OBODataProvider Class Reference

Loads ResidueModification data from an OBO ontology file (PSI-MOD or XLMOD). More...

#include <OpenMS/CHEMISTRY/OBODataProvider.h>

Inheritance diagram for OBODataProvider:

Collaboration diagram for OBODataProvider:

Public Member Functions
	OBODataProvider (const String &filename, bool cross_links_only=false)
std::vector< std::unique_ptr< ResidueModification > >	loadModifications () override
	Load modifications from whatever source this provider wraps.
Public Member Functions inherited from ModificationDataProvider
virtual	~ModificationDataProvider ()=default

Private Attributes
String	filename_
bool	cross_links_only_

Detailed Description

Loads ResidueModification data from an OBO ontology file (PSI-MOD or XLMOD).

Parses OBO format files and returns modifications as unique_ptr. The cross_links_only flag controls filtering:

• false (default): returns all modifications EXCEPT cross-linkers (reactionSites==2). Used by ModificationsDB for PSI-MOD.obo and XLMOD.obo (mono-links only).
• true: returns only cross-linkers (reactionSites==2), skipping mono-links. Used by CrossLinksDB for XLMOD.obo.

Constructor & Destructor Documentation

OBODataProvider()

OBODataProvider ( const String &  filename, bool  cross_links_only = false  )

explicit

Parameters

filename	Path to an OBO file (resolved via File::find)
cross_links_only	If true, return only cross-linkers; if false, exclude them

Member Function Documentation

loadModifications()

std::vector< std::unique_ptr< ResidueModification > > loadModifications ( )

overridevirtual

Load modifications from whatever source this provider wraps.

Returns

Vector of modifications with ownership transferred to caller.

Note

Providers may only be called once. Subsequent calls may return empty results.

Implements ModificationDataProvider.

Member Data Documentation

cross_links_only_

bool cross_links_only_

private

filename_

String filename_

private