OpenMS  2.6.0
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< DataProcessingSoftwareDataProcessingSoftwares
 
typedef IteratorWrapper< DataProcessingSoftwares::iterator > ProcessingSoftwareRef
 
typedef std::set< DataProcessingStepDataProcessingSteps
 
typedef IteratorWrapper< DataProcessingSteps::iterator > ProcessingStepRef
 
typedef std::set< DataQueryDataQueries
 
typedef IteratorWrapper< DataQueries::iterator > DataQueryRef
 
typedef std::set< DBSearchParamDBSearchParams
 
typedef IteratorWrapper< DBSearchParams::iterator > SearchParamRef
 
typedef std::map< ProcessingStepRef, SearchParamRefDBSearchSteps
 
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< AASequenceIdentifiedPeptide
 
typedef IdentifiedSequence< NASequenceIdentifiedOligo
 
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< StringInputFiles
 
typedef IteratorWrapper< InputFiles::iterator > InputFileRef
 
typedef std::map< ParentMoleculeRef, std::set< MoleculeParentMatch > > ParentMatches
 mapping: parent molecule -> match information More...
 
typedef std::vector< PeptideHit::PeakAnnotationPeakAnnotations
 
typedef std::map< boost::optional< ProcessingStepRef >, PeakAnnotationsPeakAnnotationSteps
 
typedef boost::variant< IdentifiedPeptideRef, IdentifiedCompoundRef, IdentifiedOligoRefIdentifiedMoleculeRef
 
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< ParentMoleculeGroupingParentMoleculeGroupings
 
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< ScoreTypeScoreTypes
 
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

◆ DataProcessingSteps

◆ DataQueries

typedef std::set<DataQuery> DataQueries

◆ DataQueryRef

typedef IteratorWrapper<DataQueries::iterator> DataQueryRef

◆ DBSearchParams

typedef std::set<DBSearchParam> DBSearchParams

◆ 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

◆ 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

◆ 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

◆ 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

◆ 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

Enumerator
PROTEIN 
COMPOUND 
RNA 
SIZE_OF_MOLECULETYPE