UniProtXMLFile.h File Reference

#include <OpenMS/FORMAT/XMLFile.h>
#include <functional>
#include <string>
#include <vector>

Go to the source code of this file.

Classes
struct	UniProtFeature
	A single <feature> element from a UniProtKB XML entry. More...
struct	UniProtIsoform
	One <isoform> definition from <comment type="alternative products">. More...
struct	UniProtEntry
	A single <entry> from a UniProtKB XML file, in a parser-neutral form. More...
class	UniProtXMLFile
	Reads UniProtKB XML protein databases (.xml or transparently .xml.gz). More...

Namespaces
namespace	OpenMS
	Main OpenMS namespace.

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Class Documentation

OpenMS::UniProtFeature

struct OpenMS::UniProtFeature

A single <feature> element from a UniProtKB XML entry.

Fields mirror the UniProt schema after the <location> has been collapsed: a feature is either a single point (HasPosition / position) or a range (HasRange / begin / end). A status="unknown" coordinate is encoded as 0 (the caller decides whether that is legal for its target PEFF key).

Class Members
int	begin {0}	1-based range start (0 = unknown / absent)
string	description	feature/@description (raw, before any cleanup)
int	end {0}	1-based range end (0 = unknown / absent)
bool	has_position {false}	a single <position> element was present
bool	has_range {false}	a <begin> / <end> pair was present
string	id	feature/@id, e.g. "VSP_021275" (referenced by isoform definitions)
string	location_sequence	<location sequence="...">: accession of the isoform the coordinates refer to; empty = the entry's canonical sequence
string	original	<original> text (sequence or splice variant)
int	position {0}	1-based position (0 = unknown / absent)
string	type	feature/@type, e.g. "modified residue", "disulfide bond", "sequence variant"
string	variation	<variation> text (sequence or splice variant; first occurrence only)

OpenMS::UniProtIsoform

struct OpenMS::UniProtIsoform

One <isoform> definition from <comment type="alternative products">.

UniProtKB XML does not store isoform sequences verbatim: an isoform either "displays" the canonical sequence (sequence_type "displayed") or is "described" by the splice-variant features listed in sequence_ref, which transform the canonical sequence (a referenced range without a replacement is deleted, one with a <variation> is substituted). The remaining types ("external", "not described") carry no reconstructable sequence.

Class Members
string	id	first <id> (isoform accession, e.g. "P02768-2"); later ids are secondary
string	name	first <name> (e.g. "2" or "VEGF121"); later <name> elements are synonyms
string	sequence_ref	<sequence ref="...">: space-separated <feature type="splice variant"> ids
string	sequence_type	<sequence type="...">: "displayed", "described", "external" or "not described"

OpenMS::UniProtEntry

struct OpenMS::UniProtEntry

A single <entry> from a UniProtKB XML file, in a parser-neutral form.

Captures the fields needed to build PEFF descriptor lines. The canonical sequence is stored verbatim; isoform sequences are not present in the XML and must be reconstructed by applying the splice-variant features listed in each UniProtIsoform's sequence_ref to the canonical sequence.

Class Members
string	accession	first <accession> (primary id)
vector< string >	alt_accessions	second and subsequent <accession> entries
string	dataset	entry/@dataset, e.g. "Swiss-Prot" or "TrEMBL"
string	entry_version	<entry version="...">
vector< UniProtFeature >	features	<feature> elements in document order
string	full_name	<protein>/<recommendedName>/<fullName> (first occurrence)
vector< UniProtIsoform >	isoforms	isoform definitions from <comment type="alternative products">
string	name	first <name> under <entry> (mnemonic id, e.g. "KSINK_HUMAN")
string	ncbi_tax_id	<organism>/<dbReference type="NCBI Taxonomy" id="...">
string	primary_gene	<gene>/<name type="primary"> (first occurrence)
string	protein_existence	<proteinExistence type="..."> (raw type string, e.g. "evidence at protein level")
string	sequence	canonical <sequence> text (whitespace stripped); isoform sequences are not stored in the XML
string	sequence_version	<sequence version="...">
string	tax_name	<organism>/<name type="scientific">