CrossLinksDB Class Reference

Process-wide singleton database of cross-linking modifications. More...

#include <OpenMS/CHEMISTRY/CrossLinksDB.h>

Inheritance diagram for CrossLinksDB:

Collaboration diagram for CrossLinksDB:

Public Member Functions
void	getAllSearchModifications (std::vector< std::string > &modifications) const
	Returns the IDs of all cross-linker modifications that are usable for identification searches (i.e. carry a PSI-MOD accession).
Public Member Functions inherited from ModificationsDB
	ModificationsDB (std::vector< std::unique_ptr< ModificationDataProvider > > providers)
	Construct from data providers (no file I/O performed by this constructor).
virtual	~ModificationsDB ()
	Destructor (public so non-singleton instances created via provider constructor can be destroyed)
Size	getNumberOfModifications () const
	Returns the number of modifications read from the unimod.xml file.
const ResidueModification *	getModification (Size index) const
	Returns the modification with the given index. note: out-of-bounds check is only performed in debug mode.
void	searchModifications (std::set< const ResidueModification * > &mods, const std::string &mod_name, const std::string &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const
	Collects all modifications which have the given name as synonym.
const ResidueModification *	searchModification (const ResidueModification &mod_in) const
	Returns a pointer to an exact match of the given modification if present in the DB.
const ResidueModification *	searchModificationsFast (const std::string &mod_name, bool &multiple_matches, const std::string &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const
	Returns the modification which has the given name as synonym (fast version)
const ResidueModification *	getModification (const std::string &mod_name, const std::string &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const
	Returns the modification with the given name.
bool	has (const std::string &modification) const
	Returns true if the modification exists.
const ResidueModification *	addModification (std::unique_ptr< ResidueModification > new_mod) const
	Add a new modification to ModificationsDB. If the modification already exists (based on its fullID) it is not added.
const ResidueModification *	addModification (const ResidueModification &new_mod) const
	Add a new modification to ModificationsDB. If the modification already exists (based on its fullID) it is not added. A copy will be made on the heap and added to the ModificationsDB otherwise.
Size	findModificationIndex (const std::string &mod_name) const
	Returns the index of the modification in the mods_ vector; a unique name must be given.
void	searchModificationsByDiffMonoMass (std::vector< std::string > &mods, double mass, double max_error, const std::string &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const
	Collects all modifications with delta mass inside a tolerance window.
void	searchModificationsByDiffMonoMass (std::vector< const ResidueModification * > &mods, double mass, double max_error, const std::string &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const
void	searchModificationsByDiffMonoMassSorted (std::vector< std::string > &mods, double mass, double max_error, const std::string &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const
	Collects all modifications with delta mass inside a tolerance window and adds them sorted by mass difference.
void	searchModificationsByDiffMonoMassSorted (std::vector< const ResidueModification * > &mods, double mass, double max_error, const std::string &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const
const ResidueModification *	getBestModificationByDiffMonoMass (double mass, double max_error, const std::string &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const
	Returns the best matching modification for the given delta mass and residue.
void	getAllSearchModifications (std::vector< std::string > &modifications) const
	Collects all modifications that can be used for identification searches.
void	writeTSV (const std::string &filename) const
	Writes tab separated entries: FullId,FullName,Origin,AA,TerminusSpecificity,DiffMonoMass (including header) to TSV file.

Static Public Member Functions
static const CrossLinksDB *	getInstance ()
	Returns the process-wide singleton instance.
Static Public Member Functions inherited from ModificationsDB
static const ModificationsDB *	getInstance ()
static const ModificationsDB *	initializeModificationsDB (std::string unimod_file="CHEMISTRY/unimod.xml", std::string custommod_file="CHEMISTRY/custom_mods.xml", std::string psimod_file="CHEMISTRY/PSI-MOD.obo", std::string xlmod_file="CHEMISTRY/XLMOD.obo")
	Initializes the modification DB with non-default modification files (can only be done once)
static bool	isInstantiated ()
	Check whether ModificationsDB was instantiated before.

Private Member Functions
Constructors and Destructors
	CrossLinksDB ()
	Private default constructor: parses the XLMOD ontology and forwards the resulting providers to ModificationsDB. Called once via getInstance.
	CrossLinksDB (const CrossLinksDB &residue_db)
	Private copy constructor (singleton — copying is not permitted).
	~CrossLinksDB () override
	Destructor. Never invoked in practice because the singleton is allocated with new and outlives the process.

Assignment
CrossLinksDB &	operator= (const CrossLinksDB &aa)
	Private assignment operator (singleton — assignment is not permitted).
static std::vector< std::unique_ptr< ModificationDataProvider > >	makeCrossLinkProviders_ ()
	Builds the OBO data provider list used by the base-class constructor. Loads CHEMISTRY/XLMOD.obo with the cross_links_only flag set.

Additional Inherited Members
Protected Member Functions inherited from ModificationsDB
bool	residuesMatch_ (const char residue, const ResidueModification *curr_mod) const
	Helper function to check if a residue matches the origin for a modification.
Protected Attributes inherited from ModificationsDB
std::vector< ResidueModification * >	mods_
	Stores the modifications (mutable: the singleton interns runtime-encountered mods through a const API; see getInstance())
std::unordered_map< std::string, std::set< const ResidueModification * > >	modification_names_
	Stores the mappings of (unique) names to the modifications (mutable; see mods_)
Static Protected Attributes inherited from ModificationsDB
static bool	is_instantiated_
	Stores whether ModificationsDB was instantiated before.

Detailed Description

Process-wide singleton database of cross-linking modifications.

CrossLinksDB is a specialization of ModificationsDB that loads cross-linker definitions from the PSI XLMOD ontology (CHEMISTRY/XLMOD.obo, shipped with OpenMS) instead of the general-purpose UniMod/PSI-MOD modifications. It exposes the same lookup, iteration, and matching interface as the base class but its underlying pool contains only entries flagged as cross-links by the OBO provider.

Singleton model

Like ModificationsDB, CrossLinksDB is a singleton: there is at most one instance per process. Obtain it via getInstance — the constructors, destructor, and assignment operator are intentionally private so callers cannot create additional copies. Loading of the XLMOD ontology happens once on the first call to getInstance.

Typical use

auto* db = CrossLinksDB::getInstance();
// Use any ModificationsDB API to look up cross-linkers by name,
// origin, mass, or accession:
const ResidueModification* mod = db->getModification("DSS");
 
// Or enumerate the searchable subset for ID-search UIs:
std::vector<String> ids;
db->getAllSearchModifications(ids);

Currently in OpenMS this database is used by MzIdentMLHandler when serialising cross-link identifications, by the pyOpenMS chemistry bindings, and by tests; new cross-link search algorithms should pull their candidate modification list from here rather than from the general ModificationsDB.

See also

ModificationsDB

Constructor & Destructor Documentation

CrossLinksDB() [1/2]

CrossLinksDB ( )

private

Private default constructor: parses the XLMOD ontology and forwards the resulting providers to ModificationsDB. Called once via getInstance.

CrossLinksDB() [2/2]

CrossLinksDB ( const CrossLinksDB &  residue_db )

private

Private copy constructor (singleton — copying is not permitted).

~CrossLinksDB()

~CrossLinksDB ( )

overrideprivate

Destructor. Never invoked in practice because the singleton is allocated with new and outlives the process.

Member Function Documentation

getAllSearchModifications()

void getAllSearchModifications

(

std::vector< std::string > &

modifications

)

const

Returns the IDs of all cross-linker modifications that are usable for identification searches (i.e. carry a PSI-MOD accession).

The list is sorted ascending and contains ResidueModification::getFullId values, suitable for offering to the user in a search-engine GUI dropdown or for passing to a cross-link-aware search engine.

Parameters

[out]

modifications

Sorted list of search-eligible modification full-IDs. Any previous contents are cleared.

getInstance()

static const CrossLinksDB * getInstance ( )

inlinestatic

Returns the process-wide singleton instance.

First call lazily constructs the instance and populates it from CHEMISTRY/XLMOD.obo. Subsequent calls return the same pointer. The returned pointer is owned by the database and must not be deleted by the caller.

makeCrossLinkProviders_()

static std::vector< std::unique_ptr< ModificationDataProvider > > makeCrossLinkProviders_ ( )

staticprivate

Builds the OBO data provider list used by the base-class constructor. Loads CHEMISTRY/XLMOD.obo with the cross_links_only flag set.

operator=()

CrossLinksDB & operator= ( const CrossLinksDB &  aa )

private

Private assignment operator (singleton — assignment is not permitted).