Generator of modified nucleic-acid sequences for fixed and variable modification placement. More...

#include <OpenMS/CHEMISTRY/ModifiedNASequenceGenerator.h>

Public Types
using	ConstRibonucleotidePtr = const Ribonucleotide *

Static Public Member Functions
static void	applyFixedModifications (const std::set< ConstRibonucleotidePtr > &fixed_mods, NASequence &sequence)
	Apply all compatible fixed modifications from `fixed_mods` to `sequence` in place.

static void	applyVariableModifications (const std::set< ConstRibonucleotidePtr > &var_mods, const NASequence &seq, Size max_variable_mods_per_NASequence, std::vector< NASequence > &all_modified_NASequences, bool keep_original=true)
	Enumerate all sequence variants obtained by combinatorially placing up to `max_variable_mods_per_NASequence` variable modifications.

Static Protected Member Functions
static void	recurseAndGenerateVariableModifiedSequences_ (const std::vector< int > &subset_indices, const std::map< int, std::vector< ConstRibonucleotidePtr > > &map_compatibility, int depth, const NASequence &current_NASequence, std::vector< NASequence > &modified_NASequences)
	Recursive helper for applyVariableModifications — enumerate every assignment of compatible modifications to a fixed subset of sequence sites.

static void	applyAtMostOneVariableModification_ (const std::set< ConstRibonucleotidePtr > &var_mods, const NASequence &seq, std::vector< NASequence > &all_modified_NASequences, bool keep_original=true)
	Fast specialisation of variable-modification placement for at most one modification per sequence.

Detailed Description

Generator of modified nucleic-acid sequences for fixed and variable modification placement.

Counterpart of ModifiedPeptideGenerator for NASequence. The class is a namespace in disguise: all entry points are static and operate either on a single sequence in place (fixed modifications) or by enumerating every legal combination of placements (variable modifications) into a caller-provided output vector.

Compatibility of a modification with a sequence position is determined by:

The residue's one-letter code matching the modification's origin character.
The modification's term-specificity (FIVE_PRIME / THREE_PRIME / ANYWHERE) being satisfied: ANYWHERE applies to any internal nucleotide, FIVE_PRIME / THREE_PRIME only at the corresponding sequence terminus.
The residue / terminal slot not already carrying a modification — pre-existing modifications are preserved and never overwritten.

Member Typedef Documentation

◆ ConstRibonucleotidePtr

using ConstRibonucleotidePtr = const Ribonucleotide*

Member Function Documentation

◆ applyAtMostOneVariableModification_()

static void applyAtMostOneVariableModification_	(	const std::set< ConstRibonucleotidePtr > &	var_mods,
		const NASequence &	seq,
		std::vector< NASequence > &	all_modified_NASequences,
		bool	keep_original = `true`
	)

staticprotected

Fast specialisation of variable-modification placement for at most one modification per sequence.

Emits one variant per (site, compatible modification) pair: no combinations are enumerated. Already-modified residues are skipped. The unmodified sequence is emitted first when keep_original is true.

Parameters

[in]	var_mods	Variable modifications to consider.
[in]	seq	Source sequence; not modified.
[out]	all_modified_NASequences	Generated variants are appended here.
[in]	keep_original	If `true`, also emit `seq` unchanged before any modified variants.

◆ applyFixedModifications()

static void applyFixedModifications	(	const std::set< ConstRibonucleotidePtr > &	fixed_mods,
		NASequence &	sequence
	)

static

Apply all compatible fixed modifications from fixed_mods to sequence in place.

Two passes:

Terminal modifications (FIVE_PRIME / THREE_PRIME) are installed on the corresponding terminal slot only when that slot is still empty. Pre-existing terminal modifications are preserved.
Each nucleotide is then visited: residues already carrying a modification are skipped, and residues whose one-letter code matches the modification's origin receive that modification provided its term-specificity is ANYWHERE.

When multiple fixed modifications match the same residue, the iteration order of fixed_mods (a pointer-keyed std::set) decides which placement persists.

Parameters

[in]	fixed_mods	Fixed modifications to apply.
[in,out]	sequence	Sequence modified in place.

Referenced by NucleicAcidSearchEngine::main_().

◆ applyVariableModifications()

static void applyVariableModifications	(	const std::set< ConstRibonucleotidePtr > &	var_mods,
		const NASequence &	seq,
		Size	max_variable_mods_per_NASequence,
		std::vector< NASequence > &	all_modified_NASequences,
		bool	keep_original = `true`
	)

static

Enumerate all sequence variants obtained by combinatorially placing up to max_variable_mods_per_NASequence variable modifications.

Produces every legal combination of compatible variable modifications drawn from var_mods, with the number of placements per variant ranging from 1 to min(max_variable_mods_per_NASequence, N) where N is the number of compatible sites. 5' / 3' terminal modifications participate in the enumeration as virtual sites and are considered only when the corresponding terminal slot of seq is empty; nucleotides that are already modified are skipped during compatibility analysis.

The output all_modified_NASequences is appended to (existing entries are preserved). The unmodified seq is included in the appended block iff keep_original is true. If var_mods is empty, max_variable_mods_per_NASequence is 0, or no compatible sites are found, only the unmodified sequence is appended (and only when keep_original is true). A fast specialisation is used when max_variable_mods_per_NASequence equals 1.

Parameters

[in]	var_mods	Variable modifications to consider.
[in]	seq	Source sequence; not modified.
[in]	max_variable_mods_per_NASequence	Maximum number of variable modifications per variant; `0` disables enumeration.
[out]	all_modified_NASequences	Generated variants are appended here.
[in]	keep_original	If `true`, also emit `seq` unchanged.

Referenced by NucleicAcidSearchEngine::main_().

◆ recurseAndGenerateVariableModifiedSequences_()

static void recurseAndGenerateVariableModifiedSequences_	(	const std::vector< int > &	subset_indices,
		const std::map< int, std::vector< ConstRibonucleotidePtr > > &	map_compatibility,
		int	depth,
		const NASequence &	current_NASequence,
		std::vector< NASequence > &	modified_NASequences
	)

staticprotected

Recursive helper for applyVariableModifications — enumerate every assignment of compatible modifications to a fixed subset of sequence sites.

For the position at subset_indices[depth], iterate over every modification listed in map_compatibility for that position, apply it to a copy of current_NASequence, and recurse with depth+1. When depth reaches subset_indices.size() the current sequence is appended to modified_NASequences. Sentinel indices -1 / -2 select the 5' / 3' terminal slot instead of an internal residue.

Parameters

[in]	subset_indices	Selected positions (and 5'/3' sentinels) at which to place modifications.
[in]	map_compatibility	Per-position list of compatible modifications.
[in]	depth	Current recursion depth (caller passes `0`).
[in]	current_NASequence	Sequence accumulated so far.
[in,out]	modified_NASequences	Output vector to which fully enumerated variants are appended.

Public Types

Static Public Member Functions

Static Protected Member Functions

Detailed Description

Member Typedef Documentation

◆ ConstRibonucleotidePtr

Member Function Documentation

◆ applyAtMostOneVariableModification_()

◆ applyFixedModifications()

◆ applyVariableModifications()

◆ recurseAndGenerateVariableModifiedSequences_()