IdentifierMSRunMapper Class Reference

Two-way mapping from ms-run-path to protID|pepID-identifier. More...

#include <OpenMS/METADATA/IdentifierMSRunMapper.h>

Collaboration diagram for IdentifierMSRunMapper:

Public Member Functions
	IdentifierMSRunMapper ()=default
	IdentifierMSRunMapper (const std::vector< ProteinIdentification > &prot_ids)
	Construct mapping from a vector of ProteinIdentifications.
void	create (const std::vector< ProteinIdentification > &prot_ids)
	Create/update mapping from a vector of ProteinIdentifications.
String	getPrimaryMSRunPath (const PeptideIdentification &pepid) const
	Get the primary MS run path for a PeptideIdentification (using id_merge_index metadata)
bool	hasIdentifier (const String &identifier) const
	Check if the mapping contains an entry for the given identifier.
const String &	getIdentifier (const StringList &ms_run_paths) const
	Get the identifier for a given MS run path list (throws if not found)
bool	empty () const
	Check if the mapping is empty.
Size	size () const
	Get the number of identifier mappings.
const StringList &	getMSRunPaths (const String &identifier) const
	Get the MS run paths for a given identifier (returns empty list if not found)
std::vector< String >	getIdentifiers () const
	Get all identifiers in this mapping.
bool	hasRunPath (const StringList &ms_run_paths) const
	Check if the mapping contains an entry for the given MS run paths.
bool	tryGetIdentifier (const StringList &ms_run_paths, String &identifier) const
	Try to get identifier for a given MS run path list (returns false if not found)

Private Attributes
std::map< String, StringList >	identifier_to_msrunpath_
std::map< StringList, String >	runpath_to_identifier_

Static Private Attributes
static const StringList	empty_stringlist_
	Empty list returned by getMSRunPaths when identifier not found.

Detailed Description

Two-way mapping from ms-run-path to protID|pepID-identifier.

This class encapsulates the mapping between protein identification identifiers and their associated MS run paths. It is used to resolve the correct source file for peptide identifications, especially in merged identification results.

Usage example:

// Create mapping from protein identifications
IdentifierMSRunMapper mapping(protein_ids);
 
// Get the source file for a peptide identification
String source_file = mapping.getPrimaryMSRunPath(pep_id);
 
// Build a USI using the mapping
USI usi = pep_id.buildUSI(mapping, "PXD000561");

Note

The internal data structures are private to avoid exposing nested containers that are difficult to wrap in Python bindings.

See also

ProteinIdentification, PeptideIdentification

Constructor & Destructor Documentation

IdentifierMSRunMapper() [1/2]

IdentifierMSRunMapper ( )

default

IdentifierMSRunMapper() [2/2]

IdentifierMSRunMapper ( const std::vector< ProteinIdentification > &  prot_ids )

explicit

Construct mapping from a vector of ProteinIdentifications.

Member Function Documentation

create()

void create

(

const std::vector< ProteinIdentification > &

prot_ids

)

Create/update mapping from a vector of ProteinIdentifications.

empty()

bool empty

(

)

const

Check if the mapping is empty.

getIdentifier()

const String & getIdentifier

(

const StringList &

ms_run_paths

)

const

Get the identifier for a given MS run path list (throws if not found)

getIdentifiers()

std::vector< String > getIdentifiers

(

)

const

Get all identifiers in this mapping.

getMSRunPaths()

const StringList & getMSRunPaths

(

const String &

identifier

)

const

Get the MS run paths for a given identifier (returns empty list if not found)

getPrimaryMSRunPath()

String getPrimaryMSRunPath

(

const PeptideIdentification &

pepid

)

const

Get the primary MS run path for a PeptideIdentification (using id_merge_index metadata)

hasIdentifier()

bool hasIdentifier

(

const String &

identifier

)

const

Check if the mapping contains an entry for the given identifier.

hasRunPath()

bool hasRunPath

(

const StringList &

ms_run_paths

)

const

Check if the mapping contains an entry for the given MS run paths.

size()

Size size

(

)

const

Get the number of identifier mappings.

tryGetIdentifier()

bool tryGetIdentifier	(	const StringList &	ms_run_paths,
		String &	identifier
	)		const

Try to get identifier for a given MS run path list (returns false if not found)

Member Data Documentation

empty_stringlist_

const StringList empty_stringlist_

staticprivate

Empty list returned by getMSRunPaths when identifier not found.

identifier_to_msrunpath_

std::map<String, StringList> identifier_to_msrunpath_

private

runpath_to_identifier_

std::map<StringList, String> runpath_to_identifier_

private