IdentificationData Class Reference

#include <OpenMS/METADATA/ID/IdentificationData.h>

Inheritance diagram for IdentificationData:

Collaboration diagram for IdentificationData:

Classes
struct	ModifyMultiIndexAddProcessingStep
	Helper functor for adding processing steps to elements in a boost::multi_index_container structure. More...
struct	ModifyMultiIndexAddScore
	Helper functor for adding scores to elements in a boost::multi_index_container structure. More...
struct	ModifyMultiIndexRemoveParentMatches
	Helper functor for removing invalid parent matches from elements in a boost::multi_index_container structure. More...
struct	RefTranslator
	structure that maps references of corresponding objects after copying More...

Public Types
using	MoleculeType = IdentificationDataInternal::MoleculeType
using	MassType = IdentificationDataInternal::MassType
using	InputFile = IdentificationDataInternal::InputFile
using	InputFiles = IdentificationDataInternal::InputFiles
using	InputFileRef = IdentificationDataInternal::InputFileRef
using	ProcessingSoftware = IdentificationDataInternal::ProcessingSoftware
using	ProcessingSoftwares = IdentificationDataInternal::ProcessingSoftwares
using	ProcessingSoftwareRef = IdentificationDataInternal::ProcessingSoftwareRef
using	ProcessingStep = IdentificationDataInternal::ProcessingStep
using	ProcessingSteps = IdentificationDataInternal::ProcessingSteps
using	ProcessingStepRef = IdentificationDataInternal::ProcessingStepRef
using	DBSearchParam = IdentificationDataInternal::DBSearchParam
using	DBSearchParams = IdentificationDataInternal::DBSearchParams
using	SearchParamRef = IdentificationDataInternal::SearchParamRef
using	DBSearchSteps = IdentificationDataInternal::DBSearchSteps
using	ScoreType = IdentificationDataInternal::ScoreType
using	ScoreTypes = IdentificationDataInternal::ScoreTypes
using	ScoreTypeRef = IdentificationDataInternal::ScoreTypeRef
using	ScoredProcessingResult = IdentificationDataInternal::ScoredProcessingResult
using	AppliedProcessingStep = IdentificationDataInternal::AppliedProcessingStep
using	AppliedProcessingSteps = IdentificationDataInternal::AppliedProcessingSteps
using	Observation = IdentificationDataInternal::Observation
using	Observations = IdentificationDataInternal::Observations
using	ObservationRef = IdentificationDataInternal::ObservationRef
using	ParentSequence = IdentificationDataInternal::ParentSequence
using	ParentSequences = IdentificationDataInternal::ParentSequences
using	ParentSequenceRef = IdentificationDataInternal::ParentSequenceRef
using	ParentMatch = IdentificationDataInternal::ParentMatch
using	ParentMatches = IdentificationDataInternal::ParentMatches
using	IdentifiedPeptide = IdentificationDataInternal::IdentifiedPeptide
using	IdentifiedPeptides = IdentificationDataInternal::IdentifiedPeptides
using	IdentifiedPeptideRef = IdentificationDataInternal::IdentifiedPeptideRef
using	IdentifiedCompound = IdentificationDataInternal::IdentifiedCompound
using	IdentifiedCompounds = IdentificationDataInternal::IdentifiedCompounds
using	IdentifiedCompoundRef = IdentificationDataInternal::IdentifiedCompoundRef
using	IdentifiedOligo = IdentificationDataInternal::IdentifiedOligo
using	IdentifiedOligos = IdentificationDataInternal::IdentifiedOligos
using	IdentifiedOligoRef = IdentificationDataInternal::IdentifiedOligoRef
using	IdentifiedMolecule = IdentificationDataInternal::IdentifiedMolecule
using	PeakAnnotations = IdentificationDataInternal::PeakAnnotations
using	Adducts = IdentificationDataInternal::Adducts
using	AdductRef = IdentificationDataInternal::AdductRef
using	AdductOpt = IdentificationDataInternal::AdductOpt
using	ObservationMatch = IdentificationDataInternal::ObservationMatch
using	ObservationMatches = IdentificationDataInternal::ObservationMatches
using	ObservationMatchRef = IdentificationDataInternal::ObservationMatchRef
using	ObservationMatchGroup = IdentificationDataInternal::ObservationMatchGroup
using	ObservationMatchGroups = IdentificationDataInternal::ObservationMatchGroups
using	MatchGroupRef = IdentificationDataInternal::MatchGroupRef
using	ParentGroup = IdentificationDataInternal::ParentGroup
using	ParentGroups = IdentificationDataInternal::ParentGroups
using	ParentGroupRef = IdentificationDataInternal::ParentGroupRef
using	ParentGroupSet = IdentificationDataInternal::ParentGroupSet
using	ParentGroupSets = IdentificationDataInternal::ParentGroupSets
using	AddressLookup = std::unordered_set< uintptr_t >

Public Member Functions
	IdentificationData ()
	Default constructor. More...
	IdentificationData (const IdentificationData &other)
	Copy constructor. More...
IdentificationData &	operator= (const IdentificationData &other)
	Copy assignment operator. More...
	IdentificationData (IdentificationData &&other) noexcept
	Move constructor. More...
IdentificationData &	operator= (IdentificationData &&other) noexcept
	Move assignment operator. More...
InputFileRef	registerInputFile (const InputFile &file)
	Register an input file. More...
ProcessingSoftwareRef	registerProcessingSoftware (const ProcessingSoftware &software)
	Register data processing software. More...
SearchParamRef	registerDBSearchParam (const DBSearchParam &param)
	Register database search parameters. More...
ProcessingStepRef	registerProcessingStep (const ProcessingStep &step)
	Register a data processing step. More...
ProcessingStepRef	registerProcessingStep (const ProcessingStep &step, SearchParamRef search_ref)
	Register a database search step with associated parameters. More...
ScoreTypeRef	registerScoreType (const ScoreType &score)
	Register a score type. More...
ObservationRef	registerObservation (const Observation &obs)
	Register an observation (e.g. MS2 spectrum or feature) More...
ParentSequenceRef	registerParentSequence (const ParentSequence &parent)
	Register a parent sequence (e.g. protein or intact RNA) More...
void	registerParentGroupSet (const ParentGroupSet &groups)
	Register a grouping of parent sequences (e.g. protein inference result) More...
IdentifiedPeptideRef	registerIdentifiedPeptide (const IdentifiedPeptide &peptide)
	Register an identified peptide. More...
IdentifiedCompoundRef	registerIdentifiedCompound (const IdentifiedCompound &compound)
	Register an identified compound (small molecule) More...
IdentifiedOligoRef	registerIdentifiedOligo (const IdentifiedOligo &oligo)
	Register an identified RNA oligonucleotide. More...
AdductRef	registerAdduct (const AdductInfo &adduct)
	Register an adduct. More...
ObservationMatchRef	registerObservationMatch (const ObservationMatch &match)
	Register an observation match (e.g. peptide-spectrum match) More...
MatchGroupRef	registerObservationMatchGroup (const ObservationMatchGroup &group)
	Register a group of observation matches that belong together. More...
const InputFiles &	getInputFiles () const
	Return the registered input files (immutable) More...
const ProcessingSoftwares &	getProcessingSoftwares () const
	Return the registered data processing software (immutable) More...
const ProcessingSteps &	getProcessingSteps () const
	Return the registered data processing steps (immutable) More...
const DBSearchParams &	getDBSearchParams () const
	Return the registered database search parameters (immutable) More...
const DBSearchSteps &	getDBSearchSteps () const
	Return the registered database search steps (immutable) More...
const ScoreTypes &	getScoreTypes () const
	Return the registered score types (immutable) More...
const Observations &	getObservations () const
	Return the registered observations (immutable) More...
const ParentSequences &	getParentSequences () const
	Return the registered parent sequences (immutable) More...
const ParentGroupSets &	getParentGroupSets () const
	Return the registered parent sequence groupings (immutable) More...
const IdentifiedPeptides &	getIdentifiedPeptides () const
	Return the registered identified peptides (immutable) More...
const IdentifiedCompounds &	getIdentifiedCompounds () const
	Return the registered compounds (immutable) More...
const IdentifiedOligos &	getIdentifiedOligos () const
	Return the registered identified oligonucleotides (immutable) More...
const Adducts &	getAdducts () const
	Return the registered adducts (immutable) More...
const ObservationMatches &	getObservationMatches () const
	Return the registered observation matches (immutable) More...
const ObservationMatchGroups &	getObservationMatchGroups () const
	Return the registered groups of observation matches (immutable) More...
void	addScore (ObservationMatchRef match_ref, ScoreTypeRef score_ref, double value)
	Add a score to an input match (e.g. PSM) More...
void	setCurrentProcessingStep (ProcessingStepRef step_ref)
	Set a data processing step that will apply to all subsequent "register..." calls. More...
ProcessingStepRef	getCurrentProcessingStep ()
	Return the current processing step (set via setCurrentProcessingStep()). More...
void	clearCurrentProcessingStep ()
	Cancel the effect of setCurrentProcessingStep(). More...
std::vector< ObservationMatchRef >	getBestMatchPerObservation (ScoreTypeRef score_ref, bool require_score=false) const
	Return the best match for each observation, according to a given score type. More...
std::pair< ObservationMatchRef, ObservationMatchRef >	getMatchesForObservation (ObservationRef obs_ref) const
	Get range of matches (cf. equal_range) for a given observation. More...
template<typename PredicateType >
void	removeObservationMatchesIf (PredicateType &&func)
	Helper function for filtering observation matches (e.g. PSMs) in IdentificationData. More...
template<typename PredicateType >
void	removeParentSequencesIf (PredicateType &&func)
	Helper function for filtering parent sequences (e.g. protein sequences) in IdentificationData. More...
template<typename PredicateType >
void	applyToObservations (PredicateType &&func)
ScoreTypeRef	findScoreType (const String &score_name) const
	Look up a score type by name. More...
void	calculateCoverages (bool check_molecule_length=false)
	Calculate sequence coverages of parent sequences. More...
void	cleanup (bool require_observation_match=true, bool require_identified_sequence=true, bool require_parent_match=true, bool require_parent_group=false, bool require_match_group=false)
	Clean up the data structure after filtering parts of it. More...
bool	empty () const
	Return whether the data structure is empty (no data) More...
RefTranslator	merge (const IdentificationData &other)
	Merge in data from another instance. More...
void	swap (IdentificationData &other)
	Swap contents with a second instance. More...
void	clear ()
	Clear all contents. More...
template<class ScoredProcessingResults >
ScoreTypeRef	pickScoreType (const ScoredProcessingResults &container, bool all_elements=false, bool any_score=false) const
void	setMetaValue (const ObservationMatchRef ref, const String &key, const DataValue &value)
	Set a meta value on a stored observation match (e.g. PSM) More...
void	setMetaValue (const ObservationRef ref, const String &key, const DataValue &value)
	Set a meta value on a stored observation. More...
void	setMetaValue (const IdentifiedMolecule &var, const String &key, const DataValue &value)
	Set a meta value on a stored identified molecule (variant) More...
void	removeMetaValue (const ObservationMatchRef ref, const String &key)
void	setMetaValue (const String &name, const DataValue &value)
	Sets the DataValue corresponding to a name. More...
void	setMetaValue (UInt index, const DataValue &value)
	Sets the DataValue corresponding to an index. More...
Public Member Functions inherited from MetaInfoInterface
	MetaInfoInterface ()
	Constructor. More...
	MetaInfoInterface (const MetaInfoInterface &rhs)
	Copy constructor. More...
	MetaInfoInterface (MetaInfoInterface &&) noexcept
	Move constructor. More...
	~MetaInfoInterface ()
	Destructor. More...
MetaInfoInterface &	operator= (const MetaInfoInterface &rhs)
	Assignment operator. More...
MetaInfoInterface &	operator= (MetaInfoInterface &&) noexcept
	Move assignment operator. More...
void	swap (MetaInfoInterface &rhs)
	Swap contents. More...
bool	operator== (const MetaInfoInterface &rhs) const
	Equality operator. More...
bool	operator!= (const MetaInfoInterface &rhs) const
	Equality operator. More...
const DataValue &	getMetaValue (const String &name) const
	Returns the value corresponding to a string, or DataValue::EMPTY if not found. More...
DataValue	getMetaValue (const String &name, const DataValue &default_value) const
	Returns the value corresponding to a string, or a default value (e.g.: DataValue::EMPTY) if not found More...
const DataValue &	getMetaValue (UInt index) const
	Returns the value corresponding to the index, or DataValue::EMPTY if not found. More...
DataValue	getMetaValue (UInt index, const DataValue &default_value) const
	Returns the value corresponding to the index, or a default value (e.g.: DataValue::EMPTY) if not found More...
bool	metaValueExists (const String &name) const
	Returns whether an entry with the given name exists. More...
bool	metaValueExists (UInt index) const
	Returns whether an entry with the given index exists. More...
void	setMetaValue (const String &name, const DataValue &value)
	Sets the DataValue corresponding to a name. More...
void	setMetaValue (UInt index, const DataValue &value)
	Sets the DataValue corresponding to an index. More...
void	removeMetaValue (const String &name)
	Removes the DataValue corresponding to name if it exists. More...
void	removeMetaValue (UInt index)
	Removes the DataValue corresponding to index if it exists. More...
void	addMetaValues (const MetaInfoInterface &from)
	function to copy all meta values from one object to this one More...
void	getKeys (std::vector< String > &keys) const
	Fills the given vector with a list of all keys for which a value is set. More...
void	getKeys (std::vector< UInt > &keys) const
	Fills the given vector with a list of all keys for which a value is set. More...
bool	isMetaEmpty () const
	Returns if the MetaInfo is empty. More...
void	clearMetaInfo ()
	Removes all meta values. More...

Protected Member Functions
void	checkScoreTypes_ (const std::map< ScoreTypeRef, double > &scores) const
	Helper function to check if all score types are valid. More...
void	checkAppliedProcessingSteps_ (const AppliedProcessingSteps &steps_and_scores) const
	Helper function to check if all applied processing steps are valid. More...
void	checkParentMatches_ (const ParentMatches &matches, MoleculeType expected_type) const
	Helper function to check if all parent matches are valid. More...
void	mergeScoredProcessingResults_ (ScoredProcessingResult &result, const ScoredProcessingResult &other, const RefTranslator &trans)
	Helper function to merge scored processing results while updating references (to processing steps and score types) More...
template<typename ContainerType , typename ElementType >
ContainerType::iterator	insertIntoMultiIndex_ (ContainerType &container, const ElementType &element)
	Helper function for adding entries (derived from ScoredProcessingResult) to a boost::multi_index_container structure. More...
template<typename ContainerType , typename ElementType >
ContainerType::iterator	insertIntoMultiIndex_ (ContainerType &container, const ElementType &element, AddressLookup &lookup)
	Variant of insertIntoMultiIndex_() that also updates a look-up table of valid references (addresses) More...
Protected Member Functions inherited from MetaInfoInterface
void	createIfNotExists_ ()
	Creates the MetaInfo object if it does not exist. More...

Protected Attributes
InputFiles	input_files_
ProcessingSoftwares	processing_softwares_
ProcessingSteps	processing_steps_
DBSearchParams	db_search_params_
DBSearchSteps	db_search_steps_
ScoreTypes	score_types_
Observations	observations_
ParentSequences	parents_
ParentGroupSets	parent_groups_
IdentifiedPeptides	identified_peptides_
IdentifiedCompounds	identified_compounds_
IdentifiedOligos	identified_oligos_
Adducts	adducts_
ObservationMatches	observation_matches_
ObservationMatchGroups	observation_match_groups_
ProcessingStepRef	current_step_ref_
	Reference to the current data processing step (see setCurrentProcessingStep()) More...
bool	no_checks_
	Suppress validity checks in register... calls? More...
AddressLookup	observation_lookup_
AddressLookup	parent_lookup_
AddressLookup	identified_peptide_lookup_
AddressLookup	identified_compound_lookup_
AddressLookup	identified_oligo_lookup_
AddressLookup	observation_match_lookup_
Protected Attributes inherited from MetaInfoInterface
MetaInfo *	meta_
	Pointer to the MetaInfo object (0 by default) More...

Additional Inherited Members
Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistry &	metaRegistry ()
	Returns a reference to the MetaInfoRegistry. More...

---

Class Documentation

OpenMS::IdentificationData::ModifyMultiIndexAddProcessingStep

struct OpenMS::IdentificationData::ModifyMultiIndexAddProcessingStep

template<typename ElementType>
struct OpenMS::IdentificationData::ModifyMultiIndexAddProcessingStep< ElementType >

Helper functor for adding processing steps to elements in a boost::multi_index_container structure.

The validity of the processing step reference cannot be checked here!

OpenMS::IdentificationData::ModifyMultiIndexAddScore

struct OpenMS::IdentificationData::ModifyMultiIndexAddScore

template<typename ElementType>
struct OpenMS::IdentificationData::ModifyMultiIndexAddScore< ElementType >

Helper functor for adding scores to elements in a boost::multi_index_container structure.

The validity of the score type reference cannot be checked here!

OpenMS::IdentificationData::ModifyMultiIndexRemoveParentMatches

struct OpenMS::IdentificationData::ModifyMultiIndexRemoveParentMatches

template<typename ElementType>
struct OpenMS::IdentificationData::ModifyMultiIndexRemoveParentMatches< ElementType >

Helper functor for removing invalid parent matches from elements in a boost::multi_index_container structure.

Used during filtering, to update parent matches after parents have been removed.

Member Typedef Documentation

AddressLookup

using AddressLookup = std::unordered_set<uintptr_t>

AdductOpt

using AdductOpt = IdentificationDataInternal::AdductOpt

AdductRef

using AdductRef = IdentificationDataInternal::AdductRef

Adducts

using Adducts = IdentificationDataInternal::Adducts

AppliedProcessingStep

using AppliedProcessingStep = IdentificationDataInternal::AppliedProcessingStep

AppliedProcessingSteps

using AppliedProcessingSteps = IdentificationDataInternal::AppliedProcessingSteps

DBSearchParam

using DBSearchParam = IdentificationDataInternal::DBSearchParam

DBSearchParams

using DBSearchParams = IdentificationDataInternal::DBSearchParams

DBSearchSteps

using DBSearchSteps = IdentificationDataInternal::DBSearchSteps

IdentifiedCompound

using IdentifiedCompound = IdentificationDataInternal::IdentifiedCompound

IdentifiedCompoundRef

using IdentifiedCompoundRef = IdentificationDataInternal::IdentifiedCompoundRef

IdentifiedCompounds

using IdentifiedCompounds = IdentificationDataInternal::IdentifiedCompounds

IdentifiedMolecule

using IdentifiedMolecule = IdentificationDataInternal::IdentifiedMolecule

IdentifiedOligo

using IdentifiedOligo = IdentificationDataInternal::IdentifiedOligo

IdentifiedOligoRef

using IdentifiedOligoRef = IdentificationDataInternal::IdentifiedOligoRef

IdentifiedOligos

using IdentifiedOligos = IdentificationDataInternal::IdentifiedOligos

IdentifiedPeptide

using IdentifiedPeptide = IdentificationDataInternal::IdentifiedPeptide

IdentifiedPeptideRef

using IdentifiedPeptideRef = IdentificationDataInternal::IdentifiedPeptideRef

IdentifiedPeptides

using IdentifiedPeptides = IdentificationDataInternal::IdentifiedPeptides

InputFile

using InputFile = IdentificationDataInternal::InputFile

InputFileRef

using InputFileRef = IdentificationDataInternal::InputFileRef

InputFiles

using InputFiles = IdentificationDataInternal::InputFiles

MassType

using MassType = IdentificationDataInternal::MassType

MatchGroupRef

using MatchGroupRef = IdentificationDataInternal::MatchGroupRef

MoleculeType

using MoleculeType = IdentificationDataInternal::MoleculeType

Observation

using Observation = IdentificationDataInternal::Observation

ObservationMatch

using ObservationMatch = IdentificationDataInternal::ObservationMatch

ObservationMatches

using ObservationMatches = IdentificationDataInternal::ObservationMatches

ObservationMatchGroup

using ObservationMatchGroup = IdentificationDataInternal::ObservationMatchGroup

ObservationMatchGroups

using ObservationMatchGroups = IdentificationDataInternal::ObservationMatchGroups

ObservationMatchRef

using ObservationMatchRef = IdentificationDataInternal::ObservationMatchRef

ObservationRef

using ObservationRef = IdentificationDataInternal::ObservationRef

Observations

using Observations = IdentificationDataInternal::Observations

ParentGroup

using ParentGroup = IdentificationDataInternal::ParentGroup

ParentGroupRef

using ParentGroupRef = IdentificationDataInternal::ParentGroupRef

ParentGroups

using ParentGroups = IdentificationDataInternal::ParentGroups

ParentGroupSet

using ParentGroupSet = IdentificationDataInternal::ParentGroupSet

ParentGroupSets

using ParentGroupSets = IdentificationDataInternal::ParentGroupSets

ParentMatch

using ParentMatch = IdentificationDataInternal::ParentMatch

ParentMatches

using ParentMatches = IdentificationDataInternal::ParentMatches

ParentSequence

using ParentSequence = IdentificationDataInternal::ParentSequence

ParentSequenceRef

using ParentSequenceRef = IdentificationDataInternal::ParentSequenceRef

ParentSequences

using ParentSequences = IdentificationDataInternal::ParentSequences

PeakAnnotations

using PeakAnnotations = IdentificationDataInternal::PeakAnnotations

ProcessingSoftware

using ProcessingSoftware = IdentificationDataInternal::ProcessingSoftware

ProcessingSoftwareRef

using ProcessingSoftwareRef = IdentificationDataInternal::ProcessingSoftwareRef

ProcessingSoftwares

using ProcessingSoftwares = IdentificationDataInternal::ProcessingSoftwares

ProcessingStep

using ProcessingStep = IdentificationDataInternal::ProcessingStep

ProcessingStepRef

using ProcessingStepRef = IdentificationDataInternal::ProcessingStepRef

ProcessingSteps

using ProcessingSteps = IdentificationDataInternal::ProcessingSteps

ScoredProcessingResult

using ScoredProcessingResult = IdentificationDataInternal::ScoredProcessingResult

ScoreType

using ScoreType = IdentificationDataInternal::ScoreType

ScoreTypeRef

using ScoreTypeRef = IdentificationDataInternal::ScoreTypeRef

ScoreTypes

using ScoreTypes = IdentificationDataInternal::ScoreTypes

SearchParamRef

using SearchParamRef = IdentificationDataInternal::SearchParamRef

Constructor & Destructor Documentation

IdentificationData() [1/3]

IdentificationData ( )

inline

Default constructor.

IdentificationData() [2/3]

IdentificationData

(

const IdentificationData &

other

)

Copy constructor.

Copy-constructing is expensive due to the necessary "rewiring" of references. Use the move constructor where possible.

IdentificationData() [3/3]

IdentificationData ( IdentificationData &&  other )

noexcept

Move constructor.

Member Function Documentation

addScore()

void addScore	(	ObservationMatchRef	match_ref,
		ScoreTypeRef	score_ref,
		double	value
	)

Add a score to an input match (e.g. PSM)

applyToObservations()

void applyToObservations ( PredicateType &&  func )

inline

calculateCoverages()

void calculateCoverages

(

bool

check_molecule_length = false

)

Calculate sequence coverages of parent sequences.

Referenced by NucleicAcidSearchEngine::main_().

checkAppliedProcessingSteps_()

void checkAppliedProcessingSteps_ ( const AppliedProcessingSteps &  steps_and_scores ) const

protected

Helper function to check if all applied processing steps are valid.

checkParentMatches_()

void checkParentMatches_ ( const ParentMatches &  matches, MoleculeType  expected_type  ) const

protected

Helper function to check if all parent matches are valid.

checkScoreTypes_()

void checkScoreTypes_ ( const std::map< ScoreTypeRef, double > &  scores ) const

protected

Helper function to check if all score types are valid.

cleanup()

void cleanup	(	bool	require_observation_match = true,
		bool	require_identified_sequence = true,
		bool	require_parent_match = true,
		bool	require_parent_group = false,
		bool	require_match_group = false
	)

Clean up the data structure after filtering parts of it.

Make sure there are no invalid references or "orphan" data entries.

Parameters

require_observation_match	Remove identified molecules, observations and adducts that aren't part of observation matches?
require_identified_sequence	Remove parent sequences (proteins/RNAs) that aren't referenced by identified peptides/oligonucleotides?
require_parent_match	Remove identified peptides/oligonucleotides that don't reference a parent sequence (protein/RNA)?
require_parent_group	Remove parent sequences that aren't part of parent sequence groups?
require_match_group	Remove input matches that aren't part of match groups?

Referenced by NucleicAcidSearchEngine::postProcessHits_().

clear()

void clear

(

)

Clear all contents.

clearCurrentProcessingStep()

void clearCurrentProcessingStep

(

)

Cancel the effect of setCurrentProcessingStep().

empty()

bool empty

(

)

const

Return whether the data structure is empty (no data)

findScoreType()

ScoreTypeRef findScoreType

(

const String &

score_name

)

const

Look up a score type by name.

Returns

Reference to the score type, if found; otherwise getScoreTypes().end()

Referenced by NucleicAcidSearchEngine::calculateAndFilterFDR_().

getAdducts()

const Adducts& getAdducts ( ) const

inline

Return the registered adducts (immutable)

getBestMatchPerObservation()

std::vector<ObservationMatchRef> getBestMatchPerObservation	(	ScoreTypeRef	score_ref,
		bool	require_score = false
	)		const

Return the best match for each observation, according to a given score type.

Parameters

score_ref	Score type to use
require_score	Exclude matches without score of this type, even if they are the only matches for their observations?

getCurrentProcessingStep()

ProcessingStepRef getCurrentProcessingStep

(

)

Return the current processing step (set via setCurrentProcessingStep()).

If no current processing step has been set, processing_steps.end() is returned.

Referenced by NucleicAcidSearchEngine::main_(), and NucleicAcidSearchEngine::postProcessHits_().

getDBSearchParams()

const DBSearchParams& getDBSearchParams ( ) const

inline

Return the registered database search parameters (immutable)

Referenced by NucleicAcidSearchEngine::main_().

getDBSearchSteps()

const DBSearchSteps& getDBSearchSteps ( ) const

inline

Return the registered database search steps (immutable)

getIdentifiedCompounds()

const IdentifiedCompounds& getIdentifiedCompounds ( ) const

inline

Return the registered compounds (immutable)

getIdentifiedOligos()

const IdentifiedOligos& getIdentifiedOligos ( ) const

inline

Return the registered identified oligonucleotides (immutable)

Referenced by NucleicAcidSearchEngine::main_().

getIdentifiedPeptides()

const IdentifiedPeptides& getIdentifiedPeptides ( ) const

inline

Return the registered identified peptides (immutable)

getInputFiles()

const InputFiles& getInputFiles ( ) const

inline

Return the registered input files (immutable)

Referenced by NucleicAcidSearchEngine::postProcessHits_().

getMatchesForObservation()

std::pair<ObservationMatchRef, ObservationMatchRef> getMatchesForObservation

(

ObservationRef

obs_ref

)

const

Get range of matches (cf. equal_range) for a given observation.

getObservationMatches()

const ObservationMatches& getObservationMatches ( ) const

inline

Return the registered observation matches (immutable)

Referenced by NucleicAcidSearchEngine::calculateAndFilterFDR_(), and NucleicAcidSearchEngine::generateLFQInput_().

getObservationMatchGroups()

const ObservationMatchGroups& getObservationMatchGroups ( ) const

inline

Return the registered groups of observation matches (immutable)

getObservations()

const Observations& getObservations ( ) const

inline

Return the registered observations (immutable)

Referenced by NucleicAcidSearchEngine::calculateAndFilterFDR_(), and NucleicAcidSearchEngine::main_().

getParentGroupSets()

const ParentGroupSets& getParentGroupSets ( ) const

inline

Return the registered parent sequence groupings (immutable)

getParentSequences()

const ParentSequences& getParentSequences ( ) const

inline

Return the registered parent sequences (immutable)

Referenced by NucleicAcidSearchEngine::main_().

getProcessingSoftwares()

const ProcessingSoftwares& getProcessingSoftwares ( ) const

inline

Return the registered data processing software (immutable)

getProcessingSteps()

const ProcessingSteps& getProcessingSteps ( ) const

inline

Return the registered data processing steps (immutable)

getScoreTypes()

const ScoreTypes& getScoreTypes ( ) const

inline

Return the registered score types (immutable)

Referenced by NucleicAcidSearchEngine::postProcessHits_().

insertIntoMultiIndex_() [1/2]

ContainerType::iterator insertIntoMultiIndex_ ( ContainerType &  container, const ElementType &  element  )

protected

Helper function for adding entries (derived from ScoredProcessingResult) to a boost::multi_index_container structure.

insertIntoMultiIndex_() [2/2]

ContainerType::iterator insertIntoMultiIndex_ ( ContainerType &  container, const ElementType &  element, AddressLookup &  lookup  )

protected

Variant of insertIntoMultiIndex_() that also updates a look-up table of valid references (addresses)

merge()

RefTranslator merge

(

const IdentificationData &

other

)

Merge in data from another instance.

Can be used to make a deep copy by calling merge() on an empty object. The returned translation table allows updating of references that are held externally.

Parameters

other

Instance to merge in.

Returns

Translation table for references (old -> new)

mergeScoredProcessingResults_()

void mergeScoredProcessingResults_ ( ScoredProcessingResult &  result, const ScoredProcessingResult &  other, const RefTranslator &  trans  )

protected

Helper function to merge scored processing results while updating references (to processing steps and score types)

Parameters

result	Instance that gets updated
other	Instance to merge into result
trans	Mapping of corresponding references between other and result

operator=() [1/2]

IdentificationData& operator=

(

const IdentificationData &

other

)

Copy assignment operator.

operator=() [2/2]

IdentificationData& operator= ( IdentificationData &&  other )

noexcept

Move assignment operator.

pickScoreType()

ScoreTypeRef pickScoreType ( const ScoredProcessingResults &  container, bool  all_elements = false, bool  any_score = false  ) const

inline

Pick a score type for operations (e.g. filtering) on a container of scored processing results (e.g. input matches, identified peptides, ...).

If all_elements is false, only the first element with a score will be considered (which is sufficient if all elements were processed in the same way). If all_elements is true, the score type supported by the highest number of elements will be chosen.

If any_score is false, only the primary score from the most recent processing step (that assigned a score) is taken into account. If any_score is true, all score types assigned across all elements are considered (this implies all_elements = true).

Parameters

container	Container with elements derived from ScoredProcessingResult
all_elements	Consider all elements?
any_score	Consider any score (or just primary/most recent ones)?

Returns

Reference to the chosen score type (or getScoreTypes().end() if there were no scores)

registerAdduct()

AdductRef registerAdduct

(

const AdductInfo &

adduct

)

Register an adduct.

Returns

Reference to the registered adduct

Referenced by NucleicAcidSearchEngine::main_().

registerDBSearchParam()

SearchParamRef registerDBSearchParam

(

const DBSearchParam &

param

)

Register database search parameters.

Returns

Reference to the registered search parameters

Referenced by NucleicAcidSearchEngine::main_().

registerIdentifiedCompound()

IdentifiedCompoundRef registerIdentifiedCompound

(

const IdentifiedCompound &

compound

)

Register an identified compound (small molecule)

Returns

Reference to the registered compound

registerIdentifiedOligo()

IdentifiedOligoRef registerIdentifiedOligo

(

const IdentifiedOligo &

oligo

)

Register an identified RNA oligonucleotide.

Returns

Reference to the registered oligonucleotide

Referenced by NucleicAcidSearchEngine::postProcessHits_().

registerIdentifiedPeptide()

IdentifiedPeptideRef registerIdentifiedPeptide

(

const IdentifiedPeptide &

peptide

)

Register an identified peptide.

Returns

Reference to the registered peptide

registerInputFile()

InputFileRef registerInputFile

(

const InputFile &

file

)

Register an input file.

Returns

Reference to the registered file

Referenced by NucleicAcidSearchEngine::main_().

registerObservation()

ObservationRef registerObservation

(

const Observation &

obs

)

Register an observation (e.g. MS2 spectrum or feature)

Returns

Reference to the registered observation

Referenced by NucleicAcidSearchEngine::postProcessHits_().

registerObservationMatch()

ObservationMatchRef registerObservationMatch

(

const ObservationMatch &

match

)

Register an observation match (e.g. peptide-spectrum match)

Returns

Reference to the registered observation match

Referenced by NucleicAcidSearchEngine::postProcessHits_().

registerObservationMatchGroup()

MatchGroupRef registerObservationMatchGroup

(

const ObservationMatchGroup &

group

)

Register a group of observation matches that belong together.

Returns

Reference to the registered group of observation matches

registerParentGroupSet()

void registerParentGroupSet

(

const ParentGroupSet &

groups

)

Register a grouping of parent sequences (e.g. protein inference result)

registerParentSequence()

ParentSequenceRef registerParentSequence

(

const ParentSequence &

parent

)

Register a parent sequence (e.g. protein or intact RNA)

Returns

Reference to the registered parent sequence

Referenced by NucleicAcidSearchEngine::main_().

registerProcessingSoftware()

ProcessingSoftwareRef registerProcessingSoftware

(

const ProcessingSoftware &

software

)

Register data processing software.

Returns

Reference to the registered software

Referenced by NucleicAcidSearchEngine::main_().

registerProcessingStep() [1/2]

ProcessingStepRef registerProcessingStep

(

const ProcessingStep &

step

)

Register a data processing step.

Returns

Reference to the registered processing step

Referenced by NucleicAcidSearchEngine::main_().

registerProcessingStep() [2/2]

ProcessingStepRef registerProcessingStep	(	const ProcessingStep &	step,
		SearchParamRef	search_ref
	)

Register a database search step with associated parameters.

Returns

Reference to the registered processing step

registerScoreType()

ScoreTypeRef registerScoreType

(

const ScoreType &

score

)

Register a score type.

Returns

Reference to the registered score type

Referenced by NucleicAcidSearchEngine::main_().

removeMetaValue()

void removeMetaValue	(	const ObservationMatchRef	ref,
		const String &	key
	)

Remove a meta value (if it exists) from a stored observation match (e.g. PSM)

Todo:

: return whether value existed? (requires changes in MetaInfo[Interface])

removeObservationMatchesIf()

void removeObservationMatchesIf ( PredicateType &&  func )

inline

Helper function for filtering observation matches (e.g. PSMs) in IdentificationData.

If other parts are invalidated by filtering, the data structure is automatically cleaned up (IdentificationData::cleanup) to remove any invalidated references at the end of this operation.

Parameters

func	Functor that returns true for container elements to be removed

References OpenMS::removeFromSetIf_().

removeParentSequencesIf()

void removeParentSequencesIf ( PredicateType &&  func )

inline

Helper function for filtering parent sequences (e.g. protein sequences) in IdentificationData.

If other parts are invalidated by filtering, the data structure is automatically cleaned up (IdentificationData::cleanup) to remove any invalidated references at the end of this operation.

Parameters

func	Functor that returns true for container elements to be removed

References OpenMS::removeFromSetIf_().

setCurrentProcessingStep()

void setCurrentProcessingStep

(

ProcessingStepRef

step_ref

)

Set a data processing step that will apply to all subsequent "register..." calls.

This step will be appended to the list of processing steps for all relevant elements that are registered subsequently (unless it is already the last entry in the list). If a score type without a software reference is registered, the software reference of this processing step will be applied. Effective until clearCurrentProcessingStep() is called.

Referenced by NucleicAcidSearchEngine::main_().

setMetaValue() [1/5]

void setMetaValue	(	const IdentifiedMolecule &	var,
		const String &	key,
		const DataValue &	value
	)

Set a meta value on a stored identified molecule (variant)

setMetaValue() [2/5]

void setMetaValue	(	const ObservationMatchRef	ref,
		const String &	key,
		const DataValue &	value
	)

Set a meta value on a stored observation match (e.g. PSM)

setMetaValue() [3/5]

void setMetaValue	(	const ObservationRef	ref,
		const String &	key,
		const DataValue &	value
	)

Set a meta value on a stored observation.

setMetaValue() [4/5]

void setMetaValue

Sets the DataValue corresponding to a name.

setMetaValue() [5/5]

void setMetaValue

Sets the DataValue corresponding to an index.

swap()

void swap

(

IdentificationData &

other

)

Swap contents with a second instance.

Member Data Documentation

adducts_

Adducts adducts_

protected

current_step_ref_

ProcessingStepRef current_step_ref_

protected

Reference to the current data processing step (see setCurrentProcessingStep())

db_search_params_

DBSearchParams db_search_params_

protected

db_search_steps_

DBSearchSteps db_search_steps_

protected

identified_compound_lookup_

AddressLookup identified_compound_lookup_

protected

identified_compounds_

IdentifiedCompounds identified_compounds_

protected

identified_oligo_lookup_

AddressLookup identified_oligo_lookup_

protected

identified_oligos_

IdentifiedOligos identified_oligos_

protected

identified_peptide_lookup_

AddressLookup identified_peptide_lookup_

protected

identified_peptides_

IdentifiedPeptides identified_peptides_

protected

input_files_

InputFiles input_files_

protected

no_checks_

bool no_checks_

protected

Suppress validity checks in register... calls?

This is useful in situations where validity is already guaranteed (e.g. copying).

observation_lookup_

AddressLookup observation_lookup_

protected

observation_match_groups_

ObservationMatchGroups observation_match_groups_

protected

observation_match_lookup_

AddressLookup observation_match_lookup_

protected

observation_matches_

ObservationMatches observation_matches_

protected

observations_

Observations observations_

protected

parent_groups_

ParentGroupSets parent_groups_

protected

parent_lookup_

AddressLookup parent_lookup_

protected

parents_

ParentSequences parents_

protected

processing_softwares_

ProcessingSoftwares processing_softwares_

protected

processing_steps_

ProcessingSteps processing_steps_

protected

score_types_

ScoreTypes score_types_

protected