Classes
struct	AppliedProcessingStep
	A processing step that was applied to a data item, possibly with associated scores. More...

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

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

struct	DataQuery
	Search query, e.g. spectrum or feature. More...

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

struct	IdentifiedCompound

struct	IdentifiedSequence
	Identified sequence (peptide or oligonucleotide) 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	MoleculeParentMatch
	Meta data for the association between an identified molecule (e.g. peptide) and a parent molecule (e.g. protein). More...

struct	MoleculeQueryMatch
	Meta data for a search hit (e.g. peptide-spectrum match). More...

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

struct	ParentMoleculeGroup
	: Group of ambiguously identified parent molecules (e.g. protein group) More...

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

struct	QueryMatchGroup
	: Group of related (co-identified) molecule-query matches 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, boost::optional< ProcessingStepRef >, &AppliedProcessingStep::processing_step_opt > > > >	AppliedProcessingSteps

typedef std::set< DataProcessingSoftware >	DataProcessingSoftwares

typedef IteratorWrapper< DataProcessingSoftwares::iterator >	ProcessingSoftwareRef

typedef std::set< DataProcessingStep >	DataProcessingSteps

typedef IteratorWrapper< DataProcessingSteps::iterator >	ProcessingStepRef

typedef std::set< DataQuery >	DataQueries

typedef IteratorWrapper< DataQueries::iterator >	DataQueryRef

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 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 std::set< String >	InputFiles

typedef IteratorWrapper< InputFiles::iterator >	InputFileRef

typedef std::map< ParentMoleculeRef, std::set< MoleculeParentMatch > >	ParentMatches
	mapping: parent molecule -> match information More...

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

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

typedef boost::variant< IdentifiedPeptideRef, IdentifiedCompoundRef, IdentifiedOligoRef >	IdentifiedMoleculeRef

typedef boost::multi_index_container< MoleculeQueryMatch, boost::multi_index::indexed_by< boost::multi_index::ordered_unique< boost::multi_index::composite_key< MoleculeQueryMatch, boost::multi_index::member< MoleculeQueryMatch, DataQueryRef, &MoleculeQueryMatch::data_query_ref >, boost::multi_index::member< MoleculeQueryMatch, IdentifiedMoleculeRef, &MoleculeQueryMatch::identified_molecule_ref > > > > >	MoleculeQueryMatches

typedef IteratorWrapper< MoleculeQueryMatches::iterator >	QueryMatchRef

typedef boost::multi_index_container< ParentMolecule, boost::multi_index::indexed_by< boost::multi_index::ordered_unique< boost::multi_index::member< ParentMolecule, String, &ParentMolecule::accession > > > >	ParentMolecules

typedef IteratorWrapper< ParentMolecules::iterator >	ParentMoleculeRef

typedef boost::multi_index_container< ParentMoleculeGroup, boost::multi_index::indexed_by< boost::multi_index::ordered_unique< boost::multi_index::member< ParentMoleculeGroup, std::set< ParentMoleculeRef >, &ParentMoleculeGroup::parent_molecule_refs > > > >	ParentMoleculeGroups

typedef IteratorWrapper< ParentMoleculeGroups::iterator >	ParentGroupRef

typedef std::vector< ParentMoleculeGrouping >	ParentMoleculeGroupings

typedef boost::multi_index_container< QueryMatchGroup, boost::multi_index::indexed_by< boost::multi_index::ordered_unique< boost::multi_index::member< QueryMatchGroup, std::set< QueryMatchRef >, &QueryMatchGroup::query_match_refs > > > >	QueryMatchGroups

typedef IteratorWrapper< QueryMatchGroups::iterator >	MatchGroupRef

typedef std::set< ScoreType >	ScoreTypes

typedef IteratorWrapper< ScoreTypes::iterator >	ScoreTypeRef

Enumerations
enum	MoleculeType { PROTEIN , COMPOUND , RNA , SIZE_OF_MOLECULETYPE }

enum	MassType { MONOISOTOPIC , AVERAGE , SIZE_OF_MASSTYPE }

Class Documentation

◆ OpenMS::IdentificationDataInternal::ParentMoleculeGroup

struct OpenMS::IdentificationDataInternal::ParentMoleculeGroup

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

Collaboration diagram for ParentMoleculeGroup:

[legend]

Class Members
set< ParentMoleculeRef >	parent_molecule_refs
map< ScoreTypeRef, double >	scores

Typedef Documentation

◆ 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, boost::optional<ProcessingStepRef>, &AppliedProcessingStep::processing_step_opt> > > > AppliedProcessingSteps

◆ DataProcessingSoftwares

typedef std::set<DataProcessingSoftware> DataProcessingSoftwares

◆ DataProcessingSteps

typedef std::set<DataProcessingStep> DataProcessingSteps

◆ DataQueries

typedef std::set<DataQuery> DataQueries

◆ DataQueryRef

typedef IteratorWrapper<DataQueries::iterator> DataQueryRef

◆ 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

◆ IdentifiedMoleculeRef

typedef boost::variant<IdentifiedPeptideRef, IdentifiedCompoundRef, IdentifiedOligoRef> IdentifiedMoleculeRef

◆ 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 std::set<String> InputFiles

◆ MatchGroupRef

typedef IteratorWrapper<QueryMatchGroups::iterator> MatchGroupRef

◆ MoleculeQueryMatches

typedef boost::multi_index_container< MoleculeQueryMatch, boost::multi_index::indexed_by< boost::multi_index::ordered_unique< boost::multi_index::composite_key< MoleculeQueryMatch, boost::multi_index::member<MoleculeQueryMatch, DataQueryRef, &MoleculeQueryMatch::data_query_ref>, boost::multi_index::member< MoleculeQueryMatch, IdentifiedMoleculeRef, &MoleculeQueryMatch::identified_molecule_ref> > > > > MoleculeQueryMatches

◆ ParentGroupRef

typedef IteratorWrapper<ParentMoleculeGroups::iterator> ParentGroupRef

◆ ParentMatches

typedef std::map<ParentMoleculeRef, std::set<MoleculeParentMatch> > ParentMatches

mapping: parent molecule -> match information

◆ ParentMoleculeGroupings

typedef std::vector<ParentMoleculeGrouping> ParentMoleculeGroupings

◆ ParentMoleculeGroups

typedef boost::multi_index_container< ParentMoleculeGroup, boost::multi_index::indexed_by< boost::multi_index::ordered_unique< boost::multi_index::member< ParentMoleculeGroup, std::set<ParentMoleculeRef>, &ParentMoleculeGroup::parent_molecule_refs> > > > ParentMoleculeGroups

◆ ParentMoleculeRef

typedef IteratorWrapper<ParentMolecules::iterator> ParentMoleculeRef

◆ ParentMolecules

typedef boost::multi_index_container< ParentMolecule, boost::multi_index::indexed_by< boost::multi_index::ordered_unique<boost::multi_index::member< ParentMolecule, String, &ParentMolecule::accession> > > > ParentMolecules

◆ PeakAnnotations

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

◆ PeakAnnotationSteps

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

◆ ProcessingSoftwareRef

typedef IteratorWrapper<DataProcessingSoftwares::iterator> ProcessingSoftwareRef

◆ ProcessingStepRef

typedef IteratorWrapper<DataProcessingSteps::iterator> ProcessingStepRef

◆ QueryMatchGroups

typedef boost::multi_index_container< QueryMatchGroup, boost::multi_index::indexed_by< boost::multi_index::ordered_unique< boost::multi_index::member<QueryMatchGroup, std::set<QueryMatchRef>, &QueryMatchGroup::query_match_refs> > > > QueryMatchGroups

◆ QueryMatchRef

typedef IteratorWrapper<MoleculeQueryMatches::iterator> QueryMatchRef

◆ 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
SIZE_OF_MASSTYPE

◆ MoleculeType

enum MoleculeType

Enumerator
PROTEIN
COMPOUND
RNA
SIZE_OF_MOLECULETYPE

Classes

Typedefs

Enumerations