ModifiedNASequenceGenerator Class Reference

#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)
	Applies fixed modifications to a single NASequence. More...
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)
	Applies variable modifications to a single NASequence. If keep_original is set the original (e.g. unmodified version) is also returned. More...

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)
	Recursively generate all combinatorial placements at compatible sites. More...
static void	applyAtMostOneVariableModification_ (const std::set< ConstRibonucleotidePtr > &var_mods, const NASequence &seq, std::vector< NASequence > &all_modified_NASequences, bool keep_original=true)

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 implementation of modification placement. No combinatorial placement is needed in this case

• just every site is modified once by each compatible modification. Already modified residues are skipped

applyFixedModifications()

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

static

Applies fixed modifications to a single NASequence.

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

Applies variable modifications to a single NASequence. If keep_original is set the original (e.g. unmodified version) is also returned.

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

Recursively generate all combinatorial placements at compatible sites.