Namespaces
namespace	Detail

Classes
struct	AdductCompare
	Comparator for adducts. More...

struct	AppliedProcessingStep

struct	DBSearchParam
	Parameters specific to a database search step. More...

class	IDDataContainer
	A collection of identification records, unique and ordered by the key formed from the members `KeyMembers`. More...

struct	IdentifiedCompound

struct	IdentifiedMolecule
	Variant type holding Peptide/Compound/Oligo references and convenience functions. More...

struct	IdentifiedSequence
	Representation of an identified sequence (peptide or oligonucleotide) More...

class	IDSequencedContainer
	Records kept in the order they were added, unique by the member `KeyMember`. More...

struct	InputFile
	Information about input files that were processed. More...

struct	IteratorWrapper
	Wrapper that adds `operator<` to iterators, so they can be used as (part of) keys in maps/sets or `multi_index_containers`. More...

struct	Observation
	Representation of an observation, e.g. a spectrum or feature, in an input data file. More...

struct	ObservationMatch
	Representation of a search hit (e.g. peptide-spectrum match). More...

struct	ObservationMatchGroup
	: Group of related (co-identified) input matches More...

struct	ParentGroup
	: Group of ambiguously identified parent sequences (e.g. protein group) More...

struct	ParentGroupSet
	Set of groups of ambiguously identified parent sequences (e.g. results of running a protein inference algorithm) More...

struct	ParentMatch
	Meta data for the association between an identified molecule (e.g. peptide) and a parent sequence (e.g. protein). More...

struct	ParentSequence
	Representation of a parent sequence that is identified only indirectly (e.g. a protein). More...

struct	ProcessingSoftware
	Information about software used for data processing. More...

struct	ProcessingStep
	Data processing step that is applied to the data (e.g. database search, PEP calculation, filtering, ConsensusID). More...

struct	ScoredProcessingResult
	Base class for ID data with scores and processing steps (and meta info) More...

struct	ScoreType
	Information about a score type. More...

Typedefs
using	AppliedProcessingSteps = IDSequencedContainer< AppliedProcessingStep, std::optional< ProcessingStepRef >, &AppliedProcessingStep::processing_step_opt >

typedef std::set< DBSearchParam >	DBSearchParams

typedef IteratorWrapper< DBSearchParams::iterator >	SearchParamRef

typedef std::map< ProcessingStepRef, SearchParamRef >	DBSearchSteps

using	IdentifiedCompounds = IDDataContainer< IdentifiedCompound, std::string, std::string, &IdentifiedCompound::identifier >

typedef IteratorWrapper< IdentifiedCompounds::iterator >	IdentifiedCompoundRef

typedef std::variant< IdentifiedPeptideRef, IdentifiedCompoundRef, IdentifiedOligoRef >	RefVariant

typedef IdentifiedSequence< AASequence >	IdentifiedPeptide

typedef IdentifiedSequence< NASequence >	IdentifiedOligo

using	IdentifiedPeptides = IDDataContainer< IdentifiedPeptide, AASequence, AASequence, &IdentifiedPeptide::sequence >

typedef IteratorWrapper< IdentifiedPeptides::iterator >	IdentifiedPeptideRef

using	IdentifiedOligos = IDDataContainer< IdentifiedOligo, NASequence, NASequence, &IdentifiedOligo::sequence >

typedef IteratorWrapper< IdentifiedOligos::iterator >	IdentifiedOligoRef

using	InputFiles = IDDataContainer< InputFile, std::string, std::string, &InputFile::name >

typedef IteratorWrapper< InputFiles::iterator >	InputFileRef

using	Observations = IDDataContainer< Observation, std::tuple< InputFileRef, std::string >, InputFileRef, &Observation::input_file, &Observation::data_id >

typedef IteratorWrapper< Observations::iterator >	ObservationRef

typedef std::vector< PeptideHit::PeakAnnotation >	PeakAnnotations

typedef std::map< std::optional< ProcessingStepRef >, PeakAnnotations >	PeakAnnotationSteps

typedef std::set< AdductInfo, AdductCompare >	Adducts

typedef IteratorWrapper< Adducts::iterator >	AdductRef

typedef std::optional< AdductRef >	AdductOpt

using	ObservationMatches = IDDataContainer< ObservationMatch, std::tuple< ObservationRef, IdentifiedMolecule, AdductOpt >, ObservationRef, &ObservationMatch::observation_ref, &ObservationMatch::identified_molecule_var, &ObservationMatch::adduct_opt >

typedef IteratorWrapper< ObservationMatches::iterator >	ObservationMatchRef

using	ObservationMatchGroups = IDDataContainer< ObservationMatchGroup, std::set< ObservationMatchRef >, std::set< ObservationMatchRef >, &ObservationMatchGroup::observation_match_refs >

typedef IteratorWrapper< ObservationMatchGroups::iterator >	MatchGroupRef

using	ParentGroups = IDDataContainer< ParentGroup, std::set< ParentSequenceRef >, std::set< ParentSequenceRef >, &ParentGroup::parent_refs >

typedef IteratorWrapper< ParentGroups::iterator >	ParentGroupRef

typedef std::vector< ParentGroupSet >	ParentGroupSets

typedef std::map< ParentSequenceRef, std::set< ParentMatch > >	ParentMatches
	mapping: parent sequence -> match information

using	ParentSequences = IDDataContainer< ParentSequence, std::string, std::string, &ParentSequence::accession >

typedef IteratorWrapper< ParentSequences::iterator >	ParentSequenceRef

typedef std::set< ProcessingSoftware >	ProcessingSoftwares

typedef IteratorWrapper< ProcessingSoftwares::iterator >	ProcessingSoftwareRef

typedef std::set< ProcessingStep >	ProcessingSteps

typedef IteratorWrapper< ProcessingSteps::iterator >	ProcessingStepRef

typedef std::set< ScoreType >	ScoreTypes

typedef IteratorWrapper< ScoreTypes::iterator >	ScoreTypeRef

Enumerations
enum	MoleculeType { PROTEIN , COMPOUND , RNA }

enum	MassType { MONOISOTOPIC , AVERAGE }

Functions
bool	operator== (const IdentifiedMolecule &a, const IdentifiedMolecule &b)

bool	operator!= (const IdentifiedMolecule &a, const IdentifiedMolecule &b)

bool	operator< (const IdentifiedMolecule &a, const IdentifiedMolecule &b)