A container for consensus elements. More...

#include <OpenMS/KERNEL/ConsensusMap.h>

Inheritance diagram for ConsensusMap:

Classes
struct	ColumnHeader
	Description of the columns in a consensus map. More...

Public Types
typedef std::vector< ConsensusFeature >	privvec

Type definitions
typedef std::vector< ConsensusFeature >	Base

typedef RangeManager< 2 >	RangeManagerType

typedef std::map< UInt64, ColumnHeader >	ColumnHeaders

typedef std::vector< ConsensusFeature >::iterator	Iterator
	Mutable iterator. More...

typedef std::vector< ConsensusFeature >::const_iterator	ConstIterator
	Non-mutable iterator. More...

typedef std::vector< ConsensusFeature >::reverse_iterator	ReverseIterator
	Mutable reverse iterator. More...

typedef std::vector< ConsensusFeature >::const_reverse_iterator	ConstReverseIterator
	Non-mutable reverse iterator. More...

Public Types inherited from RangeManager< 2 >
enum
	Dimension of the position range. More...

typedef DRange< D >	PositionRangeType
	Position range type. More...

typedef DPosition< D >	PositionType
	Position Type. More...

typedef DRange< 1 >	IntensityRangeType
	Intensity range type. More...

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< ConsensusMap >
typedef boost::unordered_map< UInt64, Size >	UniqueIdMap

Public Member Functions
	ConsensusMap ()
	Default constructor. More...

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

	~ConsensusMap () override
	Destructor. More...

	ConsensusMap (Base::size_type n)
	Creates a ConsensusMap with n elements. More...

ConsensusMap &	operator= (const ConsensusMap &source)
	Assignment operator. More...

ConsensusMap &	appendRows (const ConsensusMap &rhs)
	Add consensus map entries as new rows. More...

ConsensusMap &	appendColumns (const ConsensusMap &rhs)
	Add consensus map entries as new columns. More...

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

const ColumnHeaders &	getColumnHeaders () const
	Non-mutable access to the file descriptions. More...

ColumnHeaders &	getColumnHeaders ()
	Mutable access to the file descriptions. More...

void	setColumnHeaders (const ColumnHeaders &column_description)
	Mutable access to the file descriptions. More...

const String &	getExperimentType () const
	Non-mutable access to the experiment type. More...

void	setExperimentType (const String &experiment_type)
	Mutable access to the experiment type. More...

void	updateRanges () override
	Updates minimum and maximum position/intensity. More...

void	swap (ConsensusMap &from)
	Swaps the content of this map with the content of `from`. More...

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

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...

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 paths to the primary MS run (stored in ColumnHeaders) More...

void	getPrimaryMSRunPath (StringList &toFill) const
	returns the MS run path (stored in ColumnHeaders) More...

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

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

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

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

bool	isMapConsistent (Logger::LogStream *stream=nullptr) const
	checks if the given maps are unique and all FeatureHandles actually refer to a registered map More...

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

void	sortByRT ()
	Sorts the peaks to RT position. More...

void	sortByMZ ()
	Sorts the peaks to m/z position. More...

void	sortByPosition ()
	Lexicographically sorts the peaks by their position (First RT then m/z). More...

void	sortByQuality (bool reverse=false)
	Sorts the peaks according to ascending quality. More...

void	sortBySize ()
	Sorts with respect to the size (number of elements) More...

void	sortByMaps ()
	Sorts with respect to the sets of maps covered by the consensus features (lexicographically). More...

void	sortPeptideIdentificationsByMapIndex ()
	Sorts PeptideIdentifications of consensus features with respect to their map index. More...

Public Member Functions inherited from MetaInfoInterface
	MetaInfoInterface ()
	Constructor. More...

	MetaInfoInterface (const MetaInfoInterface &rhs)
	Copy constructor. More...

	~MetaInfoInterface ()
	Destructor. More...

MetaInfoInterface &	operator= (const MetaInfoInterface &rhs)
	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
	Returns the value corresponding to a string (or DataValue::EMPTY if not found) More...

const DataValue &	getMetaValue (UInt index) const
	Returns the value corresponding to an index (or 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	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 RangeManager< 2 >
	RangeManager ()
	Default constructor. More...

	RangeManager (const RangeManager &rhs)
	Copy constructor. More...

virtual	~RangeManager ()
	Destructor. More...

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

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

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

const PositionType &	getMin () const
	Returns the minimum position. More...

const PositionType &	getMax () const
	Returns the maximum position. More...

double	getMinInt () const
	Returns the minimum intensity. More...

double	getMaxInt () const
	Returns the maximum intensity. More...

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

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

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

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

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

virtual	~DocumentIdentifier ()
	destructor 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)
	Copy constructor - copies the unique id. More...

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

virtual	~UniqueIdInterface ()
	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< ConsensusMap >
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...

Protected Attributes
ColumnHeaders	column_description_
	Map from index to file description. More...

String	experiment_type_ = "label-free"
	type of experiment (label-free, labeled_MS1, labeled_MS2) More...

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

std::vector< PeptideIdentification >	unassigned_peptide_identifications_
	protein identifications More...

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

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

Protected Attributes inherited from RangeManager< 2 >
IntensityRangeType	int_range_
	Intensity range (1-dimensional) More...

PositionRangeType	pos_range_
	Position range (D-dimensional) 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< ConsensusMap >
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< 2 >
void	updateRanges_ (const PeakIteratorType &begin, const PeakIteratorType &end)
	Updates the range using data points in the iterator range. More...

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

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

Detailed Description

A container for consensus elements.

A ConsensusMap is a container holding 2-dimensional consensus elements (ConsensusFeature) which in turn represent analytes that have been quantified across multiple LC-MS/MS experiments. Each analyte in a ConsensusFeature is linked to its original LC-MS/MS run, the links are maintained by the ConsensusMap class. The map is implemented as a vector of elements of type ConsensusFeature.

To be consistent, all maps who are referenced by ConsensusFeature objects (through a unique id) need to be registered in this class.

Member Typedef Documentation

◆ Base

typedef std::vector<ConsensusFeature> Base

◆ ColumnHeaders

typedef std::map<UInt64, ColumnHeader> ColumnHeaders

◆ ConstIterator

typedef std::vector<ConsensusFeature>::const_iterator ConstIterator

Non-mutable iterator.

◆ ConstReverseIterator

typedef std::vector<ConsensusFeature>::const_reverse_iterator ConstReverseIterator

Non-mutable reverse iterator.

◆ Iterator

typedef std::vector<ConsensusFeature>::iterator Iterator

Mutable iterator.

◆ privvec

typedef std::vector<ConsensusFeature> privvec

◆ RangeManagerType

typedef RangeManager<2> RangeManagerType

◆ ReverseIterator

typedef std::vector<ConsensusFeature>::reverse_iterator ReverseIterator

Mutable reverse iterator.

Constructor & Destructor Documentation

◆ ConsensusMap() [1/3]

ConsensusMap ( )

Default constructor.

◆ ConsensusMap() [2/3]

ConsensusMap ( const ConsensusMap & source )

Copy constructor.

◆ ~ConsensusMap()

~ConsensusMap ( )

override

Destructor.

◆ ConsensusMap() [3/3]

ConsensusMap ( Base::size_type n )

explicit

Creates a ConsensusMap with n elements.

Member Function Documentation

◆ appendColumns()

ConsensusMap& appendColumns ( const ConsensusMap & rhs )

Add consensus map entries as new columns.

The number of columns (maximum map index) is the sum of both maps.

Parameters

rhs	The consensus map to be merged.

◆ appendRows()

ConsensusMap& appendRows ( const ConsensusMap & rhs )

Add consensus map entries as new rows.

Consensus elements are merged into one container, simply by appending.

The number of columns (maximum map index) stays the same.

Parameters

rhs	The consensus map to be merged.

◆ applyMemberFunction() [1/2]

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

inline

Applies a member function of Type to the container itself and all consensus features. 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):

ConsensusMap cm;
(...)
std::cout << cm.applyMemberFunction(&UniqueIdInterface::hasInvalidUniqueId) << std::endl;

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

◆ applyMemberFunction() [2/2]

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

inline

The "const" variant.

◆ 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.

◆ getColumnHeaders() [1/2]

const ColumnHeaders& getColumnHeaders ( ) const

Non-mutable access to the file descriptions.

◆ getColumnHeaders() [2/2]

ColumnHeaders& getColumnHeaders ( )

Mutable access to the file descriptions.

◆ getDataProcessing() [1/2]

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

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

◆ getDataProcessing() [2/2]

std::vector<DataProcessing>& getDataProcessing ( )

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

◆ getExperimentType()

const String& getExperimentType ( ) const

Non-mutable access to the experiment type.

◆ getPrimaryMSRunPath()

void getPrimaryMSRunPath ( StringList & toFill ) const

returns the MS run path (stored in ColumnHeaders)

◆ getProteinIdentifications() [1/2]

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

non-mutable access to the protein identifications

◆ getProteinIdentifications() [2/2]

std::vector<ProteinIdentification>& getProteinIdentifications ( )

mutable access to the protein identifications

◆ getUnassignedPeptideIdentifications() [1/2]

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

non-mutable access to the unassigned peptide identifications

◆ getUnassignedPeptideIdentifications() [2/2]

std::vector<PeptideIdentification>& getUnassignedPeptideIdentifications ( )

mutable access to the unassigned peptide identifications

◆ isMapConsistent()

bool isMapConsistent ( Logger::LogStream * stream = nullptr ) const

checks if the given maps are unique and all FeatureHandles actually refer to a registered map

To avoid inconsistencies in map IDs and make sure the maps are unique in terms of name+label

If you want some verbose output, provide a stream.

: alternative to this method we could check the features while they are added to the map directly, but

currently we can't because the interface is not designed for this (derived from std::vector, no encapsulation)
we should restrict the user to first fill the list of maps, before any datapoints can be inserted

◆ operator!=()

bool operator!= ( const ConsensusMap & rhs ) const

Equality operator.

◆ operator=()

ConsensusMap& operator= ( const ConsensusMap & source )

Assignment operator.

◆ operator==()

bool operator== ( const ConsensusMap & rhs ) const

Equality operator.

◆ setColumnHeaders()

void setColumnHeaders ( const ColumnHeaders & column_description )

Mutable access to the file descriptions.

◆ setDataProcessing()

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

sets the description of the applied data processing

◆ setExperimentType()

void setExperimentType ( const String & experiment_type )

Mutable access to the experiment type.

◆ setPrimaryMSRunPath()

void setPrimaryMSRunPath ( const StringList & s )

set the file paths to the primary MS run (stored in ColumnHeaders)

◆ 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.

◆ sortByMaps()

void sortByMaps ( )

Sorts with respect to the sets of maps covered by the consensus features (lexicographically).

◆ sortByMZ()

void sortByMZ ( )

Sorts the peaks to m/z position.

◆ sortByPosition()

void sortByPosition ( )

Lexicographically sorts the peaks by their position (First RT then m/z).

◆ sortByQuality()

void sortByQuality ( bool reverse = false )

Sorts the peaks according to ascending quality.

◆ sortByRT()

void sortByRT ( )

Sorts the peaks to RT position.

◆ sortBySize()

void sortBySize ( )

Sorts with respect to the size (number of elements)

◆ sortPeptideIdentificationsByMapIndex()

void sortPeptideIdentificationsByMapIndex ( )

Sorts PeptideIdentifications of consensus features with respect to their map index.

◆ swap()

void swap ( ConsensusMap & from )

Swaps the content of this map with the content of from.

◆ updateRanges()

void updateRanges ( )

overridevirtual

Updates minimum and maximum position/intensity.

This method is usually implemented by calling clearRanges() and updateRanges_().

Implements RangeManager< 2 >.

Member Data Documentation

◆ column_description_

ColumnHeaders column_description_

protected

Map from index to file description.

◆ data_processing_

std::vector<DataProcessing> data_processing_

protected

applied data processing

◆ experiment_type_

String experiment_type_ = "label-free"

protected

type of experiment (label-free, labeled_MS1, labeled_MS2)

◆ protein_identifications_

std::vector<ProteinIdentification> protein_identifications_

protected

protein identifications

◆ unassigned_peptide_identifications_

std::vector<PeptideIdentification> unassigned_peptide_identifications_

protected

protein identifications

Classes

Public Types

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Base

◆ ColumnHeaders

◆ ConstIterator

◆ ConstReverseIterator

◆ Iterator

◆ privvec

◆ RangeManagerType

◆ ReverseIterator

Constructor & Destructor Documentation

◆ ConsensusMap() [1/3]

◆ ConsensusMap() [2/3]

◆ ~ConsensusMap()

◆ ConsensusMap() [3/3]

Member Function Documentation

◆ appendColumns()

◆ appendRows()

◆ applyMemberFunction() [1/2]

◆ applyMemberFunction() [2/2]

◆ clear()

◆ getColumnHeaders() [1/2]

◆ getColumnHeaders() [2/2]

◆ getDataProcessing() [1/2]

◆ getDataProcessing() [2/2]

◆ getExperimentType()

◆ getPrimaryMSRunPath()

◆ getProteinIdentifications() [1/2]

◆ getProteinIdentifications() [2/2]

◆ getUnassignedPeptideIdentifications() [1/2]

◆ getUnassignedPeptideIdentifications() [2/2]

◆ isMapConsistent()

◆ operator!=()

◆ operator=()

◆ operator==()

◆ setColumnHeaders()

◆ setDataProcessing()

◆ setExperimentType()

◆ setPrimaryMSRunPath()

◆ setProteinIdentifications()

◆ setUnassignedPeptideIdentifications()

◆ sortByIntensity()

◆ sortByMaps()

◆ sortByMZ()

◆ sortByPosition()

◆ sortByQuality()

◆ sortByRT()

◆ sortBySize()

◆ sortPeptideIdentificationsByMapIndex()

◆ swap()

◆ updateRanges()

Member Data Documentation

◆ column_description_

◆ data_processing_

◆ experiment_type_

◆ protein_identifications_

◆ unassigned_peptide_identifications_