The annotations of the PEFF entries that UniPEFF writes for a UniProtKB entry: its canonical entry and the entries of its reconstructed isoforms. More...

Classes
struct	DisulfidePairItem

struct	EntryAnnotations

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

struct	IsoformScopedTracker

struct	ModResItem

struct	PreparedEntry

struct	ProcessedItem

struct	PtmEntry

struct	VariantComplexItem

struct	VariantSimpleItem

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

using	SkippedIsoformCounts = std::map< std::string, size_t >

Functions
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, 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.

Detailed Description

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

prepareEntry() classifies the features of an entry into annotations of the canonical entry or of the isoform they are annotated on; the tool writes the prepared entries.

Class Documentation

◆ 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="...">)
string	name	isoform <name>, e.g. "2" or "VEGF121"
string	sequence	canonical sequence with the referenced splice variants applied

◆ 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::PreparedEntry

struct OpenMS::UniPEFFEntries::PreparedEntry

Class Members
EntryAnnotations	annotations
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

◆ 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::PtmEntry

struct OpenMS::UniPEFFEntries::PtmEntry

Class Members
string	accession	UniProt internal accession, e.g. "PTM-0253".
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::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::VariantSimpleItem

struct OpenMS::UniPEFFEntries::VariantSimpleItem

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

Typedef Documentation

◆ PtmMap

using PtmMap = std::unordered_map<std::string, PtmEntry>

◆ SkippedIsoformCounts

using SkippedIsoformCounts = std::map<std::string, size_t>

Isoforms without a reconstructable sequence ("external": stored as its own UniProt entry; "not described": sequence unknown), counted per sequence type so the run reports them in one summary line instead of one line per isoform.

Function Documentation

◆ isResidueCode()

bool isResidueCode ( char c )

PEFF VariantSimple newAA must be an amino-acid letter (or '*').

◆ positionOrUnknown()

std::string positionOrUnknown ( int p )

0 → "?", else decimal.

◆ prepareEntry()

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,
		SkippedIsoformCounts &	skipped_isoforms
	)

Prepare one entry: reconstruct the emittable isoform sequences ("external" / "not described" isoforms are counted in skipped_isoforms), classify each feature into the canonical entry or, if its <location sequence="..."> names an emitted isoform, into that isoform's entry; then, per entry, merge halfcys, drop disulfide pairs with out-of-range endpoints and stamp annotation IDs (global in Option B, selective disulfide labels otherwise).

References IsoformEntry::accession, UniProtEntry::accession, IsoformEntry::annotations, PreparedEntry::annotations, UniProtEntry::dataset, UniProtEntry::features, PreparedEntry::isoform_scoped_applied, PreparedEntry::isoform_scoped_skipped, PreparedEntry::isoforms, UniProtEntry::isoforms, IsoformEntry::name, OPENMS_LOG_DEBUG, OPENMS_LOG_WARN, PreparedEntry::prefix, UniProtEntry::sequence, and PreparedEntry::source.

Variable Documentation

◆ kNoId

constexpr uint32_t kNoId = std::numeric_limits<uint32_t>::max()

constexpr

Sentinel for "no annotation identifier assigned": the tuple is emitted without an id: prefix.

Classes

Typedefs

Functions

Variables