Writer for ProForma v2 peptidoform notation. More...

#include <OpenMS/CHEMISTRY/ProFormaWriter.h>

Static Public Member Functions
static String	toString (const Peptidoform &peptidoform, ProFormaWriteMode mode=ProFormaWriteMode::LOSSLESS)
	Convert a Peptidoform to a ProForma string.

static String	toString (const PeptidoformIon &ion, ProFormaWriteMode mode=ProFormaWriteMode::LOSSLESS)
	Convert a PeptidoformIon to a ProForma string.

Static Private Member Functions
static void	writeGlobalMods_ (std::ostream &os, const std::vector< GlobalModEntry > &mods, ProFormaWriteMode mode)
	Write global modification entries to stream.

static void	writeIsotopeReplacement_ (std::ostream &os, const IsotopeReplacement &isotope)
	Write an isotope replacement to stream.

static void	writeGlobalModification_ (std::ostream &os, const GlobalModification &mod, ProFormaWriteMode mode)
	Write a global modification to stream.

static void	writeModification_ (std::ostream &os, const Modification &mod, ProFormaWriteMode mode)
	Write a modification (with alternatives) to stream.

static void	writeModificationTag_ (std::ostream &os, const ModificationTag &tag, ProFormaWriteMode mode)
	Write a modification tag (variant) to stream.

static void	writeCvAccession_ (std::ostream &os, const CvAccession &cv)
	Write a CV accession to stream.

static void	writeNamedMod_ (std::ostream &os, const NamedMod &named)
	Write a named modification to stream.

static void	writeMassDelta_ (std::ostream &os, const MassDelta &delta, ProFormaWriteMode mode)
	Write a mass delta to stream.

static void	writeFormulaTag_ (std::ostream &os, const FormulaTag &formula)
	Write a formula tag to stream.

static void	writeGlycanComposition_ (std::ostream &os, const GlycanComposition &glycan)
	Write a glycan composition to stream.

static void	writeInfoTag_ (std::ostream &os, const InfoTag &info)
	Write an info tag to stream.

static void	writePositionConstraint_ (std::ostream &os, const PositionConstraint &pc)
	Write a position constraint to stream.

static void	writeLabel_ (std::ostream &os, const Label &label, ProFormaWriteMode mode)
	Write a label to stream.

static void	writeUnlocalisedMods_ (std::ostream &os, const std::vector< UnlocalisedMod > &mods, ProFormaWriteMode mode)
	Write unlocalised modifications to stream.

static void	writeLabileModifications_ (std::ostream &os, const std::vector< LabileModification > &mods, ProFormaWriteMode mode)
	Write labile modifications to stream.

static void	writeNTermMods_ (std::ostream &os, const std::vector< Modification > &mods, ProFormaWriteMode mode)
	Write N-terminal modifications to stream.

static void	writeCTermMods_ (std::ostream &os, const std::vector< Modification > &mods, ProFormaWriteMode mode)
	Write C-terminal modifications to stream.

static void	writeSequence_ (std::ostream &os, const std::vector< SequenceSection > &seq, ProFormaWriteMode mode)
	Write the sequence with modifications to stream.

static void	writeSequenceElement_ (std::ostream &os, const SequenceElement &elem, ProFormaWriteMode mode)
	Write a single sequence element to stream.

static void	writeAmbiguousRegion_ (std::ostream &os, const AmbiguousRegion &region, ProFormaWriteMode mode)
	Write an ambiguous region to stream.

static void	writeModifiedRange_ (std::ostream &os, const ModifiedRange &range, ProFormaWriteMode mode)
	Write a modified range to stream.

static void	writeChargeState_ (std::ostream &os, const ChargeState &charge)
	Write a charge state to stream.

static const char *	cvDatabaseToString_ (CvDatabase db)
	Get the string representation of a CV database prefix.

static const char *	cvDatabaseToHint_ (CvDatabase db)
	Get the single-letter hint for a CV database.

static const char *	massSourceToString_ (MassDelta::Source source)
	Get the source prefix string for mass delta.

Detailed Description

Writer for ProForma v2 peptidoform notation.

This class provides serialization of ProForma AST structures back to ProForma strings. It supports lossless roundtrip conversion when the AST was populated from parsing, preserving the original notation style (e.g., using "Oxidation" vs "UNIMOD:35" based on what was originally parsed).

Output Format Rules:

Global mods: <[MOD]@A,C> or <13C> for isotope replacement
N-terminal: [mod]-SEQUENCE
C-terminal: SEQUENCE-[mod]
Modifications: A[mod1][mod2]
Alternatives: [mod1|mod2]
Cross-links: [mod#XL1]
Glycan: [Glycan:HexNAc2Hex5]
CV accession: [UNIMOD:35]
Mass delta: [+15.9949]
Formula: [Formula:C2H3NO]
Charge: /2 or /[M+2H]2+
Unlocalised: [Phospho]? or [Phospho]^2?
Labile: {Glycan:Hex}
Ambiguous region: (?DQ)
Modified range: (EOSFORMS)[+19.0523]
Multiple chains: PEPTIDE//PEPTIDE

Usage example:

Peptidoform peptidoform;
// ... populate peptidoform ...
String proforma_str = ProFormaWriter::toString(peptidoform);
 
PeptidoformIon ion;
// ... populate ion with charge ...
String ion_str = ProFormaWriter::toString(ion);

Member Function Documentation

◆ cvDatabaseToHint_()

static const char * cvDatabaseToHint_ ( CvDatabase db )

staticprivate

Get the single-letter hint for a CV database.

Parameters

db	The CV database enum

Returns: The single-letter hint (e.g., "U", "M", "X")

◆ cvDatabaseToString_()

static const char * cvDatabaseToString_ ( CvDatabase db )

staticprivate

Get the string representation of a CV database prefix.

Parameters

db	The CV database enum

Returns: The prefix string (e.g., "UNIMOD", "MOD", "XLMOD")

◆ massSourceToString_()

static const char * massSourceToString_ ( MassDelta::Source source )

staticprivate

Get the source prefix string for mass delta.

Parameters

source The mass delta source enum

Returns: The source prefix (e.g., "Obs", "U", "M") or empty for NONE

◆ toString() [1/2]

static String toString	(	const Peptidoform &	peptidoform,
		ProFormaWriteMode	mode = `ProFormaWriteMode::LOSSLESS`
	)

static

Convert a Peptidoform to a ProForma string.

Serializes a single peptide chain including all modifications, but without charge state information.

Parameters

[in]	peptidoform	The peptidoform to serialize
[in]	mode	Write mode: LOSSLESS preserves original formatting, CANONICAL produces normalized output

Returns: The ProForma string representation

◆ toString() [2/2]

static String toString	(	const PeptidoformIon &	ion,
		ProFormaWriteMode	mode = `ProFormaWriteMode::LOSSLESS`
	)

static

Convert a PeptidoformIon to a ProForma string.

Serializes one or more peptide chains with optional charge state. Multiple chains are separated by "//".

Parameters

[in]	ion	The peptidoform ion to serialize
[in]	mode	Write mode: LOSSLESS preserves original formatting, CANONICAL produces normalized output

Returns: The ProForma string representation including charge if present

◆ writeAmbiguousRegion_()

static void writeAmbiguousRegion_	(	std::ostream &	os,
		const AmbiguousRegion &	region,
		ProFormaWriteMode	mode
	)

staticprivate

Write an ambiguous region to stream.

Formats as (?AA...), e.g., (?DQ)

Parameters

os	Output stream
region	The ambiguous region
mode	Write mode

◆ writeChargeState_()

static void writeChargeState_	(	std::ostream &	os,
		const ChargeState &	charge
	)

staticprivate

Write a charge state to stream.

Formats as /CHARGE or /[ADDUCTS]CHARGE+, e.g., /2, /[M+2H]2+

Parameters

os	Output stream
charge	The charge state

◆ writeCTermMods_()

static void writeCTermMods_	(	std::ostream &	os,
		const std::vector< Modification > &	mods,
		ProFormaWriteMode	mode
	)

staticprivate

Write C-terminal modifications to stream.

Formats as -[MOD], e.g., -[Amidated]

Parameters

os	Output stream
mods	Vector of C-terminal modifications
mode	Write mode

◆ writeCvAccession_()

static void writeCvAccession_	(	std::ostream &	os,
		const CvAccession &	cv
	)

staticprivate

Write a CV accession to stream.

Formats as DATABASE:ACCESSION, e.g., UNIMOD:35, MOD:00046

Parameters

os	Output stream
cv	The CV accession

◆ writeFormulaTag_()

static void writeFormulaTag_	(	std::ostream &	os,
		const FormulaTag &	formula
	)

staticprivate

Write a formula tag to stream.

Formats as Formula:FORMULA or Formula:FORMULA:z+CHARGE

Parameters

os	Output stream
formula	The formula tag

◆ writeGlobalModification_()

static void writeGlobalModification_	(	std::ostream &	os,
		const GlobalModification &	mod,
		ProFormaWriteMode	mode
	)

staticprivate

Write a global modification to stream.

Formats as <[MOD]@TARGETS>, e.g., <[TMT6plex]@K,N-term>

Parameters

os	Output stream
mod	The global modification
mode	Write mode

◆ writeGlobalMods_()

static void writeGlobalMods_	(	std::ostream &	os,
		const std::vector< GlobalModEntry > &	mods,
		ProFormaWriteMode	mode
	)

staticprivate

Write global modification entries to stream.

Handles both IsotopeReplacement (<13C>) and GlobalModification (<[TMT6plex]@K>).

Parameters

os	Output stream
mods	Vector of global modification entries
mode	Write mode

◆ writeGlycanComposition_()

static void writeGlycanComposition_	(	std::ostream &	os,
		const GlycanComposition &	glycan
	)

staticprivate

Write a glycan composition to stream.

Formats as Glycan:COMPOSITION, e.g., Glycan:HexNAc2Hex5

Parameters

os	Output stream
glycan	The glycan composition

◆ writeInfoTag_()

static void writeInfoTag_	(	std::ostream &	os,
		const InfoTag &	info
	)

staticprivate

Write an info tag to stream.

Formats as INFO:TEXT

Parameters

os	Output stream
info	The info tag

◆ writeIsotopeReplacement_()

static void writeIsotopeReplacement_	(	std::ostream &	os,
		const IsotopeReplacement &	isotope
	)

staticprivate

Write an isotope replacement to stream.

Formats as <ISOTOPE>, e.g., <13C>, <15N>, <D>

Parameters

os	Output stream
isotope	The isotope replacement

◆ writeLabel_()

static void writeLabel_	(	std::ostream &	os,
		const Label &	label,
		ProFormaWriteMode	mode
	)

staticprivate

Write a label to stream.

Formats as #ID or #ID(SCORE), e.g., #XL1, #g1(0.90), #BRANCH

Parameters

os	Output stream
label	The label
mode	Write mode

◆ writeLabileModifications_()

static void writeLabileModifications_	(	std::ostream &	os,
		const std::vector< LabileModification > &	mods,
		ProFormaWriteMode	mode
	)

staticprivate

Write labile modifications to stream.

Formats as {MOD}, e.g., {Glycan:Hex}

Parameters

os	Output stream
mods	Vector of labile modifications
mode	Write mode

◆ writeMassDelta_()

static void writeMassDelta_	(	std::ostream &	os,
		const MassDelta &	delta,
		ProFormaWriteMode	mode
	)

staticprivate

Write a mass delta to stream.

In LOSSLESS mode, uses original_text if available. In CANONICAL mode, formats with 4 decimal places.

Parameters

os	Output stream
delta	The mass delta
mode	Write mode

◆ writeModification_()

static void writeModification_	(	std::ostream &	os,
		const Modification &	mod,
		ProFormaWriteMode	mode
	)

staticprivate

Write a modification (with alternatives) to stream.

Handles single modifications and alternatives separated by |. Includes labels like #XL1 or #g1(0.90) if present.

Parameters

os	Output stream
mod	The modification with its alternatives
mode	Write mode

◆ writeModificationTag_()

static void writeModificationTag_	(	std::ostream &	os,
		const ModificationTag &	tag,
		ProFormaWriteMode	mode
	)

staticprivate

Write a modification tag (variant) to stream.

Dispatches to the appropriate writer based on tag type: CvAccession, NamedMod, MassDelta, FormulaTag, GlycanComposition, InfoTag

Parameters

os	Output stream
tag	The modification tag variant
mode	Write mode

◆ writeModifiedRange_()

static void writeModifiedRange_	(	std::ostream &	os,
		const ModifiedRange &	range,
		ProFormaWriteMode	mode
	)

staticprivate

Write a modified range to stream.

Formats as (SEQ)[MOD], e.g., (EOSFORMS)[+19.0523]

Parameters

os	Output stream
range	The modified range
mode	Write mode

◆ writeNamedMod_()

static void writeNamedMod_	(	std::ostream &	os,
		const NamedMod &	named
	)

staticprivate

Write a named modification to stream.

Formats as NAME or PREFIX:NAME, e.g., Oxidation, U:Oxidation

Parameters

os	Output stream
named	The named modification

◆ writeNTermMods_()

static void writeNTermMods_	(	std::ostream &	os,
		const std::vector< Modification > &	mods,
		ProFormaWriteMode	mode
	)

staticprivate

Write N-terminal modifications to stream.

Formats as [MOD]-, e.g., [Acetyl]-

Parameters

os	Output stream
mods	Vector of N-terminal modifications
mode	Write mode

◆ writePositionConstraint_()

static void writePositionConstraint_	(	std::ostream &	os,
		const PositionConstraint &	pc
	)

staticprivate

Write a position constraint to stream.

Formats as Position:RESIDUES, e.g., Position:MKC

Parameters

os	Output stream
pc	The position constraint

◆ writeSequence_()

static void writeSequence_	(	std::ostream &	os,
		const std::vector< SequenceSection > &	seq,
		ProFormaWriteMode	mode
	)

staticprivate

Write the sequence with modifications to stream.

Handles SequenceElement, AmbiguousRegion, and ModifiedRange.

Parameters

os	Output stream
seq	Vector of sequence sections
mode	Write mode

◆ writeSequenceElement_()

static void writeSequenceElement_	(	std::ostream &	os,
		const SequenceElement &	elem,
		ProFormaWriteMode	mode
	)

staticprivate

Write a single sequence element to stream.

Formats as AA[MOD][MOD]..., e.g., M[Oxidation], K[TMT6plex]

Parameters

os	Output stream
elem	The sequence element
mode	Write mode

◆ writeUnlocalisedMods_()

static void writeUnlocalisedMods_	(	std::ostream &	os,
		const std::vector< UnlocalisedMod > &	mods,
		ProFormaWriteMode	mode
	)

staticprivate

Write unlocalised modifications to stream.

Formats as [MOD]? or [MOD]^N?, e.g., [Phospho]?, [Phospho]^2?

Parameters

os	Output stream
mods	Vector of unlocalised modifications
mode	Write mode

Static Public Member Functions

Static Private Member Functions

Detailed Description

Member Function Documentation

◆ cvDatabaseToHint_()

◆ cvDatabaseToString_()

◆ massSourceToString_()

◆ toString() [1/2]

◆ toString() [2/2]

◆ writeAmbiguousRegion_()

◆ writeChargeState_()

◆ writeCTermMods_()

◆ writeCvAccession_()

◆ writeFormulaTag_()

◆ writeGlobalModification_()

◆ writeGlobalMods_()

◆ writeGlycanComposition_()

◆ writeInfoTag_()

◆ writeIsotopeReplacement_()

◆ writeLabel_()

◆ writeLabileModifications_()

◆ writeMassDelta_()

◆ writeModification_()

◆ writeModificationTag_()

◆ writeModifiedRange_()

◆ writeNamedMod_()

◆ writeNTermMods_()

◆ writePositionConstraint_()

◆ writeSequence_()

◆ writeSequenceElement_()

◆ writeUnlocalisedMods_()