear () noexcept
	Clear all elements. More...
reverse_iterator	rbegin () noexcept
	Get reverse iterator to beginning. More...
const_reverse_iterator	rbegin () const noexcept
	Get const reverse iterator to beginning. More...
reverse_iterator	rend () noexcept
	Get reverse iterator to end. More...
const_reverse_iterator	rend () const noexcept
	Get const reverse iterator to end. More...
const_reverse_iterator	crbegin () const noexcept
	Get const reverse iterator to beginning. More...
const_reverse_iterator	crend () const noexcept
	Get const reverse iterator to end. More...
void	swap (ExposedVector &other) noexcept
	Swap contents with another ExposedVector. More...
void	assign (InputIt first, InputIt last)
	Assign values from iterators. More...
void	assign (size_type count, const PeptideIdentification &value)
	Assign n copies of value. More...
void	assign (std::initializer_list< PeptideIdentification > init)
	Assign from initializer list. More...
PeptideIdentification &	front () noexcept
	Get first element. More...
const PeptideIdentification &	front () const noexcept
	Get first element (const) More...
size_type	max_size () const noexcept
	Get maximum possible size. More...
size_type	capacity () const noexcept
	Get current capacity. More...
void	shrink_to_fit ()
	Shrink capacity to fit size. More...
iterator	emplace (const_iterator pos, Args &&... args)
	Emplace element at position. More...
const VecMember &	getData () const
	read-only access to the underlying data More...
VecMember &	getData ()
	read access to the underlying data More...
bool	operator== (const ExposedVector &other) const
	Equality comparison. More...
bool	operator!= (const ExposedVector &other) const
	Inequality comparison. More...
bool	operator< (const ExposedVector &other) const requires LessThanComparable< PeptideIdentification >
bool	operator<= (const ExposedVector &other) const requires LessThanComparable< PeptideIdentification >
bool	operator> (const ExposedVector &other) const requires LessThanComparable< PeptideIdentification >
bool	operator>= (const ExposedVector &other) const requires LessThanComparable< PeptideIdentification >

Additional Inherited Members
Public Types inherited from ExposedVector< PeptideIdentification >
using	VecMember = std::vector< PeptideIdentification >
using	value_type = typename VecMember::value_type
using	iterator = typename VecMember::iterator
using	const_iterator = typename VecMember::const_iterator
using	reverse_iterator = typename VecMember::reverse_iterator
using	const_reverse_iterator = typename VecMember::const_reverse_iterator
using	size_type = typename VecMember::size_type
using	pointer = typename VecMember::pointer
using	reference = typename VecMember::reference
using	const_reference = typename VecMember::const_reference
using	difference_type = typename VecMember::difference_type
Protected Attributes inherited from ExposedVector< PeptideIdentification >
VecMember	data_
	the container which holds all the data More...

Detailed Description

Container for peptide identifications from multiple spectra.

This class represents a collection of PeptideIdentification objects, typically originating from multiple spectra within a single identification run or experiment.

PeptideIdentificationList is commonly used in scenarios where multiple spectra have been searched against a database, resulting in a list of identifications that need to be processed together. Examples include:

• Storing all peptide identifications from an LC-MS/MS run
• Collecting identifications for protein inference algorithms
• Aggregating results from multiple search engines
• Managing identifications in feature mapping workflows

Note: The class uses composition over inheritance (via ExposedVector) to avoid the well-known pitfalls of inheriting directly from STL containers

Usage example:

PeptideIdentificationList peptide_ids;
 
// Add identifications from search results
PeptideIdentification id1, id2;
id1.setRT(1234.5);
id1.setMZ(567.8);
peptide_ids.push_back(id1);
peptide_ids.push_back(id2);
 
// Process all identifications
for (auto& id : peptide_ids)
{
  // Apply filtering, scoring, etc.
  IDFilter::keepNBestHits(id, 5);
}
 
// Use with algorithms that operate on collections
IDFilter::keepNBestHits(peptide_ids, 1);
BasicProteinInferenceAlgorithm algo;
algo.run(peptide_ids, protein_ids);

The container provides full vector-like functionality including element access, iteration, size management, and all standard algorithms.

See also

PeptideIdentification, ProteinIdentification, IDFilter, BasicProteinInferenceAlgorithm, ExposedVector

Constructor & Destructor Documentation

PeptideIdentificationList() [1/3]

PeptideIdentificationList ( const std::vector< PeptideIdentification > &  vec )

inline

Constructor from std::vector.

PeptideIdentificationList() [2/3]

PeptideIdentificationList ( std::vector< PeptideIdentification > &&  vec )

inline

Move constructor from std::vector.

PeptideIdentificationList() [3/3]

PeptideIdentificationList ( std::initializer_list< PeptideIdentification >  init )

inline

Constructor from initializer list.

Member Function Documentation

operator=() [1/3]

PeptideIdentificationList& operator= ( const std::vector< PeptideIdentification > &  vec )

inline

Assignment from std::vector.

operator=() [2/3]

PeptideIdentificationList& operator= ( std::initializer_list< PeptideIdentification >  init )

inline

Assignment from initializer list.

operator=() [3/3]

PeptideIdentificationList& operator= ( std::vector< PeptideIdentification > &&  vec )

inline

Move assignment from std::vector.