#include <OpenMS/CHEMISTRY/CrossLinksDB.h>

Inheritance diagram for CrossLinksDB:

Collaboration diagram for CrossLinksDB:

Public Member Functions
void	readFromOBOFile (const String &filename)
	Adds modifications from a given file in OBO format. More...

void	getAllSearchModifications (std::vector< String > &modifications) const
	Collects all modifications that can be used for identification searches. More...

Public Member Functions inherited from ModificationsDB
Size	getNumberOfModifications () const
	Returns the number of modifications read from the unimod.xml file. More...

const ResidueModification *	getModification (Size index) const
	Returns the modification with the given index. note: out-of-bounds check is only performed in debug mode. More...

void	searchModifications (std::set< const ResidueModification * > &mods, const String &mod_name, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const
	Collects all modifications which have the given name as synonym. More...

const ResidueModification *	searchModification (const ResidueModification &mod_in) const
	Returns a pointer to an exact match of the given modification if present in the DB. More...

const ResidueModification *	searchModificationsFast (const String &mod_name, bool &multiple_matches, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const
	Returns the modification which has the given name as synonym (fast version) More...

const ResidueModification *	getModification (const String &mod_name, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const
	Returns the modification with the given name. More...

bool	has (const String &modification) const
	Returns true if the modification exists. More...

const ResidueModification *	addModification (std::unique_ptr< ResidueModification > new_mod)
	Add a new modification to ModificationsDB. If the modification already exists (based on its fullID) it is not added. More...

const ResidueModification *	addModification (const ResidueModification &new_mod)
	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. More...

Size	findModificationIndex (const String &mod_name) const
	Returns the index of the modification in the mods_ vector; a unique name must be given. More...

void	searchModificationsByDiffMonoMass (std::vector< String > &mods, double mass, double max_error, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY)
	Collects all modifications with delta mass inside a tolerance window. More...

void	searchModificationsByDiffMonoMass (std::vector< const ResidueModification * > &mods, double mass, double max_error, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY)

void	searchModificationsByDiffMonoMassSorted (std::vector< String > &mods, double mass, double max_error, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY)
	Collects all modifications with delta mass inside a tolerance window and adds them sorted by mass difference. More...

void	searchModificationsByDiffMonoMassSorted (std::vector< const ResidueModification * > &mods, double mass, double max_error, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY)

const ResidueModification *	getBestModificationByDiffMonoMass (double mass, double max_error, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY)
	Returns the best matching modification for the given delta mass and residue. More...

void	getAllSearchModifications (std::vector< String > &modifications) const
	Collects all modifications that can be used for identification searches. More...

void	writeTSV (const String &filename)
	Writes tab separated entries: FullId,FullName,Origin,AA,TerminusSpecificity,DiffMonoMass (including header) to TSV file. More...

Static Public Member Functions
static CrossLinksDB *	getInstance ()
	Returns a pointer to the modifications DB (singleton) More...

Static Public Member Functions inherited from ModificationsDB
static ModificationsDB *	getInstance ()
	Returns a pointer to the modifications DB (singleton) More...

static ModificationsDB *	initializeModificationsDB (OpenMS::String unimod_file="CHEMISTRY/unimod.xml", OpenMS::String custommod_file="CHEMISTRY/custom_mods.xml", OpenMS::String psimod_file="CHEMISTRY/PSI-MOD.obo", OpenMS::String xlmod_file="CHEMISTRY/XLMOD.obo")
	Initializes the modification DB with non-default modification files (can only be done once) More...

static bool	isInstantiated ()
	Check whether ModificationsDB was instantiated before. More...

Private Member Functions
Constructors and Destructors
	CrossLinksDB ()
	Default constructor. More...

	CrossLinksDB (const CrossLinksDB &residue_db)
	Copy constructor. More...

	~CrossLinksDB () override
	Destructor. More...

Assignment
CrossLinksDB &	operator= (const CrossLinksDB &aa)
	Assignment operator. More...

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. More...

Protected Attributes inherited from ModificationsDB
std::vector< ResidueModification * >	mods_
	Stores the modifications. More...

std::unordered_map< String, std::set< const ResidueModification * > >	modification_names_
	Stores the mappings of (unique) names to the modifications. More...

Static Protected Attributes inherited from ModificationsDB
static bool	is_instantiated_
	Stores whether ModificationsDB was instantiated before. More...

Constructor & Destructor Documentation

◆ CrossLinksDB() [1/2]

CrossLinksDB ( )

private

Default constructor.

◆ CrossLinksDB() [2/2]

CrossLinksDB ( const CrossLinksDB & residue_db )

private

Copy constructor.

◆ ~CrossLinksDB()

~CrossLinksDB ( )

overrideprivate

Destructor.

Member Function Documentation

◆ getAllSearchModifications()

void getAllSearchModifications ( std::vector< String > & modifications ) const

Collects all modifications that can be used for identification searches.

◆ getInstance()

static CrossLinksDB* getInstance ( )

inlinestatic

Returns a pointer to the modifications DB (singleton)

◆ operator=()

CrossLinksDB& operator= ( const CrossLinksDB & aa )

private

Assignment operator.

◆ readFromOBOFile()

void readFromOBOFile ( const String & filename )

Adds modifications from a given file in OBO format.

Note: readFromOBOFile should be called in a single threaded context with no other threads accessing the CrossLinkDB

Exceptions

Exception::ParseError if the file cannot be parsed correctly

Public Member Functions

Static Public Member Functions

Private Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

◆ CrossLinksDB() [1/2]

◆ CrossLinksDB() [2/2]

◆ ~CrossLinksDB()

Member Function Documentation

◆ getAllSearchModifications()

◆ getInstance()

◆ operator=()

◆ readFromOBOFile()