OpenMS  2.8.0
Classes | Typedefs | Enumerations | Functions
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< 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 std::variant< IdentifiedPeptideRef, IdentifiedCompoundRef, IdentifiedOligoRefRefVariant
 
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 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::PeakAnnotationPeakAnnotations
 
typedef std::map< std::optional< ProcessingStepRef >, PeakAnnotationsPeakAnnotationSteps
 
typedef std::set< AdductInfo, AdductCompareAdducts
 
typedef IteratorWrapper< Adducts::iterator > AdductRef
 
typedef std::optional< AdductRefAdductOpt
 
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< ParentGroupSetParentGroupSets
 
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< ProcessingSoftwareProcessingSoftwares
 
typedef IteratorWrapper< ProcessingSoftwares::iterator > ProcessingSoftwareRef
 
typedef std::set< ProcessingStepProcessingSteps
 
typedef IteratorWrapper< ProcessingSteps::iterator > ProcessingStepRef
 
typedef std::set< ScoreTypeScoreTypes
 
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)
 

Class Documentation

◆ OpenMS::IdentificationDataInternal::ParentGroup

struct OpenMS::IdentificationDataInternal::ParentGroup

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

Collaboration diagram for ParentGroup:
[legend]
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

◆ 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

◆ 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 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

◆ PeakAnnotationSteps

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

◆ ProcessingSoftwareRef

typedef IteratorWrapper<ProcessingSoftwares::iterator> ProcessingSoftwareRef

◆ ProcessingSoftwares

◆ ProcessingStepRef

typedef IteratorWrapper<ProcessingSteps::iterator> ProcessingStepRef

◆ ProcessingSteps

typedef std::set<ProcessingStep> ProcessingSteps

◆ 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

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 
)