UniProtXMLFile.h File Reference

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

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Classes
struct	UniProtFeature
	A single <feature> element from a UniProtKB XML entry. 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).

Collaboration diagram for UniProtFeature:

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	original	<original> text (sequence 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 variant; first occurrence only)

OpenMS::UniProtEntry

struct OpenMS::UniProtEntry

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

Captures only the fields needed to build a PEFF descriptor line; isoforms (sequences without a "length" attribute) and splice-variant features are intentionally not represented because UniPEFF's PEFF emission ignores them.

Collaboration diagram for UniProtEntry:

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)
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 skipped
string	sequence_version	<sequence version="...">
string	tax_name	<organism>/<name type="scientific">