#include <OpenMS/METADATA/ID/IdentificationDataConverter.h>

Classes
struct	PepIDCompare
	Functor for ordering peptide IDs by RT and m/z (if available) More...

struct	StepOptCompare
	Functor for ordering `StepOpt` (by date of the steps, if available): More...

Static Public Member Functions
static void	importIDs (IdentificationData &id_data, const std::vector< ProteinIdentification > &proteins, const std::vector< PeptideIdentification > &peptides)
	Import from legacy peptide/protein identifications. More...

static void	exportIDs (const IdentificationData &id_data, std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides, bool export_ids_wo_scores=false)
	Export to legacy peptide/protein identifications. More...

static MzTab	exportMzTab (const IdentificationData &id_data)
	Export to mzTab format. More...

static void	importSequences (IdentificationData &id_data, const std::vector< FASTAFile::FASTAEntry > &fasta, IdentificationData::MoleculeType type=IdentificationData::MoleculeType::PROTEIN, const String &decoy_pattern="")
	Import FASTA sequences as parent sequences. More...

static void	exportParentMatches (const IdentificationData::ParentMatches &parent_matches, PeptideHit &hit)
	Convert parent matches to peptide evidences. More...

static void	importFeatureIDs (FeatureMap &features, bool clear_original=true)
	Convert IDs from legacy peptide/protein identifications in a feature map. More...

static void	exportFeatureIDs (FeatureMap &features, bool clear_original=true)
	Convert IDs in a feature map to legacy peptide/protein identifications. More...

Protected Types
using	StepOpt = std::optional< IdentificationData::ProcessingStepRef >

Static Protected Member Functions
template<typename MzTabSectionRow >
static void	exportParentSequenceToMzTab_ (const IdentificationData::ParentSequence &parent, std::vector< MzTabSectionRow > &output, std::map< IdentificationData::ScoreTypeRef, Size > &score_map)
	Export a parent sequence (protein or nucleic acid) to mzTab. More...

template<typename MzTabSectionRow , typename IdentSeq >
static void	exportPeptideOrOligoToMzTab_ (const IdentSeq &identified, std::vector< MzTabSectionRow > &output, std::map< IdentificationData::ScoreTypeRef, Size > &score_map)
	Export an identified sequence (peptide or oligonucleotide, but not small molecule/compound) to mzTab. More...

template<typename MzTabSectionRow >
static void	exportObservationMatchToMzTab_ (const String &sequence, const IdentificationData::ObservationMatch &match, double calc_mass, std::vector< MzTabSectionRow > &output, std::map< IdentificationData::ScoreTypeRef, Size > &score_map, std::map< IdentificationData::InputFileRef, Size > &file_map)
	Export an input match (peptide- or oligonucleotide-spectrum match) to mzTab. More...

static void	exportStepsAndScoresToMzTab_ (const IdentificationData::AppliedProcessingSteps &steps_and_scores, MzTabParameterList &steps_out, std::map< Size, MzTabDouble > &scores_out, std::map< IdentificationData::ScoreTypeRef, Size > &score_map)
	Helper function to add processing steps (search engines) and their scores to MzTab. More...

static void	addMzTabSEScores_ (const std::map< IdentificationData::ScoreTypeRef, Size > &scores, std::map< Size, MzTabParameter > &output)
	Helper function to add search engine score entries to MzTab's meta data section. More...

static void	addMzTabMoleculeParentContext_ (const IdentificationData::ParentMatch &match, MzTabOligonucleotideSectionRow &row)
	Helper function for exportPeptideOrOligoToMzTab_() - oligonucleotide variant. More...

static void	addMzTabMoleculeParentContext_ (const IdentificationData::ParentMatch &match, MzTabPeptideSectionRow &row)
	Helper function for exportPeptideOrOligoToMzTab_() - peptide variant. More...

static IdentificationData::SearchParamRef	importDBSearchParameters_ (const ProteinIdentification::SearchParameters &pisp, IdentificationData &id_data)
	Helper function to import DB search parameters from legacy format. More...

static ProteinIdentification::SearchParameters	exportDBSearchParameters_ (IdentificationData::SearchParamRef ref)
	Helper function to export DB search parameters to legacy format. More...

static void	exportMSRunInformation_ (IdentificationData::ProcessingStepRef step_ref, ProteinIdentification &protein)
	Helper function to export (primary) MS run information to legacy format. More...

static void	handleFeatureImport_ (Feature &feature, IntList indexes, std::vector< PeptideIdentification > &peptides, Size &id_counter, bool clear_original)

static void	handleFeatureExport_ (Feature &feature, const IntList &indexes, IdentificationData &id_data, Size &id_counter)

Member Typedef Documentation

◆ StepOpt

using StepOpt = std::optional<IdentificationData::ProcessingStepRef>

protected

Member Function Documentation

◆ addMzTabMoleculeParentContext_() [1/2]

static void addMzTabMoleculeParentContext_	(	const IdentificationData::ParentMatch &	match,
		MzTabOligonucleotideSectionRow &	row
	)

staticprotected

Helper function for exportPeptideOrOligoToMzTab_() - oligonucleotide variant.

◆ addMzTabMoleculeParentContext_() [2/2]

static void addMzTabMoleculeParentContext_	(	const IdentificationData::ParentMatch &	match,
		MzTabPeptideSectionRow &	row
	)

staticprotected

Helper function for exportPeptideOrOligoToMzTab_() - peptide variant.

◆ addMzTabSEScores_()

static void addMzTabSEScores_	(	const std::map< IdentificationData::ScoreTypeRef, Size > &	scores,
		std::map< Size, MzTabParameter > &	output
	)

staticprotected

Helper function to add search engine score entries to MzTab's meta data section.

◆ exportDBSearchParameters_()

static ProteinIdentification::SearchParameters exportDBSearchParameters_ ( IdentificationData::SearchParamRef ref )

staticprotected

Helper function to export DB search parameters to legacy format.

◆ exportFeatureIDs()

static void exportFeatureIDs	(	FeatureMap &	features,
		bool	clear_original = `true`
	)

static

Convert IDs in a feature map to legacy peptide/protein identifications.

Parameters

features	Feature map containing IDs in new format
clear_original	Clear original IDs after conversion?

◆ exportIDs()

static void exportIDs	(	const IdentificationData &	id_data,
		std::vector< ProteinIdentification > &	proteins,
		std::vector< PeptideIdentification > &	peptides,
		bool	export_ids_wo_scores = `false`
	)

static

Export to legacy peptide/protein identifications.

Results are added to existing data (if any) in proteins and peptides.

Referenced by NucleicAcidSearchEngine::main_().

◆ exportMSRunInformation_()

static void exportMSRunInformation_	(	IdentificationData::ProcessingStepRef	step_ref,
		ProteinIdentification &	protein
	)

staticprotected

Helper function to export (primary) MS run information to legacy format.

◆ exportMzTab()

static MzTab exportMzTab ( const IdentificationData & id_data )

static

Export to mzTab format.

Referenced by NucleicAcidSearchEngine::main_().

◆ exportObservationMatchToMzTab_()

static void exportObservationMatchToMzTab_	(	const String &	sequence,
		const IdentificationData::ObservationMatch &	match,
		double	calc_mass,
		std::vector< MzTabSectionRow > &	output,
		std::map< IdentificationData::ScoreTypeRef, Size > &	score_map,
		std::map< IdentificationData::InputFileRef, Size > &	file_map
	)

inlinestaticprotected

Export an input match (peptide- or oligonucleotide-spectrum match) to mzTab.

References ObservationMatch::adduct_opt, ObservationMatch::charge, Observation::data_id, MetaInfoInterface::getMetaValue(), Observation::input_file, MetaInfoInterface::metaValueExists(), Observation::mz, ObservationMatch::observation_ref, Observation::rt, and ScoredProcessingResult::steps_and_scores.

◆ exportParentMatches()

static void exportParentMatches	(	const IdentificationData::ParentMatches &	parent_matches,
		PeptideHit &	hit
	)

static

Convert parent matches to peptide evidences.

◆ exportParentSequenceToMzTab_()

static void exportParentSequenceToMzTab_	(	const IdentificationData::ParentSequence &	parent,
		std::vector< MzTabSectionRow > &	output,
		std::map< IdentificationData::ScoreTypeRef, Size > &	score_map
	)

inlinestaticprotected

Export a parent sequence (protein or nucleic acid) to mzTab.

References ParentSequence::accession, ParentSequence::coverage, ParentSequence::description, ParentSequence::sequence, and ScoredProcessingResult::steps_and_scores.

◆ exportPeptideOrOligoToMzTab_()

static void exportPeptideOrOligoToMzTab_	(	const IdentSeq &	identified,
		std::vector< MzTabSectionRow > &	output,
		std::map< IdentificationData::ScoreTypeRef, Size > &	score_map
	)

inlinestaticprotected

Export an identified sequence (peptide or oligonucleotide, but not small molecule/compound) to mzTab.

◆ exportStepsAndScoresToMzTab_()

static void exportStepsAndScoresToMzTab_	(	const IdentificationData::AppliedProcessingSteps &	steps_and_scores,
		MzTabParameterList &	steps_out,
		std::map< Size, MzTabDouble > &	scores_out,
		std::map< IdentificationData::ScoreTypeRef, Size > &	score_map
	)

staticprotected

Helper function to add processing steps (search engines) and their scores to MzTab.

◆ handleFeatureExport_()

static void handleFeatureExport_	(	Feature &	feature,
		const IntList &	indexes,
		IdentificationData &	id_data,
		Size &	id_counter
	)

staticprotected

◆ handleFeatureImport_()

static void handleFeatureImport_	(	Feature &	feature,
		IntList	indexes,
		std::vector< PeptideIdentification > &	peptides,
		Size &	id_counter,
		bool	clear_original
	)

staticprotected

◆ importDBSearchParameters_()

static IdentificationData::SearchParamRef importDBSearchParameters_	(	const ProteinIdentification::SearchParameters &	pisp,
		IdentificationData &	id_data
	)

staticprotected

Helper function to import DB search parameters from legacy format.

◆ importFeatureIDs()

static void importFeatureIDs	(	FeatureMap &	features,
		bool	clear_original = `true`
	)

static

Convert IDs from legacy peptide/protein identifications in a feature map.

Parameters

features	Feature map containing IDs in legacy format
clear_original	Clear original IDs after conversion?

◆ importIDs()

static void importIDs	(	IdentificationData &	id_data,
		const std::vector< ProteinIdentification > &	proteins,
		const std::vector< PeptideIdentification > &	peptides
	)

static

Import from legacy peptide/protein identifications.

◆ importSequences()

static void importSequences	(	IdentificationData &	id_data,
		const std::vector< FASTAFile::FASTAEntry > &	fasta,
		IdentificationData::MoleculeType	type = `IdentificationData::MoleculeType::PROTEIN`,
		const String &	decoy_pattern = `""`
	)

static

Import FASTA sequences as parent sequences.

Referenced by NucleicAcidSearchEngine::main_().

Classes

Static Public Member Functions

Protected Types

Static Protected Member Functions

Member Typedef Documentation

◆ StepOpt

Member Function Documentation

◆ addMzTabMoleculeParentContext_() [1/2]

◆ addMzTabMoleculeParentContext_() [2/2]

◆ addMzTabSEScores_()

◆ exportDBSearchParameters_()

◆ exportFeatureIDs()

◆ exportIDs()

◆ exportMSRunInformation_()

◆ exportMzTab()

◆ exportObservationMatchToMzTab_()

◆ exportParentMatches()

◆ exportParentSequenceToMzTab_()

◆ exportPeptideOrOligoToMzTab_()

◆ exportStepsAndScoresToMzTab_()

◆ handleFeatureExport_()

◆ handleFeatureImport_()

◆ importDBSearchParameters_()

◆ importFeatureIDs()

◆ importIDs()

◆ importSequences()