| OpenMS 2.5.0

Classes | Typedefs | Enumerations
OpenMS::IdentificationDataInternal Namespace Reference

## 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)

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 |