PEFFEntry Struct Reference

Represents a single entry in a PEFF file with all annotations. More...

#include <OpenMS/FORMAT/PEFFFile.h>

Collaboration diagram for PEFFEntry:

Public Member Functions
	PEFFEntry ()=default
	PEFFEntry (const PEFFEntry &rhs)=default
	PEFFEntry (PEFFEntry &&rhs) noexcept=default
PEFFEntry &	operator= (const PEFFEntry &rhs)=default
PEFFEntry &	operator= (PEFFEntry &&rhs) noexcept=default
bool	operator== (const PEFFEntry &rhs) const
FASTAFile::FASTAEntry	toFASTAEntry () const
	Convert to a FASTAFile::FASTAEntry (loses PEFF-specific annotations)
AASequence	getSequence () const
	Get the base AASequence for this entry (unmodified sequence).
AASequence	getModifiedSequence () const
	Get an AASequence with all annotated modifications applied.
void	getVariantSequences (std::vector< std::string > &descriptions, std::vector< AASequence > &sequences, bool include_complex=false) const
	Get all variant sequences (each variant applied individually).
AASequence	getProcessedSequence (const String &region_accession="PEFF:0001021") const
	Get processed sequence (e.g., mature protein without signal peptide).
void	digestWithVariants (const ProteaseDigestion &digestor, std::vector< std::string > &descriptions, std::vector< AASequence > &sequences, Size min_length=6, Size max_length=40, bool include_reference=true, bool include_variants=true, bool include_modifications=false) const
	Generate all variant and/or modification peptides by digesting with a given protease.
void	generatePeptides (const ProteaseDigestion &digestor, std::vector< std::string > &descriptions, std::vector< AASequence > &sequences, const std::vector< std::string > &fixed_mods={}, const std::vector< std::string > &variable_mods={}, Size max_variable_mods_per_peptide=2, Size min_length=6, Size max_length=40, bool include_reference=true, bool include_peff_variants=true, bool include_peff_modifications=true) const
	Generate peptides with PEFF annotations and optional sample handling modifications.

Static Public Member Functions
static PEFFEntry	fromFASTAEntry (const FASTAFile::FASTAEntry &fasta)
	Create a PEFFEntry from a FASTAEntry (basic fields only)

Public Attributes
String	prefix
	Database prefix from description line (e.g., "sp" from ">sp:P12345")
String	identifier
String	sequence
std::vector< String >	protein_names
	\PName - may have multiple names
String	gene_name
	\GName
Int	ncbi_tax_id {0}
	\NcbiTaxId or \OX
String	taxonomy_name
	\TaxName
Size	sequence_length {0}
	\Length
String	sequence_version
	\SV
String	entry_version
	\EV
Int	protein_existence {0}
	\PE (1-5)
String	db_unique_id
	\DbUniqueId
String	entry_id
	\ID (e.g., NPM_HUMAN)
std::vector< String >	alt_accessions
	\AltAC - alternative accessions
std::vector< PEFFModification >	modifications
std::vector< PEFFVariantSimple >	simple_variants
std::vector< PEFFVariantComplex >	complex_variants
std::vector< PEFFProcessedRegion >	processed_regions
std::vector< PEFFDisulfideBond >	disulfide_bonds
	\DisulfideBond
std::vector< String >	proteoforms
	ProForma notation.
std::map< String, String >	custom_annotations

Static Private Member Functions
static std::vector< std::pair< String, AASequence > >	enumeratePEFFModifications_ (const AASequence &peptide, const std::vector< std::pair< Size, const PEFFModification * > > &peff_mods, const String &base_description)
	Apply PEFF modifications at specific positions to a peptide.

Detailed Description

Represents a single entry in a PEFF file with all annotations.

Each entry corresponds to one description line and sequence in the PEFF file. The description line format per the PEFF spec is:

>Prefix:DbUniqueId \key=value \key=value ...

Where Prefix is the database prefix defined in the header block and DbUniqueId is the unique identifier within that database. The identifier field stores the full "Prefix:DbUniqueId" string, and the prefix field stores just the prefix portion.

Constructor & Destructor Documentation

PEFFEntry() [1/3]

PEFFEntry ( )

default

PEFFEntry() [2/3]

PEFFEntry ( const PEFFEntry &  rhs )

default

PEFFEntry() [3/3]

PEFFEntry ( PEFFEntry &&  rhs )

defaultnoexcept

Member Function Documentation

digestWithVariants()

void digestWithVariants	(	const ProteaseDigestion &	digestor,
		std::vector< std::string > &	descriptions,
		std::vector< AASequence > &	sequences,
		Size	min_length = 6,
		Size	max_length = 40,
		bool	include_reference = true,
		bool	include_variants = true,
		bool	include_modifications = false
	)		const

Generate all variant and/or modification peptides by digesting with a given protease.

This method performs enzymatic digestion on the reference sequence and then generates all combinations of simple variants and/or modifications within each peptide.

Parameters

digestor	The protease digestion object (must be configured with enzyme, missed cleavages, etc.)
descriptions	Output vector for peptide descriptions (empty for reference peptides)
sequences	Output vector for peptide sequences
min_length	Minimum peptide length to include (default: 6)
max_length	Maximum peptide length to include (default: 40, 0 = no limit)
include_reference	If true, include reference peptides (default: true)
include_variants	If true, generate variant combinations (default: true)
include_modifications	If true, generate modification combinations (default: false)

enumeratePEFFModifications_()

static std::vector< std::pair< String, AASequence > > enumeratePEFFModifications_ ( const AASequence &  peptide, const std::vector< std::pair< Size, const PEFFModification * > > &  peff_mods, const String &  base_description  )

staticprivate

Apply PEFF modifications at specific positions to a peptide.

Helper method that generates all 2^n combinations of PEFF modifications for a given peptide, where n is the number of PEFF modifications within the peptide's range.

Parameters

peptide	The base peptide sequence
peff_mods	PEFF modifications with positions relative to the peptide (0-based)
base_description	Base description to prepend to modification descriptions

Returns

Vector of pairs: (description, modified AASequence)

fromFASTAEntry()

static PEFFEntry fromFASTAEntry ( const FASTAFile::FASTAEntry &  fasta )

static

Create a PEFFEntry from a FASTAEntry (basic fields only)

generatePeptides()

void generatePeptides	(	const ProteaseDigestion &	digestor,
		std::vector< std::string > &	descriptions,
		std::vector< AASequence > &	sequences,
		const std::vector< std::string > &	fixed_mods = {},
		const std::vector< std::string > &	variable_mods = {},
		Size	max_variable_mods_per_peptide = 2,
		Size	min_length = 6,
		Size	max_length = 40,
		bool	include_reference = true,
		bool	include_peff_variants = true,
		bool	include_peff_modifications = true
	)		const

Generate peptides with PEFF annotations and optional sample handling modifications.

Combines enzymatic digestion, PEFF variants/modifications, and sample handling mods.

Parameters

digestor	The protease digestion object (configured with enzyme, missed cleavages)
descriptions	Output vector for peptide descriptions
sequences	Output vector for peptide sequences
fixed_mods	Fixed modifications (e.g., {"Carbamidomethyl (C)"})
variable_mods	Variable modifications (e.g., {"Oxidation (M)"})
max_variable_mods_per_peptide	Maximum variable mods per peptide (default: 2)
min_length	Minimum peptide length (default: 6)
max_length	Maximum peptide length (default: 40, 0 = no limit)
include_reference	Include reference peptides (default: true)
include_peff_variants	Enumerate PEFF variants (default: true)
include_peff_modifications	Enumerate PEFF modifications (default: true)

getModifiedSequence()

AASequence getModifiedSequence

(

)

const

Get an AASequence with all annotated modifications applied.

Uses the modifications vector to apply modifications to the sequence. Modifications with unknown positions (position == 0) are skipped. Modifications that cannot be resolved are logged as warnings and skipped.

Returns

AASequence with modifications applied

getProcessedSequence()

AASequence getProcessedSequence

(

const String &

region_accession = "PEFF:0001021"

)

const

Get processed sequence (e.g., mature protein without signal peptide).

Applies the first processed region of the given type to extract the processed sequence segment.

Parameters

region_accession

PEFF CV accession for the region type (e.g., "PEFF:0001021" for signal peptide)

Returns

Processed AASequence, or empty if region not found

getSequence()

AASequence getSequence

(

)

const

Get the base AASequence for this entry (unmodified sequence).

Returns

AASequence representing the protein sequence

getVariantSequences()

void getVariantSequences	(	std::vector< std::string > &	descriptions,
		std::vector< AASequence > &	sequences,
		bool	include_complex = false
	)		const

Get all variant sequences (each variant applied individually).

Parameters

descriptions	Output vector for variant descriptions
sequences	Output vector for variant sequences
include_complex	If true, also include complex variants (default: false)

operator=() [1/2]

PEFFEntry & operator= ( const PEFFEntry &  rhs )

default

operator=() [2/2]

PEFFEntry & operator= ( PEFFEntry &&  rhs )

defaultnoexcept

operator==()

bool operator== ( const PEFFEntry &  rhs ) const

inline

References PEFFEntry::alt_accessions, PEFFEntry::complex_variants, PEFFEntry::custom_annotations, PEFFEntry::db_unique_id, PEFFEntry::disulfide_bonds, PEFFEntry::entry_id, PEFFEntry::entry_version, PEFFEntry::gene_name, PEFFEntry::identifier, PEFFEntry::modifications, PEFFEntry::ncbi_tax_id, PEFFEntry::prefix, PEFFEntry::processed_regions, PEFFEntry::protein_existence, PEFFEntry::protein_names, PEFFEntry::proteoforms, PEFFEntry::sequence, PEFFEntry::sequence_length, PEFFEntry::sequence_version, PEFFEntry::simple_variants, and PEFFEntry::taxonomy_name.

toFASTAEntry()

FASTAFile::FASTAEntry toFASTAEntry

(

)

const

Convert to a FASTAFile::FASTAEntry (loses PEFF-specific annotations)

Member Data Documentation

alt_accessions

std::vector<String> alt_accessions

\AltAC - alternative accessions

Referenced by PEFFEntry::operator==().

complex_variants

std::vector<PEFFVariantComplex> complex_variants

Referenced by PEFFEntry::operator==().

custom_annotations

std::map<String, String> custom_annotations

Referenced by PEFFEntry::operator==().

db_unique_id

String db_unique_id

\DbUniqueId

Referenced by PEFFEntry::operator==().

disulfide_bonds

std::vector<PEFFDisulfideBond> disulfide_bonds

\DisulfideBond

Referenced by PEFFEntry::operator==().

entry_id

String entry_id

\ID (e.g., NPM_HUMAN)

Referenced by PEFFEntry::operator==().

entry_version

String entry_version

\EV

Referenced by PEFFEntry::operator==().

gene_name

String gene_name

\GName

Referenced by PEFFEntry::operator==().

identifier

String identifier

Referenced by PEFFEntry::operator==().

modifications

std::vector<PEFFModification> modifications

Referenced by PEFFEntry::operator==().

ncbi_tax_id

Int ncbi_tax_id {0}

\NcbiTaxId or \OX

Referenced by PEFFEntry::operator==().

prefix

String prefix

Database prefix from description line (e.g., "sp" from ">sp:P12345")

Referenced by PEFFEntry::operator==().

processed_regions

std::vector<PEFFProcessedRegion> processed_regions

Referenced by PEFFEntry::operator==().

protein_existence

Int protein_existence {0}

\PE (1-5)

Referenced by PEFFEntry::operator==().

protein_names

std::vector<String> protein_names

\PName - may have multiple names

Referenced by PEFFEntry::operator==().

proteoforms

std::vector<String> proteoforms

ProForma notation.

Referenced by PEFFEntry::operator==().

sequence

String sequence

Referenced by PEFFEntry::operator==().

sequence_length

Size sequence_length {0}

\Length

Referenced by PEFFEntry::operator==().

sequence_version

String sequence_version

\SV

Referenced by PEFFEntry::operator==().

simple_variants

std::vector<PEFFVariantSimple> simple_variants

Referenced by PEFFEntry::operator==().

taxonomy_name

String taxonomy_name

\TaxName

Referenced by PEFFEntry::operator==().