Representation of spectrum identification results and associated data. More...

#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 @t 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 (IdentificationData &&other) noexcept
	Move constructor. 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...

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 input match. More...

void	setMetaValue (const ObservationRef ref, const String &key, const DataValue &value)
	Set a meta value on a stored input item. More...

void	setMetaValue (const IdentifiedMolecule &var, const String &key, const DataValue &value)
	Set a meta value on a stored identified molecule (variant) 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...

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 DataValue &default_value=DataValue::EMPTY) const
	Returns the value corresponding to a string, or a default value (default: DataValue::EMPTY) if not found. More...

const DataValue &	getMetaValue (UInt index, const DataValue &default_value=DataValue::EMPTY) const
	Returns the value corresponding to an index, or a default value (default: 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...

template<typename RefType , typename ContainerType >
void	setMetaValue_ (const RefType ref, const String &key, const DataValue &value, ContainerType &container, const AddressLookup &lookup=AddressLookup())
	Helper function to add a meta value to an element in a multi-index container. More...

Protected Member Functions inherited from MetaInfoInterface
void	createIfNotExists_ ()
	Creates the MetaInfo object if it does not exist. More...

Static Protected Member Functions
template<typename RefType , typename ContainerType >
static bool	isValidReference_ (RefType ref, ContainerType &container)
	Check whether a reference points to an element in a container. More...

template<typename RefType >
static bool	isValidHashedReference_ (RefType ref, const AddressLookup &lookup)
	Check validity of a reference based on a look-up table of addresses. More...

template<typename ContainerType , typename PredicateType >
static void	removeFromSetIf_ (ContainerType &container, PredicateType predicate)
	Remove elements from a set (or ordered multi_index_container) if they fulfill a predicate. More...

template<typename ContainerType >
static void	removeFromSetIfNotHashed_ (ContainerType &container, const AddressLookup &lookup)
	Remove elements from a set (or ordered multi_index_container) if they don't occur in a look-up table. More...

template<typename ContainerType >
static void	updateAddressLookup_ (const ContainerType &container, AddressLookup &lookup)
	Recreate the address look-up table for a container. 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...

Friends
class	IDFilter

class	MapAlignmentTransformer

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

Detailed Description

Representation of spectrum identification results and associated data.

This class provides capabilities for storing spectrum identification results from different types of experiments/molecules (proteomics: peptides/proteins, metabolomics: small molecules, "nucleomics": RNA).

The class design has the following goals:

Provide one structure for storing all relevant data for spectrum identification results.
Store data non-redundantly.
Ensure consistency (e.g. no conflicting information; no "dangling references").
Allow convenient and efficient querying.
Support different types of experiments, as mentioned above, in one common framework.

The following important subordinate classes are provided to represent different types of data:

Class	Represents	Key	Proteomics example	Corresponding legacy class
ProcessingStep	Information about a data processing step that was applied (e.g. input files, software used, parameters)	Combined information	Mascot search	ProteinIdentification
Observation	A search query (with identifier, RT, m/z) from an input file, i.e. an MS2 spectrum or feature (for accurate mass search)	File/Identifier	MS2 spectrum	PeptideIdentification
ParentSequence	An entry in a FASTA file with associated information (sequence, coverage, etc.)	Accession	Protein	ProteinHit
IdentifiedPeptide/-Oligo/-Compound	An identified molecule of the respective type	Sequence (or identifier for a compound)	Peptide	PeptideHit
ObservationMatch	A match between a query (Observation), identified molecule (Identified...), and optionally adduct	Combination of query/molecule/adduct references	Peptide-spectrum match (PSM)	PeptideIdentification/PeptideHit

To populate an IdentificationData instance with data, "register..." functions are used. These functions return "references" (implemented as iterators) that can be used to refer to stored data items and thus form connections. For example, a protein can be stored using registerParentSequence, which returns a corresponding reference. This reference can be used to build an IdentifiedPeptide object that references the protein. An identified peptide referencing a protein can only be registered if that protein has been registered already, to ensure data consistency. Given the identified peptide, information about the associated protein can be retrieved efficiently by simply dereferencing the reference.

To ensure non-redundancy, many data types have a "key" (see table above) to which a uniqueness constraint applies. This means only one item of such a type with a given key can be stored in an IdentificationData object. If items with an existing key are registered subsequently, attempts are made to merge new information (e.g. additional scores) into the existing entry. The details of this merging are handled in the merge function in each data class.

Warning: This class is not thread-safe while being modified.

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 )

inlinenoexcept

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)

◆ 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 IDFilter::filterObservationMatchesByFunctor(), and 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
	)

inlineprotected

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
	)

inlineprotected

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

◆ isValidHashedReference_()

static bool isValidHashedReference_	(	RefType	ref,
		const AddressLookup &	lookup
	)

inlinestaticprotected

Check validity of a reference based on a look-up table of addresses.

◆ isValidReference_()

static bool isValidReference_	(	RefType	ref,
		ContainerType &	container
	)

inlinestaticprotected

Check whether a reference points to an element in a container.

◆ 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`

◆ 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_().

◆ removeFromSetIf_()

static void removeFromSetIf_	(	ContainerType &	container,
		PredicateType	predicate
	)

inlinestaticprotected

Remove elements from a set (or ordered multi_index_container) if they fulfill a predicate.

Referenced by IDFilter::filterObservationMatchesByFunctor().

◆ removeFromSetIfNotHashed_()

static void removeFromSetIfNotHashed_	(	ContainerType &	container,
		const AddressLookup &	lookup
	)

inlinestaticprotected

Remove elements from a set (or ordered multi_index_container) if they don't occur in a look-up table.

◆ 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 input match.

◆ setMetaValue() [3/5]

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

Set a meta value on a stored input item.

◆ setMetaValue() [4/5]

void setMetaValue

Sets the DataValue corresponding to a name.

◆ setMetaValue() [5/5]

void setMetaValue

Sets the DataValue corresponding to an index.

◆ setMetaValue_()

void setMetaValue_	(	const RefType	ref,
		const String &	key,
		const DataValue &	value,
		ContainerType &	container,
		const AddressLookup &	lookup = `AddressLookup()`
	)

inlineprotected

Helper function to add a meta value to an element in a multi-index container.

◆ swap()

void swap ( IdentificationData & other )

Swap contents with a second instance.

◆ updateAddressLookup_()

static void updateAddressLookup_	(	const ContainerType &	container,
		AddressLookup &	lookup
	)

inlinestaticprotected

Recreate the address look-up table for a container.

Friends And Related Function Documentation

◆ IDFilter

friend class IDFilter

friend

◆ MapAlignmentTransformer

friend class MapAlignmentTransformer

friend

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

Referenced by IDFilter::filterObservationMatchesByFunctor().

◆ 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

Classes

Public Types

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Friends

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ AddressLookup

◆ AdductOpt

◆ AdductRef

◆ Adducts

◆ AppliedProcessingStep

◆ AppliedProcessingSteps

◆ DBSearchParam

◆ DBSearchParams

◆ DBSearchSteps

◆ IdentifiedCompound

◆ IdentifiedCompoundRef

◆ IdentifiedCompounds

◆ IdentifiedMolecule

◆ IdentifiedOligo

◆ IdentifiedOligoRef

◆ IdentifiedOligos

◆ IdentifiedPeptide

◆ IdentifiedPeptideRef

◆ IdentifiedPeptides

◆ InputFile

◆ InputFileRef

◆ InputFiles

◆ MassType

◆ MatchGroupRef

◆ MoleculeType

◆ Observation

◆ ObservationMatch

◆ ObservationMatches

◆ ObservationMatchGroup

◆ ObservationMatchGroups

◆ ObservationMatchRef

◆ ObservationRef

◆ Observations

◆ ParentGroup

◆ ParentGroupRef

◆ ParentGroups

◆ ParentGroupSet

◆ ParentGroupSets

◆ ParentMatch

◆ ParentMatches

◆ ParentSequence

◆ ParentSequenceRef

◆ ParentSequences

◆ PeakAnnotations

◆ ProcessingSoftware

◆ ProcessingSoftwareRef

◆ ProcessingSoftwares

◆ ProcessingStep

◆ ProcessingStepRef

◆ ProcessingSteps

◆ ScoredProcessingResult

◆ ScoreType

◆ ScoreTypeRef

◆ ScoreTypes

◆ SearchParamRef

Constructor & Destructor Documentation

◆ IdentificationData() [1/3]

◆ IdentificationData() [2/3]

◆ IdentificationData() [3/3]

Member Function Documentation

◆ addScore()

◆ calculateCoverages()

◆ checkAppliedProcessingSteps_()

◆ checkParentMatches_()

◆ checkScoreTypes_()

◆ cleanup()

◆ clear()

◆ clearCurrentProcessingStep()

◆ empty()

◆ findScoreType()