OpenMS::IdentificationDataInternal Namespace Reference

Classes
struct	AppliedProcessingStep
struct	DBSearchParam
	Parameters specific to a database search step. 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...
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	AdductCompare
	Comparator for adducts. 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
typedef boost::multi_index_container< AppliedProcessingStep, boost::multi_index::indexed_by< boost::multi_index::sequenced<>, boost::multi_index::ordered_unique< boost::multi_index::member< AppliedProcessingStep, std::optional< ProcessingStepRef >, &AppliedProcessingStep::processing_step_opt > > > >	AppliedProcessingSteps
typedef std::set< DBSearchParam >	DBSearchParams
typedef IteratorWrapper< DBSearchParams::iterator >	SearchParamRef
typedef std::map< ProcessingStepRef, SearchParamRef >	DBSearchSteps
typedef boost::multi_index_container< IdentifiedCompound, boost::multi_index::indexed_by< boost::multi_index::ordered_unique< boost::multi_index::member< IdentifiedCompound, String, &IdentifiedCompound::identifier > > > >	IdentifiedCompounds
typedef IteratorWrapper< IdentifiedCompounds::iterator >	IdentifiedCompoundRef
typedef std::variant< IdentifiedPeptideRef, IdentifiedCompoundRef, IdentifiedOligoRef >	RefVariant
typedef IdentifiedSequence< AASequence >	IdentifiedPeptide
typedef IdentifiedSequence< NASequence >	IdentifiedOligo
typedef boost::multi_index_container< IdentifiedPeptide, boost::multi_index::indexed_by< boost::multi_index::ordered_unique< boost::multi_index::member< IdentifiedPeptide, AASequence, &IdentifiedPeptide::sequence > > > >	IdentifiedPeptides
typedef IteratorWrapper< IdentifiedPeptides::iterator >	IdentifiedPeptideRef
typedef boost::multi_index_container< IdentifiedOligo, boost::multi_index::indexed_by< boost::multi_index::ordered_unique< boost::multi_index::member< IdentifiedOligo, NASequence, &IdentifiedOligo::sequence > > > >	IdentifiedOligos
typedef IteratorWrapper< IdentifiedOligos::iterator >	IdentifiedOligoRef
typedef boost::multi_index_container< InputFile, boost::multi_index::indexed_by< boost::multi_index::ordered_unique< boost::multi_index::member< InputFile, String, &InputFile::name > > > >	InputFiles
typedef IteratorWrapper< InputFiles::iterator >	InputFileRef
typedef boost::multi_index_container< Observation, boost::multi_index::indexed_by< boost::multi_index::ordered_unique< boost::multi_index::composite_key< Observation, boost::multi_index::member< Observation, InputFileRef, &Observation::input_file >, boost::multi_index::member< Observation, String, &Observation::data_id > > > > >	Observations
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
typedef boost::multi_index_container< ObservationMatch, boost::multi_index::indexed_by< boost::multi_index::ordered_unique< boost::multi_index::composite_key< ObservationMatch, boost::multi_index::member< ObservationMatch, ObservationRef, &ObservationMatch::observation_ref >, boost::multi_index::member< ObservationMatch, IdentifiedMolecule, &ObservationMatch::identified_molecule_var >, boost::multi_index::member< ObservationMatch, AdductOpt, &ObservationMatch::adduct_opt > > > > >	ObservationMatches
typedef IteratorWrapper< ObservationMatches::iterator >	ObservationMatchRef
typedef boost::multi_index_container< ObservationMatchGroup, boost::multi_index::indexed_by< boost::multi_index::ordered_unique< boost::multi_index::member< ObservationMatchGroup, std::set< ObservationMatchRef >, &ObservationMatchGroup::observation_match_refs > > > >	ObservationMatchGroups
typedef IteratorWrapper< ObservationMatchGroups::iterator >	MatchGroupRef
typedef boost::multi_index_container< ParentGroup, boost::multi_index::indexed_by< boost::multi_index::ordered_unique< boost::multi_index::member< ParentGroup, std::set< ParentSequenceRef >, &ParentGroup::parent_refs > > > >	ParentGroups
typedef IteratorWrapper< ParentGroups::iterator >	ParentGroupRef
typedef std::vector< ParentGroupSet >	ParentGroupSets
typedef std::map< ParentSequenceRef, std::set< ParentMatch > >	ParentMatches
	mapping: parent sequence -> match information More...
typedef boost::multi_index_container< ParentSequence, boost::multi_index::indexed_by< boost::multi_index::ordered_unique< boost::multi_index::member< ParentSequence, String, &ParentSequence::accession > > > >	ParentSequences
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)

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Class Documentation

OpenMS::IdentificationDataInternal::ParentGroup

struct OpenMS::IdentificationDataInternal::ParentGroup

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

Collaboration diagram for ParentGroup:

Class Members
set< ParentSequenceRef >	parent_refs
map< ScoreTypeRef, double >	scores

Typedef Documentation

AdductOpt

typedef std::optional<AdductRef> AdductOpt

AdductRef

typedef IteratorWrapper<Adducts::iterator> AdductRef

Adducts

typedef std::set<AdductInfo, AdductCompare> Adducts

AppliedProcessingSteps

typedef boost::multi_index_container< AppliedProcessingStep, boost::multi_index::indexed_by< boost::multi_index::sequenced<>, boost::multi_index::ordered_unique< boost::multi_index::member< AppliedProcessingStep, std::optional<ProcessingStepRef>, &AppliedProcessingStep::processing_step_opt> > > > AppliedProcessingSteps

DBSearchParams

typedef std::set<DBSearchParam> DBSearchParams

DBSearchSteps

typedef std::map<ProcessingStepRef, SearchParamRef> DBSearchSteps

IdentifiedCompoundRef

typedef IteratorWrapper<IdentifiedCompounds::iterator> IdentifiedCompoundRef

IdentifiedCompounds

typedef boost::multi_index_container< IdentifiedCompound, boost::multi_index::indexed_by< boost::multi_index::ordered_unique<boost::multi_index::member< IdentifiedCompound, String, &IdentifiedCompound::identifier> > > > IdentifiedCompounds

IdentifiedOligo

typedef IdentifiedSequence<NASequence> IdentifiedOligo

IdentifiedOligoRef

typedef IteratorWrapper<IdentifiedOligos::iterator> IdentifiedOligoRef

IdentifiedOligos

typedef boost::multi_index_container< IdentifiedOligo, boost::multi_index::indexed_by< boost::multi_index::ordered_unique<boost::multi_index::member< IdentifiedOligo, NASequence, &IdentifiedOligo::sequence> > > > IdentifiedOligos

IdentifiedPeptide

typedef IdentifiedSequence<AASequence> IdentifiedPeptide

IdentifiedPeptideRef

typedef IteratorWrapper<IdentifiedPeptides::iterator> IdentifiedPeptideRef

IdentifiedPeptides

typedef boost::multi_index_container< IdentifiedPeptide, boost::multi_index::indexed_by< boost::multi_index::ordered_unique<boost::multi_index::member< IdentifiedPeptide, AASequence, &IdentifiedPeptide::sequence> > > > IdentifiedPeptides

InputFileRef

typedef IteratorWrapper<InputFiles::iterator> InputFileRef

InputFiles

typedef boost::multi_index_container< InputFile, boost::multi_index::indexed_by< boost::multi_index::ordered_unique<boost::multi_index::member< InputFile, String, &InputFile::name> > > > InputFiles

MatchGroupRef

typedef IteratorWrapper<ObservationMatchGroups::iterator> MatchGroupRef

ObservationMatches

typedef boost::multi_index_container< ObservationMatch, boost::multi_index::indexed_by< boost::multi_index::ordered_unique< boost::multi_index::composite_key< ObservationMatch, boost::multi_index::member<ObservationMatch, ObservationRef, &ObservationMatch::observation_ref>, boost::multi_index::member< ObservationMatch, IdentifiedMolecule, &ObservationMatch::identified_molecule_var>, boost::multi_index::member<ObservationMatch, AdductOpt, &ObservationMatch::adduct_opt> > > > > ObservationMatches

ObservationMatchGroups

typedef boost::multi_index_container< ObservationMatchGroup, boost::multi_index::indexed_by< boost::multi_index::ordered_unique< boost::multi_index::member<ObservationMatchGroup, std::set<ObservationMatchRef>, &ObservationMatchGroup::observation_match_refs> > > > ObservationMatchGroups

ObservationMatchRef

typedef IteratorWrapper<ObservationMatches::iterator> ObservationMatchRef

ObservationRef

typedef IteratorWrapper<Observations::iterator> ObservationRef

Observations

typedef boost::multi_index_container< Observation, boost::multi_index::indexed_by< boost::multi_index::ordered_unique< boost::multi_index::composite_key< Observation, boost::multi_index::member<Observation, InputFileRef, &Observation::input_file>, boost::multi_index::member<Observation, String, &Observation::data_id> > > > > Observations

ParentGroupRef

typedef IteratorWrapper<ParentGroups::iterator> ParentGroupRef

ParentGroups

typedef boost::multi_index_container< ParentGroup, boost::multi_index::indexed_by< boost::multi_index::ordered_unique< boost::multi_index::member< ParentGroup, std::set<ParentSequenceRef>, &ParentGroup::parent_refs> > > > ParentGroups

ParentGroupSets

typedef std::vector<ParentGroupSet> ParentGroupSets

ParentMatches

typedef std::map<ParentSequenceRef, std::set<ParentMatch> > ParentMatches

mapping: parent sequence -> match information

ParentSequenceRef

typedef IteratorWrapper<ParentSequences::iterator> ParentSequenceRef

ParentSequences

typedef boost::multi_index_container< ParentSequence, boost::multi_index::indexed_by< boost::multi_index::ordered_unique<boost::multi_index::member< ParentSequence, String, &ParentSequence::accession> > > > ParentSequences

PeakAnnotations

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

PeakAnnotationSteps

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

ProcessingSoftwareRef

typedef IteratorWrapper<ProcessingSoftwares::iterator> ProcessingSoftwareRef

ProcessingSoftwares

typedef std::set<ProcessingSoftware> ProcessingSoftwares

ProcessingStepRef

typedef IteratorWrapper<ProcessingSteps::iterator> ProcessingStepRef

ProcessingSteps

typedef std::set<ProcessingStep> ProcessingSteps

RefVariant

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

ScoreTypeRef

typedef IteratorWrapper<ScoreTypes::iterator> ScoreTypeRef

ScoreTypes

typedef std::set<ScoreType> ScoreTypes

SearchParamRef

typedef IteratorWrapper<DBSearchParams::iterator> SearchParamRef

Enumeration Type Documentation

MassType

enum MassType

Enumerator
MONOISOTOPIC
AVERAGE

MoleculeType

enum MoleculeType

Enumerator
PROTEIN
COMPOUND
RNA

Function Documentation

operator!=()

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

operator<()

bool OpenMS::IdentificationDataInternal::operator<	(	const IdentifiedMolecule &	a,
		const IdentifiedMolecule &	b
	)

operator==()

bool OpenMS::IdentificationDataInternal::operator==	(	const IdentifiedMolecule &	a,
		const IdentifiedMolecule &	b
	)