Reads UniProtKB XML protein databases (.xml or transparently .xml.gz). More...

#include <OpenMS/FORMAT/UniProtXMLFile.h>

Inheritance diagram for UniProtXMLFile:

Collaboration diagram for UniProtXMLFile:

Public Member Functions
	UniProtXMLFile ()
	Default constructor.

	~UniProtXMLFile () override
	Destructor.

void	load (const std::string &filename, std::vector< UniProtEntry > &entries)
	Load all entries from a UniProtKB XML file into memory.

void	loadStreaming (const std::string &filename, const std::function< void(UniProtEntry &&)> &callback)
	Stream entries one at a time via a user-supplied callback.

Public Member Functions inherited from XMLFile
	XMLFile ()
	Construct an XMLFile without schema info; `schema_location_` remains unset, so isValid cannot be used until derived-class logic initializes `schema_location_` before calling isValid.

	XMLFile (const std::string &schema_location, const std::string &version)
	Construct with a schema location for later isValid calls.

virtual	~XMLFile ()
	Virtual destructor — defaulted; allows safe deletion through a base-class pointer.

bool	isValid (const std::string &filename, std::ostream &os)
	Check if `filename` validates against the bound XML schema.

const std::string &	getVersion () const
	Return the schema version string passed to the parameterised constructor; empty for default-constructed instances.

Private Member Functions
	UniProtXMLFile (const UniProtXMLFile &)=delete

UniProtXMLFile &	operator= (const UniProtXMLFile &)=delete

Additional Inherited Members
Protected Member Functions inherited from XMLFile
void	parse_ (const std::string &filename, XMLHandler *handler)
	Parse the XML file at `filename` through `handler`.

void	parseBuffer_ (const std::string &buffer, XMLHandler *handler)
	Parse an in-memory XML buffer through `handler`.

void	save_ (const std::string &filename, XMLHandler *handler) const
	Stores the contents of the XML handler given by `handler` in the file given by `filename`.

void	enforceEncoding_ (const std::string &encoding)
	Set or clear the XML-encoding override applied to subsequent parse_ / parseBuffer_ calls.

Protected Attributes inherited from XMLFile
std::string	schema_location_
	Path of the XML schema for validation; empty when the default constructor was used (isValid then throws `NotImplemented`).

std::string	schema_version_
	Schema version string returned by getVersion.

std::string	enforced_encoding_
	Optional XML encoding override applied to the `InputSource` in parse_ and parseBuffer_; empty disables the override. Used as a workaround for XTandem output XML which carries an encoding the parser otherwise stumbles on.

Detailed Description

Reads UniProtKB XML protein databases (.xml or transparently .xml.gz).

Streams the document via Xerces SAX. The on-disk format is the UniProtKB XML release schema; isoforms (sequences without the "length" attribute on <sequence>) and the <comment type="alternative products"> subtree are skipped, matching UniPEFF's PEFF-emission behaviour. Gzip is detected by magic-byte sniffing in the inherited XMLFile parser, so no special handling is required for .xml.gz inputs.

Constructor & Destructor Documentation

◆ UniProtXMLFile() [1/2]

UniProtXMLFile ( )

Default constructor.

◆ ~UniProtXMLFile()

~UniProtXMLFile ( )

override

Destructor.

◆ UniProtXMLFile() [2/2]

UniProtXMLFile ( const UniProtXMLFile & )

privatedelete

Member Function Documentation

◆ load()

void load	(	const std::string &	filename,
		std::vector< UniProtEntry > &	entries
	)

Load all entries from a UniProtKB XML file into memory.

Parameters

[in]	filename	Path to a .xml or .xml.gz UniProtKB file (gzip auto-detected).
[out]	entries	Filled with one UniProtEntry per <entry> element.

Exceptions

Exception::FileNotFound	if `filename` does not exist.
Exception::ParseError	if the file is not well-formed XML.

◆ loadStreaming()

void loadStreaming	(	const std::string &	filename,
		const std::function< void(UniProtEntry &&)> &	callback
	)

Stream entries one at a time via a user-supplied callback.

The callback receives ownership of each fully populated UniProtEntry as soon as its </entry> is reached. This is the preferred path for databases too large to materialise in full (e.g. TrEMBL).