A container for features. More...

#include <OpenMS/KERNEL/FeatureMap.h>

Inheritance diagram for FeatureMap:

Collaboration diagram for FeatureMap:

Public Types
Type definitions
typedef std::vector< Feature >	Base

typedef RangeManagerContainer< RangeRT, RangeMZ, RangeIntensity >	RangeManagerContainerType

typedef RangeManager< RangeRT, RangeMZ, RangeIntensity >	RangeManagerType

typedef Base::iterator	Iterator

typedef Base::const_iterator	ConstIterator

typedef Base::reverse_iterator	ReverseIterator

typedef Base::const_reverse_iterator	ConstReverseIterator

Public Types inherited from UniqueIdInterface
enum	{ INVALID = 0 }
	This is the invalid unique id (cast it to a UInt64 if you like) More...

Public Types inherited from UniqueIdIndexer< FeatureMap >
typedef std::unordered_map< UInt64, Size >	UniqueIdMap

Public Member Functions
const std::vector< DataProcessing > &	getDataProcessing () const
	returns a const reference to the description of the applied data processing More...

std::vector< DataProcessing > &	getDataProcessing ()
	returns a mutable reference to the description of the applied data processing More...

void	setDataProcessing (const std::vector< DataProcessing > &processing_method)
	sets the description of the applied data processing More...

void	setPrimaryMSRunPath (const StringList &s)
	set the file path to the primary MS run (usually the mzML file obtained after data conversion from raw files) More...

void	setPrimaryMSRunPath (const StringList &s, MSExperiment &e)

void	getPrimaryMSRunPath (StringList &toFill) const
	get the file path to the first MS run More...

void	clear (bool clear_meta_data=true)
	Clears all data and meta data. More...

template<typename Type >
Size	applyMemberFunction (Size(Type::*member_function)())
	Applies a member function of Type to the container itself and all features (including subordinates). The returned values are accumulated. More...

template<typename Type >
Size	applyMemberFunction (Size(Type::*member_function)() const) const
	The "const" variant. More...

AnnotationStatistics	getAnnotationStatistics () const

Constructors and Destructor
	FeatureMap ()
	Default constructor. More...

	FeatureMap (const FeatureMap &source)
	Copy constructor. More...

	FeatureMap (FeatureMap &&source)
	Move constructor. More...

	~FeatureMap () override
	Destructor. More...

FeatureMap &	operator= (const FeatureMap &rhs)
	Assignment operator. More...

bool	operator== (const FeatureMap &rhs) const
	Equality operator. More...

bool	operator!= (const FeatureMap &rhs) const
	Equality operator. More...

FeatureMap	operator+ (const FeatureMap &rhs) const
	Joins two feature maps. More...

FeatureMap &	operator+= (const FeatureMap &rhs)
	Add one feature map to another. More...

Sorting.
These simplified sorting methods are supported in addition to the standard sorting methods of std::vector.
void	sortByIntensity (bool reverse=false)
	Sorts the peaks according to ascending intensity. More...

void	sortByPosition ()
	Sort features by position. Lexicographical comparison (first RT then m/z) is done. More...

void	sortByRT ()
	Sort features by RT position. More...

void	sortByMZ ()
	Sort features by m/z position. More...

void	sortByOverallQuality (bool reverse=false)
	Sort features by ascending overall quality. More...

void	updateRanges () override

void	swapFeaturesOnly (FeatureMap &from)
	Swaps the feature content (plus its range information) of this map with the content of `from`. More...

void	swap (FeatureMap &from)

Functions for dealing with identifications in legacy format
non-mutable access to the protein identifications
const std::vector< ProteinIdentification > &	getProteinIdentifications () const

std::vector< ProteinIdentification > &	getProteinIdentifications ()
	mutable access to the protein identifications More...

void	setProteinIdentifications (const std::vector< ProteinIdentification > &protein_identifications)
	sets the protein identifications More...

const std::vector< PeptideIdentification > &	getUnassignedPeptideIdentifications () const
	non-mutable access to the unassigned peptide identifications More...

std::vector< PeptideIdentification > &	getUnassignedPeptideIdentifications ()
	mutable access to the unassigned peptide identifications More...

void	setUnassignedPeptideIdentifications (const std::vector< PeptideIdentification > &unassigned_peptide_identifications)
	sets the unassigned peptide identifications More...

Functions for dealing with identifications in new format
std::set< IdentificationData::ObservationMatchRef >	getUnassignedIDMatches () const
	Return observation matches (e.g. PSMs) from the identification data that are not assigned to any feature in the map. More...

const IdentificationData &	getIdentificationData () const
	Immutable access to the contained identification data. More...

IdentificationData &	getIdentificationData ()
	Mutable access to the contained identification data. 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...

Public Member Functions inherited from RangeManagerContainer< RangeRT, RangeMZ, RangeIntensity >
const RangeManager< RangeBases... > &	getRange () const
	get range of current data (call updateRanges() before to ensure the range is accurate) More...

RangeManager< RangeBases... > &	getRange ()
	get mutable range, provided for efficiency reasons (avoid updateRanges(), if only minor changes were made) More...

Public Member Functions inherited from RangeManager< RangeBases... >
bool	operator== (const RangeManager &rhs) const

bool	assignUnsafe (const RangeManager< RangeBasesOther... > &rhs)

void	assign (const RangeManager< RangeBasesOther... > &rhs)

bool	extendUnsafe (const RangeManager< RangeBasesOther... > &rhs)

void	extend (const RangeManager< RangeBasesOther... > &rhs)

void	scaleBy (const double factor)
	calls RangeBase::scale() for each dimension More...

RangeBase &	getRangeForDim (MSDim dim)
	obtain a range dimension at runtime using `dim` More...

HasRangeType	hasRange () const
	is any/some/all dimension in this range populated? More...

bool	containsAll (const RangeManager< RangeBasesOther... > &rhs) const

void	clearRanges ()
	Resets all ranges. More...

void	printRange (std::ostream &out) const
	print each dimension (base classes) to a stream More...

Public Member Functions inherited from DocumentIdentifier
	DocumentIdentifier ()
	Default constructor. More...

	DocumentIdentifier (const DocumentIdentifier &)=default
	Copy constructor. More...

	DocumentIdentifier (DocumentIdentifier &&)=default
	Move constructor. More...

virtual	~DocumentIdentifier ()
	Destructor. More...

DocumentIdentifier &	operator= (const DocumentIdentifier &)=default
	Assignment operator. More...

DocumentIdentifier &	operator= (DocumentIdentifier &&) &=default
	Move assignment operator. More...

bool	operator== (const DocumentIdentifier &rhs) const
	Equality operator. More...

void	setIdentifier (const String &id)
	set document identifier (e.g. an LSID) More...

const String &	getIdentifier () const
	retrieve document identifier (e.g. an LSID) More...

void	swap (DocumentIdentifier &from)
	exchange content with `from` More...

void	setLoadedFilePath (const String &file_name)
	set the file_name_ according to absolute path of the file loaded from preferably done whilst loading More...

const String &	getLoadedFilePath () const
	get the file_name_ which is the absolute path to the file loaded from More...

void	setLoadedFileType (const String &file_name)
	set the file_type according to the type of the file loaded from (see FileHandler::Type) preferably done whilst loading More...

const FileTypes::Type &	getLoadedFileType () const
	get the file_type (e.g. featureXML, consensusXML, mzData, mzXML, mzML, ...) of the file loaded from More...

Public Member Functions inherited from UniqueIdInterface
	UniqueIdInterface ()
	Default constructor - the unique id will be invalid More...

	UniqueIdInterface (const UniqueIdInterface &rhs)=default
	Copy constructor - copies the unique id. More...

	UniqueIdInterface (UniqueIdInterface &&rhs)=default
	Move constructor. More...

UniqueIdInterface &	operator= (UniqueIdInterface const &rhs)=default
	Assignment operator - copies the unique id. More...

UniqueIdInterface &	operator= (UniqueIdInterface &&) &=default
	Move Assignment operator - copies the unique id. More...

virtual	~UniqueIdInterface ()=default
	Destructor. More...

bool	operator== (UniqueIdInterface const &rhs) const
	Equality comparison operator - the unique ids must be equal (!) More...

UInt64	getUniqueId () const
	Non-mutable access to unique id - returns the unique id. More...

Size	clearUniqueId ()
	Clear the unique id. The new unique id will be invalid. Returns 1 if the unique id was changed, 0 otherwise. More...

void	swap (UniqueIdInterface &from)

Size	hasValidUniqueId () const
	Returns whether the unique id is valid. Returns 1 if the unique id is valid, 0 otherwise. More...

Size	hasInvalidUniqueId () const
	Returns whether the unique id is invalid. Returns 1 if the unique id is invalid, 0 otherwise. More...

Size	setUniqueId ()
	Assigns a new, valid unique id. Always returns 1. More...

Size	ensureUniqueId ()
	Assigns a valid unique id, but only if the present one is invalid. Returns 1 if the unique id was changed, 0 otherwise. More...

void	setUniqueId (UInt64 rhs)
	Assigns the given unique id. More...

void	setUniqueId (const String &rhs)
	Mutable access to unique id. More...

Public Member Functions inherited from UniqueIdIndexer< FeatureMap >
Size	uniqueIdToIndex (UInt64 unique_id) const
	Returns the index of the feature with the given unique id, or Size(-1) if none exists in this random access container. More...

void	updateUniqueIdToIndex () const
	Updates the hash map from unique id to index. More...

Size	resolveUniqueIdConflicts ()
	Assign new UID's to doubly occurring UID's. More...

void	swap (UniqueIdIndexer &rhs)
	Swap. More...

Public Member Functions inherited from MapUtilities< FeatureMap >
void	applyFunctionOnPeptideHits (T &&f, bool include_unassigned=true)
	applies a function on all PeptideHits or only assigned ones More...

void	applyFunctionOnPeptideHits (T &&f, bool include_unassigned=true) const
	applies a const function on all PeptideHits or only assigned ones More...

void	applyFunctionOnPeptideIDs (T &&f, bool include_unassigned=true)
	applies a function on all PeptideIDs or only assigned ones More...

void	applyFunctionOnPeptideIDs (T &&f, bool include_unassigned=true) const
	applies a const function on all PeptideIDs or only assigned ones More...

Protected Attributes
std::vector< ProteinIdentification >	protein_identifications_
	protein identifications More...

std::vector< PeptideIdentification >	unassigned_peptide_identifications_
	peptide identifications not matched to a specific feature More...

std::vector< DataProcessing >	data_processing_
	applied data processing More...

IdentificationData	id_data_
	general identification results (peptides/proteins, RNA, compounds) More...

Protected Attributes inherited from MetaInfoInterface
MetaInfo *	meta_
	Pointer to the MetaInfo object (0 by default) More...

Protected Attributes inherited from DocumentIdentifier
String	id_
	the ID (e.g. LSID) More...

String	file_path_
	the path to the loaded file More...

FileTypes::Type	file_type_
	the type of the loaded file More...

Protected Attributes inherited from UniqueIdInterface
UInt64	unique_id_
	the unique id More...

Protected Attributes inherited from UniqueIdIndexer< FeatureMap >
UniqueIdMap	uniqueid_to_index_
	hash map from unique id to index of features More...

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

Static Public Member Functions inherited from UniqueIdInterface
static bool	isValid (UInt64 unique_id)
	Returns true if the unique_id is valid, false otherwise. More...

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

Protected Member Functions inherited from RangeManager< RangeBases... >
void	for_each_base_ (Visitor &&visitor)
	use fold expression to iterate over all RangeBases of RangeManager and apply a lambda (Visitor) for each one More...

void	for_each_base_ (Visitor &&visitor) const
	.. and a const version More...

Protected Member Functions inherited from UniqueIdIndexer< FeatureMap >
const FeatureMap &	getBase_ () const
	A little helper to get access to the base (!) class RandomAccessContainer. More...

FeatureMap &	getBase_ ()
	A little helper to get access to the base (!) class RandomAccessContainer. More...

Static Protected Member Functions inherited from RangeManager< RangeBases... >
static void	static_for_each_base_ (Visitor &&visitor)
	use fold expression to iterate over all RangeBases of RangeManager and apply a lambda (Visitor) for each one (for static members) More...

Detailed Description

A container for features.

A feature map is a container holding features, which represent chemical entities (peptides, proteins, small molecules etc.) found in an LC-MS/MS experiment.

Maps are implemented as vectors of features and have basically the same interface as an STL vector has (model of Random Access Container and Back Insertion Sequence).

Feature maps are typically created from peak data of 2D runs through the FeatureFinder.

Member Typedef Documentation

◆ Base

typedef std::vector<Feature> Base

◆ ConstIterator

typedef Base::const_iterator ConstIterator

◆ ConstReverseIterator

typedef Base::const_reverse_iterator ConstReverseIterator

◆ Iterator

typedef Base::iterator Iterator

◆ RangeManagerContainerType

typedef RangeManagerContainer<RangeRT, RangeMZ, RangeIntensity> RangeManagerContainerType

◆ RangeManagerType

typedef RangeManager<RangeRT, RangeMZ, RangeIntensity> RangeManagerType

◆ ReverseIterator

typedef Base::reverse_iterator ReverseIterator

Constructor & Destructor Documentation

◆ FeatureMap() [1/3]

FeatureMap ( )

Default constructor.

◆ FeatureMap() [2/3]

FeatureMap ( const FeatureMap & source )

Copy constructor.

◆ FeatureMap() [3/3]

FeatureMap ( FeatureMap && source )

Move constructor.

◆ ~FeatureMap()

~FeatureMap ( )

override

Destructor.

Member Function Documentation

◆ applyMemberFunction() [1/2]

Size applyMemberFunction ( Size(Type::*)() const member_function ) const

inline

The "const" variant.

◆ applyMemberFunction() [2/2]

Size applyMemberFunction ( Size(Type::*)() member_function )

inline

Applies a member function of Type to the container itself and all features (including subordinates). The returned values are accumulated.

Example: The following will print the number of features with invalid unique ids (plus 1 if the container has an invalid UID as well):

FeatureMap fm;
(...)
std::cout << fm.applyMemberFunction(&UniqueIdInterface::hasInvalidUniqueId) << std::endl;

See e.g. UniqueIdInterface for what else can be done this way.

◆ clear()

void clear ( bool clear_meta_data = true )

Clears all data and meta data.

Parameters

clear_meta_data If true, all meta data is cleared in addition to the data.

◆ getAnnotationStatistics()

AnnotationStatistics getAnnotationStatistics ( ) const

◆ getDataProcessing() [1/2]

std::vector<DataProcessing>& getDataProcessing ( )

returns a mutable reference to the description of the applied data processing

◆ getDataProcessing() [2/2]

const std::vector<DataProcessing>& getDataProcessing ( ) const

returns a const reference to the description of the applied data processing

◆ getIdentificationData() [1/2]

IdentificationData& getIdentificationData ( )

Mutable access to the contained identification data.

◆ getIdentificationData() [2/2]

const IdentificationData& getIdentificationData ( ) const

Immutable access to the contained identification data.

◆ getPrimaryMSRunPath()

void getPrimaryMSRunPath ( StringList & toFill ) const

get the file path to the first MS run

◆ getProteinIdentifications() [1/2]

std::vector<ProteinIdentification>& getProteinIdentifications ( )

mutable access to the protein identifications

◆ getProteinIdentifications() [2/2]

const std::vector<ProteinIdentification>& getProteinIdentifications ( ) const

Referenced by MetaDataBrowser::add().

◆ getUnassignedIDMatches()

std::set<IdentificationData::ObservationMatchRef> getUnassignedIDMatches ( ) const

Return observation matches (e.g. PSMs) from the identification data that are not assigned to any feature in the map.

Only top-level features are considered, i.e. no subordinates.

See also: BaseFeature::getIDMatches()

◆ getUnassignedPeptideIdentifications() [1/2]

std::vector<PeptideIdentification>& getUnassignedPeptideIdentifications ( )

mutable access to the unassigned peptide identifications

◆ getUnassignedPeptideIdentifications() [2/2]

const std::vector<PeptideIdentification>& getUnassignedPeptideIdentifications ( ) const

non-mutable access to the unassigned peptide identifications

Referenced by MetaDataBrowser::add().

◆ operator!=()

bool operator!= ( const FeatureMap & rhs ) const

Equality operator.

◆ operator+()

FeatureMap operator+ ( const FeatureMap & rhs ) const

Joins two feature maps.

Features are merged into one container (see operator+= for details).

◆ operator+=()

FeatureMap& operator+= ( const FeatureMap & rhs )

Add one feature map to another.

Features are merged into one container, simply by appending. UnassignedPeptides and ProteinIdentifications are appended. Information on DocumentIdentifier, UniqueIdInterface (of container only) are reset to default.

For conflicting UID's, new UID's will be assigned.

Parameters

rhs	The feature to add to this one.

◆ operator=()

FeatureMap& operator= ( const FeatureMap & rhs )

Assignment operator.

◆ operator==()

bool operator== ( const FeatureMap & rhs ) const

Equality operator.

◆ setDataProcessing()

void setDataProcessing ( const std::vector< DataProcessing > & processing_method )

sets the description of the applied data processing

◆ setPrimaryMSRunPath() [1/2]

void setPrimaryMSRunPath ( const StringList & s )

set the file path to the primary MS run (usually the mzML file obtained after data conversion from raw files)

◆ setPrimaryMSRunPath() [2/2]

void setPrimaryMSRunPath	(	const StringList &	s,
		MSExperiment &	e
	)

set the file path to the primary MS run using the mzML annotated in the MSExperiment

Parameters

e.	If it doesn't exist, fallback to
s.

◆ setProteinIdentifications()

void setProteinIdentifications ( const std::vector< ProteinIdentification > & protein_identifications )

sets the protein identifications

◆ setUnassignedPeptideIdentifications()

void setUnassignedPeptideIdentifications ( const std::vector< PeptideIdentification > & unassigned_peptide_identifications )

sets the unassigned peptide identifications

◆ sortByIntensity()

void sortByIntensity ( bool reverse = false )

Sorts the peaks according to ascending intensity.

◆ sortByMZ()

void sortByMZ ( )

Sort features by m/z position.

◆ sortByOverallQuality()

void sortByOverallQuality ( bool reverse = false )

Sort features by ascending overall quality.

◆ sortByPosition()

void sortByPosition ( )

Sort features by position. Lexicographical comparison (first RT then m/z) is done.

◆ sortByRT()

void sortByRT ( )

Sort features by RT position.

◆ swap()

void swap ( FeatureMap & from )

◆ swapFeaturesOnly()

void swapFeaturesOnly ( FeatureMap & from )

Swaps the feature content (plus its range information) of this map with the content of from.

◆ updateRanges()

void updateRanges ( )

overridevirtual

implement this function to reflect the underlying data of the derived class (e.g. an MSSpectrum) Usually, call clearRanges() internally and then populate the dimensions.

Implements RangeManagerContainer< RangeRT, RangeMZ, RangeIntensity >.

Member Data Documentation

◆ data_processing_

std::vector<DataProcessing> data_processing_

protected

applied data processing

◆ id_data_

IdentificationData id_data_

protected

general identification results (peptides/proteins, RNA, compounds)

◆ protein_identifications_

std::vector<ProteinIdentification> protein_identifications_

protected

protein identifications

◆ unassigned_peptide_identifications_

std::vector<PeptideIdentification> unassigned_peptide_identifications_

protected

peptide identifications not matched to a specific feature

Public Types

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Base

◆ ConstIterator

◆ ConstReverseIterator

◆ Iterator

◆ RangeManagerContainerType

◆ RangeManagerType

◆ ReverseIterator

Constructor & Destructor Documentation

◆ FeatureMap() [1/3]

◆ FeatureMap() [2/3]

◆ FeatureMap() [3/3]

◆ ~FeatureMap()

Member Function Documentation

◆ applyMemberFunction() [1/2]

◆ applyMemberFunction() [2/2]

◆ clear()

◆ getAnnotationStatistics()

◆ getDataProcessing() [1/2]

◆ getDataProcessing() [2/2]

◆ getIdentificationData() [1/2]

◆ getIdentificationData() [2/2]

◆ getPrimaryMSRunPath()

◆ getProteinIdentifications() [1/2]

◆ getProteinIdentifications() [2/2]

◆ getUnassignedIDMatches()

◆ getUnassignedPeptideIdentifications() [1/2]

◆ getUnassignedPeptideIdentifications() [2/2]

◆ operator!=()

◆ operator+()

◆ operator+=()

◆ operator=()

◆ operator==()

◆ setDataProcessing()

◆ setPrimaryMSRunPath() [1/2]

◆ setPrimaryMSRunPath() [2/2]

◆ setProteinIdentifications()

◆ setUnassignedPeptideIdentifications()

◆ sortByIntensity()

◆ sortByMZ()

◆ sortByOverallQuality()

◆ sortByPosition()

◆ sortByRT()

◆ swap()

◆ swapFeaturesOnly()

◆ updateRanges()

Member Data Documentation

◆ data_processing_

◆ id_data_

◆ protein_identifications_

◆ unassigned_peptide_identifications_