IdentificationData Class Reference

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 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...

Public Types
using	MoleculeType = IdentificationDataInternal::MoleculeType
using	MassType = IdentificationDataInternal::MassType
using	InputFiles = IdentificationDataInternal::InputFiles
using	InputFileRef = IdentificationDataInternal::InputFileRef
using	DataProcessingSoftware = IdentificationDataInternal::DataProcessingSoftware
using	DataProcessingSoftwares = IdentificationDataInternal::DataProcessingSoftwares
using	ProcessingSoftwareRef = IdentificationDataInternal::ProcessingSoftwareRef
using	DataProcessingStep = IdentificationDataInternal::DataProcessingStep
using	DataProcessingSteps = IdentificationDataInternal::DataProcessingSteps
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	AppliedProcessingStep = IdentificationDataInternal::AppliedProcessingStep
using	AppliedProcessingSteps = IdentificationDataInternal::AppliedProcessingSteps
using	DataQuery = IdentificationDataInternal::DataQuery
using	DataQueries = IdentificationDataInternal::DataQueries
using	DataQueryRef = IdentificationDataInternal::DataQueryRef
using	ParentMolecule = IdentificationDataInternal::ParentMolecule
using	ParentMolecules = IdentificationDataInternal::ParentMolecules
using	ParentMoleculeRef = IdentificationDataInternal::ParentMoleculeRef
using	MoleculeParentMatch = IdentificationDataInternal::MoleculeParentMatch
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	PeakAnnotations = IdentificationDataInternal::PeakAnnotations
using	IdentifiedMoleculeRef = IdentificationDataInternal::IdentifiedMoleculeRef
using	MoleculeQueryMatch = IdentificationDataInternal::MoleculeQueryMatch
using	MoleculeQueryMatches = IdentificationDataInternal::MoleculeQueryMatches
using	QueryMatchRef = IdentificationDataInternal::QueryMatchRef
using	QueryMatchGroup = IdentificationDataInternal::QueryMatchGroup
using	QueryMatchGroups = IdentificationDataInternal::QueryMatchGroups
using	MatchGroupRef = IdentificationDataInternal::MatchGroupRef
using	ParentMoleculeGroup = IdentificationDataInternal::ParentMoleculeGroup
using	ParentMoleculeGroups = IdentificationDataInternal::ParentMoleculeGroups
using	ParentGroupRef = IdentificationDataInternal::ParentGroupRef
using	ParentMoleculeGrouping = IdentificationDataInternal::ParentMoleculeGrouping
using	ParentMoleculeGroupings = IdentificationDataInternal::ParentMoleculeGroupings
using	AddressLookup = boost::unordered_set< uintptr_t >

Public Member Functions
	IdentificationData ()
	Default constructor. More...
	IdentificationData (const IdentificationData &other)=delete
	IdentificationData (IdentificationData &&other)
	Move constructor. More...
InputFileRef	registerInputFile (const String &file)
	Register an input file. More...
ProcessingSoftwareRef	registerDataProcessingSoftware (const DataProcessingSoftware &software)
	Register data processing software. More...
SearchParamRef	registerDBSearchParam (const DBSearchParam &param)
	Register database search parameters. More...
ProcessingStepRef	registerDataProcessingStep (const DataProcessingStep &step)
	Register a data processing step. More...
ProcessingStepRef	registerDataProcessingStep (const DataProcessingStep &step, SearchParamRef search_ref)
	Register a database search step with associated parameters. More...
ScoreTypeRef	registerScoreType (const ScoreType &score)
	Register a score type. More...
DataQueryRef	registerDataQuery (const DataQuery &query)
	Register a data query (e.g. MS2 spectrum or feature) More...
ParentMoleculeRef	registerParentMolecule (const ParentMolecule &parent)
	Register a parent molecule (e.g. protein or intact RNA) More...
void	registerParentMoleculeGrouping (const ParentMoleculeGrouping &grouping)
	Register a grouping of parent molecules (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...
QueryMatchRef	registerMoleculeQueryMatch (const MoleculeQueryMatch &match)
	Register a molecule-query match (e.g. peptide-spectrum match) More...
MatchGroupRef	registerQueryMatchGroup (const QueryMatchGroup &group)
	Register a group of associated molecule-query matches. More...
const InputFiles &	getInputFiles () const
	Return the registered input files (immutable) More...
const DataProcessingSoftwares &	getDataProcessingSoftwares () const
	Return the registered data processing software (immutable) More...
const DataProcessingSteps &	getDataProcessingSteps () 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 DataQueries &	getDataQueries () const
	Return the registered data queries (immutable) More...
const ParentMolecules &	getParentMolecules () const
	Return the registered parent molecules (immutable) More...
const ParentMoleculeGroupings &	getParentMoleculeGroupings () const
	Return the registered parent molecule 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 MoleculeQueryMatches &	getMoleculeQueryMatches () const
	Return the registered molecule-query matches (immutable) More...
const QueryMatchGroups &	getQueryMatchGroups () const
	Return the registered groups of molecule-query matches (immutable) More...
void	addScore (QueryMatchRef match_ref, ScoreTypeRef score_ref, double value)
	Add a score to a molecule-query 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 ()
void	clearCurrentProcessingStep ()
	Cancel the effect of setCurrentProcessingStep(). More...
std::vector< QueryMatchRef >	getBestMatchPerQuery (ScoreTypeRef score_ref) const
	Return the best match for each data query, according to a given score type. More...
std::pair< ScoreTypeRef, bool >	findScoreType (const String &score_name) const
	Look up a score type by name. More...
void	calculateCoverages (bool check_molecule_length=false)
	Calculate sequence coverage of parent molecules. More...
void	cleanup (bool require_query_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...
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...
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...

Static Public Member Functions
static bool	isBetterScore (double first, double second, bool higher_better)
	Helper function to compare two scores. More...
Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistry &	metaRegistry ()
	Returns a reference to the MetaInfoRegistry. 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...
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...

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_
DataProcessingSoftwares	processing_softwares_
DataProcessingSteps	processing_steps_
DBSearchParams	db_search_params_
DBSearchSteps	db_search_steps_
ScoreTypes	score_types_
DataQueries	data_queries_
ParentMolecules	parent_molecules_
ParentMoleculeGroupings	parent_molecule_groupings_
IdentifiedPeptides	identified_peptides_
IdentifiedCompounds	identified_compounds_
IdentifiedOligos	identified_oligos_
MoleculeQueryMatches	query_matches_
QueryMatchGroups	query_match_groups_
ProcessingStepRef	current_step_ref_
	Reference to the current data processing step (see setCurrentProcessingStep()) More...
AddressLookup	data_query_lookup_
AddressLookup	parent_molecule_lookup_
AddressLookup	identified_peptide_lookup_
AddressLookup	identified_compound_lookup_
AddressLookup	identified_oligo_lookup_
AddressLookup	query_match_lookup_
Protected Attributes inherited from MetaInfoInterface
MetaInfo *	meta_
	Pointer to the MetaInfo object (0 by default) More...

Friends
class	IDFilter

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
DataProcessingStep	Information about a data processing step that was applied (e.g. input files, software used, parameters)	Combined information	Mascot search	ProteinIdentification
DataQuery	A search query (with identifier, RT, m/z), i.e. an MS2 spectrum or feature (for accurate mass search)	Identifier	MS2 spectrum	PeptideIdentification
ParentMolecule	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
MoleculeQueryMatch	A match between a query (DataQuery) and identified molecule (Identified...)	Combination of query and molecule 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 registerParentMolecule, 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.

Member Typedef Documentation

AddressLookup

using AddressLookup = boost::unordered_set<uintptr_t>

AppliedProcessingStep

using AppliedProcessingStep = IdentificationDataInternal::AppliedProcessingStep

AppliedProcessingSteps

using AppliedProcessingSteps = IdentificationDataInternal::AppliedProcessingSteps

DataProcessingSoftware

using DataProcessingSoftware = IdentificationDataInternal::DataProcessingSoftware

DataProcessingSoftwares

using DataProcessingSoftwares = IdentificationDataInternal::DataProcessingSoftwares

DataProcessingStep

using DataProcessingStep = IdentificationDataInternal::DataProcessingStep

DataProcessingSteps

using DataProcessingSteps = IdentificationDataInternal::DataProcessingSteps

DataQueries

using DataQueries = IdentificationDataInternal::DataQueries

DataQuery

using DataQuery = IdentificationDataInternal::DataQuery

DataQueryRef

using DataQueryRef = IdentificationDataInternal::DataQueryRef

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

IdentifiedMoleculeRef

using IdentifiedMoleculeRef = IdentificationDataInternal::IdentifiedMoleculeRef

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

InputFileRef

using InputFileRef = IdentificationDataInternal::InputFileRef

InputFiles

using InputFiles = IdentificationDataInternal::InputFiles

MassType

using MassType = IdentificationDataInternal::MassType

MatchGroupRef

using MatchGroupRef = IdentificationDataInternal::MatchGroupRef

MoleculeParentMatch

using MoleculeParentMatch = IdentificationDataInternal::MoleculeParentMatch

MoleculeQueryMatch

using MoleculeQueryMatch = IdentificationDataInternal::MoleculeQueryMatch

MoleculeQueryMatches

using MoleculeQueryMatches = IdentificationDataInternal::MoleculeQueryMatches

MoleculeType

using MoleculeType = IdentificationDataInternal::MoleculeType

ParentGroupRef

using ParentGroupRef = IdentificationDataInternal::ParentGroupRef

ParentMatches

using ParentMatches = IdentificationDataInternal::ParentMatches

ParentMolecule

using ParentMolecule = IdentificationDataInternal::ParentMolecule

ParentMoleculeGroup

using ParentMoleculeGroup = IdentificationDataInternal::ParentMoleculeGroup

ParentMoleculeGrouping

using ParentMoleculeGrouping = IdentificationDataInternal::ParentMoleculeGrouping

ParentMoleculeGroupings

using ParentMoleculeGroupings = IdentificationDataInternal::ParentMoleculeGroupings

ParentMoleculeGroups

using ParentMoleculeGroups = IdentificationDataInternal::ParentMoleculeGroups

ParentMoleculeRef

using ParentMoleculeRef = IdentificationDataInternal::ParentMoleculeRef

ParentMolecules

using ParentMolecules = IdentificationDataInternal::ParentMolecules

PeakAnnotations

using PeakAnnotations = IdentificationDataInternal::PeakAnnotations

ProcessingSoftwareRef

using ProcessingSoftwareRef = IdentificationDataInternal::ProcessingSoftwareRef

ProcessingStepRef

using ProcessingStepRef = IdentificationDataInternal::ProcessingStepRef

QueryMatchGroup

using QueryMatchGroup = IdentificationDataInternal::QueryMatchGroup

QueryMatchGroups

using QueryMatchGroups = IdentificationDataInternal::QueryMatchGroups

QueryMatchRef

using QueryMatchRef = IdentificationDataInternal::QueryMatchRef

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 )

delete

IdentificationData() [3/3]

IdentificationData ( IdentificationData &&  other )

inline

Move constructor.

Member Function Documentation

addScore()

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

Add a score to a molecule-query match (e.g. PSM)

calculateCoverages()

void calculateCoverages

(

bool

check_molecule_length = false

)

Calculate sequence coverage of parent molecules.

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_query_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_query_match	Remove identified molecules and data queries that aren't part of molecule-query matches?
require_identified_sequence	Remove parent molecules (proteins/RNAs) that aren't referenced by identified peptides/oligonucleotides?
require_parent_match	Remove identified peptides/oligonucleotides that don't reference a parent molecule (protein/RNA)?
require_parent_group	Remove parent molecules that aren't part of parent molecule groups?
require_match_group	Remove molecule-query matches that aren't part of match groups?

Referenced by NucleicAcidSearchEngine::postProcessHits_().

clearCurrentProcessingStep()

void clearCurrentProcessingStep

(

)

Cancel the effect of setCurrentProcessingStep().

findScoreType()

std::pair<ScoreTypeRef, bool> findScoreType

(

const String &

score_name

)

const

Look up a score type by name.

Returns

A pair: 1. Reference to the score type, if found; 2. Boolean indicating success or failure

Referenced by NucleicAcidSearchEngine::calculateAndFilterFDR_().

getBestMatchPerQuery()

std::vector<QueryMatchRef> getBestMatchPerQuery

(

ScoreTypeRef

score_ref

)

const

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

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::postProcessHits_().

getDataProcessingSoftwares()

const DataProcessingSoftwares& getDataProcessingSoftwares ( ) const

inline

Return the registered data processing software (immutable)

getDataProcessingSteps()

const DataProcessingSteps& getDataProcessingSteps ( ) const

inline

Return the registered data processing steps (immutable)

getDataQueries()

const DataQueries& getDataQueries ( ) const

inline

Return the registered data queries (immutable)

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

getDBSearchParams()

const DBSearchParams& getDBSearchParams ( ) const

inline

Return the registered database search parameters (immutable)

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_().

getMoleculeQueryMatches()

const MoleculeQueryMatches& getMoleculeQueryMatches ( ) const

inline

Return the registered molecule-query matches (immutable)

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

getParentMoleculeGroupings()

const ParentMoleculeGroupings& getParentMoleculeGroupings ( ) const

inline

Return the registered parent molecule groupings (immutable)

getParentMolecules()

const ParentMolecules& getParentMolecules ( ) const

inline

Return the registered parent molecules (immutable)

getQueryMatchGroups()

const QueryMatchGroups& getQueryMatchGroups ( ) const

inline

Return the registered groups of molecule-query matches (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)

isBetterScore()

static bool isBetterScore ( double  first, double  second, bool  higher_better  )

inlinestatic

Helper function to compare two scores.

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.

registerDataProcessingSoftware()

ProcessingSoftwareRef registerDataProcessingSoftware

(

const DataProcessingSoftware &

software

)

Register data processing software.

Returns

Reference to the registered software

Referenced by NucleicAcidSearchEngine::registerIDMetaData_().

registerDataProcessingStep() [1/2]

ProcessingStepRef registerDataProcessingStep

(

const DataProcessingStep &

step

)

Register a data processing step.

Returns

Reference to the registered processing step

Referenced by NucleicAcidSearchEngine::registerIDMetaData_().

registerDataProcessingStep() [2/2]

ProcessingStepRef registerDataProcessingStep	(	const DataProcessingStep &	step,
		SearchParamRef	search_ref
	)

Register a database search step with associated parameters.

Returns

Reference to the registered processing step

registerDataQuery()

DataQueryRef registerDataQuery

(

const DataQuery &

query

)

Register a data query (e.g. MS2 spectrum or feature)

Returns

Reference to the registered data query

Referenced by NucleicAcidSearchEngine::postProcessHits_().

registerDBSearchParam()

SearchParamRef registerDBSearchParam

(

const DBSearchParam &

param

)

Register database search parameters.

Returns

Reference to the registered search parameters

Referenced by NucleicAcidSearchEngine::registerIDMetaData_().

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 String &

file

)

Register an input file.

Returns

Reference to the registered file

Referenced by NucleicAcidSearchEngine::registerIDMetaData_().

registerMoleculeQueryMatch()

QueryMatchRef registerMoleculeQueryMatch

(

const MoleculeQueryMatch &

match

)

Register a molecule-query match (e.g. peptide-spectrum match)

Returns

Reference to the registered molecule-query match

Referenced by NucleicAcidSearchEngine::postProcessHits_().

registerParentMolecule()

ParentMoleculeRef registerParentMolecule

(

const ParentMolecule &

parent

)

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

Returns

Reference to the registered parent molecule

registerParentMoleculeGrouping()

void registerParentMoleculeGrouping

(

const ParentMoleculeGrouping &

grouping

)

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

registerQueryMatchGroup()

MatchGroupRef registerQueryMatchGroup

(

const QueryMatchGroup &

group

)

Register a group of associated molecule-query matches.

Returns

Reference to the registered group of matches

registerScoreType()

ScoreTypeRef registerScoreType

(

const ScoreType &

score

)

Register a score type.

Returns

Reference to the registered score type

Referenced by NucleicAcidSearchEngine::registerIDMetaData_().

removeFromSetIf_()

static void removeFromSetIf_ ( ContainerType &  container, PredicateType  predicate  )

inlinestaticprotected

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

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::registerIDMetaData_().

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

Member Data Documentation

current_step_ref_

ProcessingStepRef current_step_ref_

protected

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

data_queries_

DataQueries data_queries_

protected

data_query_lookup_

AddressLookup data_query_lookup_

protected

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

parent_molecule_groupings_

ParentMoleculeGroupings parent_molecule_groupings_

protected

parent_molecule_lookup_

AddressLookup parent_molecule_lookup_

protected

parent_molecules_

ParentMolecules parent_molecules_

protected

processing_softwares_

DataProcessingSoftwares processing_softwares_

protected

processing_steps_

DataProcessingSteps processing_steps_

protected

query_match_groups_

QueryMatchGroups query_match_groups_

protected

query_match_lookup_

AddressLookup query_match_lookup_

protected

query_matches_

MoleculeQueryMatches query_matches_

protected

score_types_

ScoreTypes score_types_

protected