UniPEFFEntries.h File Reference

#include "UniProtXMLFile.h"
#include <cstdint>
#include <limits>
#include <map>
#include <string>
#include <unordered_map>
#include <vector>

Go to the source code of this file.

Classes
struct	PtmEntry
struct	ModResItem
struct	VariantSimpleItem
struct	VariantComplexItem
struct	ProcessedItem
struct	DisulfidePairItem
struct	EntryAnnotations
struct	IsoformEntry
	One reconstructed isoform, ready for emission as its own PEFF entry. More...
struct	PreparedEntry
struct	IsoformScopedTracker

Namespaces
namespace	OpenMS
	Main OpenMS namespace.
namespace	OpenMS::UniPEFFEntries
	The annotations of the PEFF entries that UniPEFF writes for a UniProtKB entry: its canonical entry and the entries of its reconstructed isoforms.

Typedefs
using	PtmMap = std::unordered_map< std::string, PtmEntry >
using	SkippedIsoformCounts = std::map< std::string, size_t >

Enumerations
enum class	ChainPosition { Anywhere , NTerminal , CTerminal }
	Where the ptmlist places a residue of a modification in the polypeptide (one part of its "PP" line) More...

Functions
std::vector< ChainPosition >	parseChainPositions (const std::string &pp)
bool	isResidueCode (char c)
	PEFF VariantSimple newAA must be an amino-acid letter (or '*').
std::string	positionOrUnknown (int p)
	0 → "?", else decimal.
PreparedEntry	prepareEntry (UniProtEntry &&e, const PtmMap &ptms, const std::string &prefix_override, bool option_b, bool record_processing, bool record_aa_mods, bool record_variants, bool record_isoforms, bool map_canonical_features, SkippedIsoformCounts &skipped_isoforms)

Variables
constexpr uint32_t	kNoId = std::numeric_limits<uint32_t>::max()
	Sentinel for "no annotation identifier assigned": the tuple is emitted without an id: prefix.

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Class Documentation

OpenMS::UniPEFFEntries::PtmEntry

struct OpenMS::UniPEFFEntries::PtmEntry

Class Members
string	accession	UniProt internal accession, e.g. "PTM-0253".
vector< ChainPosition >	chain_positions {}	ptmlist "PP" line (position of the modification in the polypeptide, see parseChainPositions()): one value per residue, in the order the ID names them, e.g. {NTerminal} for N-acetylalanine ("PP N-terminal.") or {Anywhere, CTerminal} for the cross-link S-(2-aminovinyl)-D-cysteine (Cys-Cys) of lantibiotics ("PP Anywhere-C-terminal."). Empty if the line is missing or not understood.
string	id	UniProt PTM name (the lookup key from feature/@description)
string	psi_mod	"MOD:xxxxx" or empty
string	unimod	"N" (numeric Unimod id) or empty (NOT prefixed with "UNIMOD:")

OpenMS::UniPEFFEntries::ModResItem

struct OpenMS::UniPEFFEntries::ModResItem

Class Members
uint32_t	annotation_id {kNoId}	0-based; all tuples in Option B, paired half-cystines in default mode
bool	is_halfcys {false}	for stable tie-break on merge
string	name	display name (UniProt PTM ID or fallback description)
int	position {0}	0 = unknown ('?')
const PtmEntry *	ptm {nullptr}	nullptr = generic (no accession), description in name

OpenMS::UniPEFFEntries::VariantSimpleItem

struct OpenMS::UniPEFFEntries::VariantSimpleItem

Class Members
uint32_t	annotation_id {kNoId}	assigned in Option B only
char	new_aa {'?'}
int	position {0}

OpenMS::UniPEFFEntries::VariantComplexItem

struct OpenMS::UniPEFFEntries::VariantComplexItem

Class Members
uint32_t	annotation_id {kNoId}	assigned in Option B only
int	begin {0}
int	end {0}
string	new_seq

OpenMS::UniPEFFEntries::ProcessedItem

struct OpenMS::UniPEFFEntries::ProcessedItem

Class Members
uint32_t	annotation_id {kNoId}	assigned in Option B only
int	begin {0}
string	cv	PEFF CV accession, e.g. "PEFF:0001021".
int	end {0}
string	type_name	human name, e.g. "signal peptide"

OpenMS::UniPEFFEntries::DisulfidePairItem

struct OpenMS::UniPEFFEntries::DisulfidePairItem

Class Members
uint32_t	annotation_id {kNoId}	id of the \DisulfideBond tuple itself (kNoId = not emitted)
size_t	idx_a {0}	Indices into EntryAnnotations::mods after merge — resolved to annotation_ids during emission.
size_t	idx_b {0}
bool	valid {false}	true when both endpoints come from a <begin>/<end> location; cleared by invalidateOutOfRangeDisulfides()

OpenMS::UniPEFFEntries::EntryAnnotations

struct OpenMS::UniPEFFEntries::EntryAnnotations

Class Members
vector< VariantComplexItem >	complex_variants
vector< DisulfidePairItem >	disulfides	indices reference halfcys before merge, mods after merge
vector< ModResItem >	halfcys
vector< ModResItem >	mods	Final merged + sorted list (built by classifyAndMerge).
vector< ProcessedItem >	processed
vector< ModResItem >	regular_mods
vector< VariantSimpleItem >	simple_variants

OpenMS::UniPEFFEntries::IsoformEntry

struct OpenMS::UniPEFFEntries::IsoformEntry

One reconstructed isoform, ready for emission as its own PEFF entry.

Class Members
string	accession	isoform accession, e.g. "P02768-2"
EntryAnnotations	annotations	features UniProt annotates on this isoform (<location sequence="...">), plus, unless -omit_canonical_features is set, the canonical ones mapped onto it
string	name	isoform <name>, e.g. "2" or "VEGF121"
string	sequence	canonical sequence with the referenced splice variants applied

OpenMS::UniPEFFEntries::PreparedEntry

struct OpenMS::UniPEFFEntries::PreparedEntry

Class Members
EntryAnnotations	annotations
size_t	canonical_mapped {0}	canonical mapping: canonical annotations written to an isoform entry (counted once per isoform)
size_t	canonical_unmapped {0}	canonical mapping: canonical annotations not written to an isoform entry because they lie in or cross one of its splice variants (or one changes the cleavage site or chain terminus they depend on), have an unknown position, or contradict an annotation UniProt makes on that isoform itself (counted once per isoform)
size_t	isoform_scoped_applied {0}	isoform-scoped features written to their isoform's entry
size_t	isoform_scoped_skipped {0}	isoform-scoped features left out (isoform not written) that would otherwise have become annotations
vector< IsoformEntry >	isoforms	reconstructed alternative products (emitted after the entry)
string	prefix	sp/tr or user override
UniProtEntry	source