ConsensusMap Class Reference

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
enum class	SplitMeta { DISCARD , COPY_ALL , COPY_FIRST }
Public Types inherited from MetaInfoInterface
using	MetaInfoConstIterator = MetaInfo::const_iterator
	Const iterator type for iterating over meta info entries.
Public Types inherited from RangeManagerContainer< RangeRT, RangeMZ, RangeIntensity >
using	ThisRangeType = typename RangeManager< RangeBases... >::ThisRangeType
Public Types inherited from RangeManager< RangeBases... >
using	ThisRangeType = RangeManager< RangeBases... >
Public Types inherited from ExposedVector< ConsensusFeature >
using	VecMember = std::vector< ConsensusFeature >
using	value_type = typename VecMember::value_type
using	iterator = typename VecMember::iterator
using	const_iterator = typename VecMember::const_iterator
using	reverse_iterator = typename VecMember::reverse_iterator
using	const_reverse_iterator = typename VecMember::const_reverse_iterator
using	size_type = typename VecMember::size_type
using	pointer = typename VecMember::pointer
using	reference = typename VecMember::reference
using	const_reference = typename VecMember::const_reference
using	difference_type = typename VecMember::difference_type
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 std::unordered_map< UInt64, Size >	UniqueIdMap

Public Member Functions
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.
void	sortByRT ()
	Sorts the peaks to RT position.
void	sortByMZ ()
	Sorts the peaks to m/z position.
void	sortByPosition ()
	Lexicographically sorts the peaks by their position (First RT then m/z).
void	sortByQuality (bool reverse=false)
	Sorts the peaks according to ascending quality.
void	sortBySize ()
	Sorts with respect to the size (number of elements)
void	sortByMaps ()
	Sorts with respect to the sets of maps covered by the consensus features (lexicographically).
void	sortPeptideIdentificationsByMapIndex ()
	Sorts PeptideIdentifications of consensus features with respect to their map index.
void	updateRanges () override
void	swap (ConsensusMap &from)
	Swaps the content of this map with the content of from.
const std::vector< ProteinIdentification > &	getProteinIdentifications () const
	non-mutable access to the protein identifications
std::vector< ProteinIdentification > &	getProteinIdentifications ()
	mutable access to the protein identifications
void	setProteinIdentifications (const std::vector< ProteinIdentification > &protein_identifications)
	sets the protein identifications
void	setProteinIdentifications (std::vector< ProteinIdentification > &&protein_identifications)
	sets the protein identifications by moving
const ProteinIdentification *	findProteinIdentification (const std::string &identifier) const
	finds a protein identification by its identifier (returns nullptr if not found)
ProteinIdentification *	findProteinIdentification (const std::string &identifier)
	finds a protein identification by its identifier (returns nullptr if not found)
const PeptideIdentificationList &	getUnassignedPeptideIdentifications () const
	non-mutable access to the unassigned peptide identifications
PeptideIdentificationList &	getUnassignedPeptideIdentifications ()
	mutable access to the unassigned peptide identifications
void	setUnassignedPeptideIdentifications (const PeptideIdentificationList &unassigned_peptide_identifications)
	sets the unassigned peptide identifications
const std::vector< DataProcessing > &	getDataProcessing () const
	returns a const reference to the description of the applied data processing
std::vector< DataProcessing > &	getDataProcessing ()
	returns a mutable reference to the description of the applied data processing
void	setDataProcessing (const std::vector< DataProcessing > &processing_method)
	sets the description of the applied data processing
void	setPrimaryMSRunPath (const StringList &s)
	set the file paths to the primary MS run (stored in ColumnHeaders)
void	setPrimaryMSRunPath (const StringList &s, MSExperiment &e)
void	getPrimaryMSRunPath (StringList &toFill) const
	returns the MS run path (stored in ColumnHeaders)
bool	operator== (const ConsensusMap &rhs) const
	Equality operator.
bool	operator!= (const ConsensusMap &rhs) const
	Equality operator.
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.
template<typename Type >
Size	applyMemberFunction (Size(Type::*member_function)() const) const
	The "const" variant.
bool	isMapConsistent (Logger::LogStream *stream=nullptr) const
	checks if the given maps are unique and all FeatureHandles actually refer to a registered map
std::vector< FeatureMap >	split (SplitMeta mode=SplitMeta::DISCARD) const
	splits ConsensusMap into its original FeatureMaps
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.
const IdentificationData &	getIdentificationData () const
	Immutable access to the contained identification data.
IdentificationData &	getIdentificationData ()
	Mutable access to the contained identification data.
Public Member Functions inherited from MetaInfoInterface
	MetaInfoInterface ()=default
	Constructor.
	MetaInfoInterface (const MetaInfoInterface &rhs)
	Copy constructor.
	MetaInfoInterface (MetaInfoInterface &&) noexcept
	Move constructor.
	~MetaInfoInterface ()
	Destructor.
MetaInfoInterface &	operator= (const MetaInfoInterface &rhs)
	Assignment operator.
MetaInfoInterface &	operator= (MetaInfoInterface &&) noexcept
	Move assignment operator.
void	swap (MetaInfoInterface &rhs)
	Swap contents.
bool	operator== (const MetaInfoInterface &rhs) const
	Equality operator.
bool	operator!= (const MetaInfoInterface &rhs) const
	Equality operator.
const DataValue &	getMetaValue (const std::string &name) const
	Returns the value corresponding to a string, or DataValue::EMPTY if not found.
DataValue	getMetaValue (const std::string &name, const DataValue &default_value) const
	Returns the value corresponding to a string, or a default value (e.g.: DataValue::EMPTY) if not found
const DataValue &	getMetaValue (UInt index) const
	Returns the value corresponding to the index, or DataValue::EMPTY if not found.
DataValue	getMetaValue (UInt index, const DataValue &default_value) const
	Returns the value corresponding to the index, or a default value (e.g.: DataValue::EMPTY) if not found
bool	metaValueExists (const std::string &name) const
	Returns whether an entry with the given name exists.
bool	metaValueExists (UInt index) const
	Returns whether an entry with the given index exists.
void	setMetaValue (const std::string &name, const DataValue &value)
	Sets the DataValue corresponding to a name.
void	setMetaValue (UInt index, const DataValue &value)
	Sets the DataValue corresponding to an index.
void	removeMetaValue (const std::string &name)
	Removes the DataValue corresponding to name if it exists.
void	removeMetaValue (UInt index)
	Removes the DataValue corresponding to index if it exists.
void	addMetaValues (const MetaInfoInterface &from)
void	getKeys (std::vector< std::string > &keys) const
	Fills the given vector with a list of all keys for which a value is set.
void	getKeys (std::vector< UInt > &keys) const
	Fills the given vector with a list of all keys for which a value is set.
bool	isMetaEmpty () const
	Returns if the MetaInfo is empty.
void	clearMetaInfo ()
	Removes all meta values.
MetaInfoConstIterator	metaBegin () const
	Returns a const iterator to the beginning of the meta info entries.
MetaInfoConstIterator	metaEnd () const
	Returns a const iterator to the end of the meta info entries.
Size	metaSize () const
	Returns the number of meta info entries.
Public Member Functions inherited from RangeManagerContainer< RangeRT, RangeMZ, RangeIntensity >
virtual	~RangeManagerContainer ()=default
	D'tor.
const ThisRangeType &	getRange () const
	get range of current data (call updateRanges() before to ensure the range is accurate)
ThisRangeType &	getRange ()
	get mutable range, provided for efficiency reasons (avoid updateRanges(), if only minor changes were made)
Public Member Functions inherited from RangeManager< RangeBases... >
bool	operator== (const RangeManager &rhs) const
bool	operator!= (const RangeManager &rhs) const
bool	assignUnsafe (const RangeManager< RangeBasesOther... > &rhs)
auto &	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
void	minSpanIfSingular (const double min_span)
	If any dimension is a single point, e.g. min==max, then extend this dimension by min_span / 2 on either side.
bool	pushIntoUnsafe (const RangeManager< RangeBasesOther... > &rhs)
void	pushInto (const RangeManager< RangeBasesOther... > &sandbox)
bool	clampToUnsafe (const RangeManager< RangeBasesOther... > &rhs)
void	clampTo (const RangeManager< RangeBasesOther... > &rhs)
const RangeBase &	getRangeForDim (MSDim dim) const
	obtain a range dimension at runtime using dim
RangeBase &	getRangeForDim (MSDim dim)
	obtain a range dimension at runtime using dim
HasRangeType	hasRange () const
	is any/some/all dimension in this range populated?
bool	containsAll (const RangeManager< RangeBasesOther... > &rhs) const
void	clearRanges ()
	Resets all ranges.
ThisRangeType &	clear (const DIM_UNIT range)
void	printRange (std::ostream &out) const
	print each dimension (base classes) to a stream
Public Member Functions inherited from DocumentIdentifier
	DocumentIdentifier ()
	Default constructor.
	DocumentIdentifier (const DocumentIdentifier &)=default
	Copy constructor.
	DocumentIdentifier (DocumentIdentifier &&)=default
	Move constructor.
virtual	~DocumentIdentifier ()
	Destructor.
DocumentIdentifier &	operator= (const DocumentIdentifier &)=default
	Assignment operator.
DocumentIdentifier &	operator= (DocumentIdentifier &&) &=default
	Move assignment operator.
bool	operator== (const DocumentIdentifier &rhs) const
	Equality operator.
void	setIdentifier (const std::string &id)
	set document identifier (e.g. an LSID)
const std::string &	getIdentifier () const
	retrieve document identifier (e.g. an LSID)
void	swap (DocumentIdentifier &from)
	exchange content with from
void	setLoadedFilePath (const std::string &file_name)
	set the file_name_ according to absolute path of the file loaded from preferably done whilst loading
const std::string &	getLoadedFilePath () const
	get the file_name_ which is the absolute path to the file loaded from
void	setLoadedFileType (const std::string &file_name)
	set the file_type according to the type of the file loaded from (see FileHandler::Type) preferably done whilst loading
const FileTypes::Type &	getLoadedFileType () const
	get the file_type (e.g. featureXML, consensusXML, mzData, mzXML, mzML, ...) of the file loaded from
Public Member Functions inherited from ExposedVector< ConsensusFeature >
	ExposedVector ()=default
	ExposedVector (const size_t n)
	ExposedVector (const size_t n, const ConsensusFeature &val)
	ExposedVector (Iter begin, Iter end)
	ExposedVector (const ExposedVector &rhs)=default
	Copy C'tor.
	ExposedVector (ExposedVector &&rhs) noexcept=default
	Move C'tor.
ExposedVector &	operator= (const ExposedVector &rhs)=default
	Assignment.
ExposedVector &	operator= (ExposedVector &&rhs) noexcept=default
	Move Assignment.
iterator	begin () noexcept
const_iterator	begin () const noexcept
iterator	end () noexcept
const_iterator	end () const noexcept
const_iterator	cbegin () const noexcept
const_iterator	cend () const noexcept
size_t	size () const noexcept
void	resize (const size_t new_size)
void	reserve (const size_t new_size)
bool	empty () const noexcept
ConsensusFeature &	operator[] (size_t i) noexcept
const ConsensusFeature &	operator[] (size_t i) const noexcept
ConsensusFeature &	at (size_t i)
const ConsensusFeature &	at (size_t i) const
ConsensusFeature &	back () noexcept
const ConsensusFeature &	back () const noexcept
void	push_back (const ConsensusFeature &f)
void	push_back (ConsensusFeature &&f)
decltype(auto)	emplace_back (Args &&... args)
void	pop_back () noexcept
iterator	erase (const_iterator where) noexcept
iterator	erase (const_iterator from, const_iterator to) noexcept
iterator	insert (const_iterator where, T from, T to)
iterator	insert (const_iterator pos, const ConsensusFeature &value)
	Insert single element.
iterator	insert (const_iterator pos, ConsensusFeature &&value)
	Insert single element (move)
iterator	insert (const_iterator pos, size_type count, const ConsensusFeature &value)
	Insert n copies of value.
iterator	insert (const_iterator pos, std::initializer_list< ConsensusFeature > init)
	Insert from initializer list.
void	clear () noexcept
	Clear all elements.
reverse_iterator	rbegin () noexcept
	Get reverse iterator to beginning.
const_reverse_iterator	rbegin () const noexcept
	Get const reverse iterator to beginning.
reverse_iterator	rend () noexcept
	Get reverse iterator to end.
const_reverse_iterator	rend () const noexcept
	Get const reverse iterator to end.
const_reverse_iterator	crbegin () const noexcept
	Get const reverse iterator to beginning.
const_reverse_iterator	crend () const noexcept
	Get const reverse iterator to end.
void	swap (ExposedVector &other) noexcept
	Swap contents with another ExposedVector.
void	assign (InputIt first, InputIt last)
	Assign values from iterators.
void	assign (size_type count, const ConsensusFeature &value)
	Assign n copies of value.
void	assign (std::initializer_list< ConsensusFeature > init)
	Assign from initializer list.
ConsensusFeature &	front () noexcept
	Get first element.
const ConsensusFeature &	front () const noexcept
	Get first element (const)
size_type	max_size () const noexcept
	Get maximum possible size.
size_type	capacity () const noexcept
	Get current capacity.
void	shrink_to_fit ()
	Shrink capacity to fit size.
iterator	emplace (const_iterator pos, Args &&... args)
	Emplace element at position.
const VecMember &	getData () const
	read-only access to the underlying data
VecMember &	getData ()
	read access to the underlying data
bool	operator== (const ExposedVector &other) const
	Equality comparison.
bool	operator!= (const ExposedVector &other) const
	Inequality comparison.
bool	operator< (const ExposedVector &other) const
bool	operator<= (const ExposedVector &other) const
bool	operator> (const ExposedVector &other) const
bool	operator>= (const ExposedVector &other) const
Public Member Functions inherited from UniqueIdInterface
	UniqueIdInterface ()
	Default constructor - the unique id will be invalid
	UniqueIdInterface (const UniqueIdInterface &rhs)=default
	Copy constructor - copies the unique id.
	UniqueIdInterface (UniqueIdInterface &&rhs)=default
	Move constructor.
UniqueIdInterface &	operator= (UniqueIdInterface const &rhs)=default
	Assignment operator - copies the unique id.
UniqueIdInterface &	operator= (UniqueIdInterface &&) &=default
	Move Assignment operator - copies the unique id.
virtual	~UniqueIdInterface ()=default
	Destructor.
bool	operator== (UniqueIdInterface const &rhs) const
	Equality comparison operator - the unique ids must be equal (!)
UInt64	getUniqueId () const
	Non-mutable access to unique id - returns the unique id.
Size	clearUniqueId ()
	Clear the unique id. The new unique id will be invalid. Returns 1 if the unique id was changed, 0 otherwise.
void	swap (UniqueIdInterface &from)
Size	hasValidUniqueId () const
	Returns whether the unique id is valid. Returns 1 if the unique id is valid, 0 otherwise.
Size	hasInvalidUniqueId () const
	Returns whether the unique id is invalid. Returns 1 if the unique id is invalid, 0 otherwise.
Size	setUniqueId ()
	Assigns a new, valid unique id. Always returns 1.
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.
void	setUniqueId (UInt64 rhs)
	Assigns the given unique id.
void	setUniqueId (const std::string &rhs)
	Mutable access to unique id.
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.
void	updateUniqueIdToIndex () const
	Updates the hash map from unique id to index.
Size	resolveUniqueIdConflicts ()
	Assign new UID's to doubly occurring UID's.
void	swap (UniqueIdIndexer &rhs)
	Swap.
Public Member Functions inherited from MapUtilities< ConsensusMap >
void	applyFunctionOnPeptideHits (T &&f, bool include_unassigned=true)
	applies a function on all PeptideHits or only assigned ones
void	applyFunctionOnPeptideHits (T &&f, bool include_unassigned=true) const
	applies a const function on all PeptideHits or only assigned ones
void	applyFunctionOnPeptideIDs (T &&f, bool include_unassigned=true)
	applies a function on all PeptideIDs or only assigned ones
void	applyFunctionOnPeptideIDs (T &&f, bool include_unassigned=true) const
	applies a const function on all PeptideIDs or only assigned ones

Protected Attributes
ColumnHeaders	column_description_
	Map from index to file description.
std::string	experiment_type_ = "label-free"
	type of experiment (label-free, labeled_MS1, labeled_MS2)
std::vector< ProteinIdentification >	protein_identifications_
	protein identifications
PeptideIdentificationList	unassigned_peptide_identifications_
	unassigned peptide identifications (without feature)
std::vector< DataProcessing >	data_processing_
	applied data processing
IdentificationData	id_data_
	general identification results (peptides/proteins, RNA, compounds)
Protected Attributes inherited from MetaInfoInterface
MetaInfo *	meta_ = nullptr
	Pointer to the MetaInfo object.
Protected Attributes inherited from DocumentIdentifier
std::string	id_
	the ID (e.g. LSID)
std::string	file_path_
	the path to the loaded file
FileTypes::Type	file_type_
	the type of the loaded file
Protected Attributes inherited from ExposedVector< ConsensusFeature >
VecMember	data_
	the container which holds all the data
Protected Attributes inherited from UniqueIdInterface
UInt64	unique_id_
	the unique id
Protected Attributes inherited from UniqueIdIndexer< ConsensusMap >
UniqueIdMap	uniqueid_to_index_
	hash map from unique id to index of features

Type definitions
typedef ConsensusFeature	FeatureType
typedef std::map< UInt64, ColumnHeader >	ColumnHeaders
typedef RangeManagerContainer< RangeRT, RangeMZ, RangeIntensity >	RangeManagerContainerType
typedef RangeManager< RangeRT, RangeMZ, RangeIntensity >	RangeManagerType
typedef iterator	Iterator
typedef const_iterator	ConstIterator
typedef reverse_iterator	ReverseIterator
typedef const_reverse_iterator	ConstReverseIterator
	ConsensusMap ()
	Default constructor.
	ConsensusMap (const ConsensusMap &source)
	Copy constructor.
	ConsensusMap (ConsensusMap &&source)
	Move constructor.
	~ConsensusMap () override
	Destructor.
	ConsensusMap (size_type n)
	Creates a ConsensusMap with n elements.
ConsensusMap &	operator= (const ConsensusMap &source)
	Assignment operator.
ConsensusMap &	operator= (ConsensusMap &&source)=default
	MoveAssignment operator.
ConsensusMap &	appendRows (const ConsensusMap &rhs)
	Add consensus map entries as new rows.
ConsensusMap &	appendColumns (const ConsensusMap &rhs)
	Add consensus map entries as new columns.
void	clear (bool clear_meta_data=true)
	Clears all data and meta data.
const ColumnHeaders &	getColumnHeaders () const
	Non-mutable access to the file descriptions.
ColumnHeaders &	getColumnHeaders ()
	Mutable access to the file descriptions.
void	setColumnHeaders (const ColumnHeaders &column_description)
	Mutable access to the file descriptions.
const std::string &	getExperimentType () const
	Non-mutable access to the experiment type.
void	setExperimentType (const std::string &experiment_type)
	Mutable access to the experiment type.

Additional Inherited Members
Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistry &	metaRegistry ()
	Returns a reference to the MetaInfoRegistry.
Static Public Member Functions inherited from UniqueIdInterface
static bool	isValid (UInt64 unique_id)
	Returns true if the unique_id is valid, false otherwise.
Protected Member Functions inherited from MetaInfoInterface
void	createIfNotExists_ ()
	Creates the MetaInfo object if it does not exist.
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
void	for_each_base_ (Visitor &&visitor) const
	.. and a const version
Protected Member Functions inherited from UniqueIdIndexer< ConsensusMap >
const auto &	getBase_ () const
	A little helper to get access to the base (!) class RandomAccessContainer.
auto &	getBase_ ()
	A little helper to get access to the base (!) class RandomAccessContainer.
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)

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

ColumnHeaders

typedef std::map<UInt64, ColumnHeader> ColumnHeaders

ConstIterator

typedef const_iterator ConstIterator

ConstReverseIterator

typedef const_reverse_iterator ConstReverseIterator

FeatureType

typedef ConsensusFeature FeatureType

Iterator

typedef iterator Iterator

RangeManagerContainerType

typedef RangeManagerContainer<RangeRT, RangeMZ, RangeIntensity> RangeManagerContainerType

RangeManagerType

typedef RangeManager<RangeRT, RangeMZ, RangeIntensity> RangeManagerType

ReverseIterator

typedef reverse_iterator ReverseIterator

Member Enumeration Documentation

SplitMeta

enum class SplitMeta

strong

Enumerator
DISCARD	do not copy any meta values
COPY_ALL	copy all meta values to all feature maps
COPY_FIRST	copy all meta values to first feature map

Constructor & Destructor Documentation

ConsensusMap() [1/4]

ConsensusMap

(

)

Default constructor.

ConsensusMap() [2/4]

ConsensusMap

(

const ConsensusMap &

source

)

Copy constructor.

ConsensusMap() [3/4]

ConsensusMap

(

ConsensusMap &&

source

)

Move constructor.

~ConsensusMap()

~ConsensusMap ( )

override

Destructor.

ConsensusMap() [4/4]

ConsensusMap ( 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

[in]

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

[in]

rhs

The consensus map to be merged.

applyMemberFunction() [1/2]

template<typename Type >

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

inline

The "const" variant.

applyMemberFunction() [2/2]

template<typename Type >

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.

clear()

void clear

(

bool

clear_meta_data = true

)

Clears all data and meta data.

Parameters

[in]

clear_meta_data

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

Referenced by MS1LabeledFAIMS::annotate(), and MS1LabeledFAIMS::group().

findProteinIdentification() [1/2]

ProteinIdentification * findProteinIdentification

(

const std::string &

identifier

)

finds a protein identification by its identifier (returns nullptr if not found)

findProteinIdentification() [2/2]

const ProteinIdentification * findProteinIdentification

(

const std::string &

identifier

)

const

finds a protein identification by its identifier (returns nullptr if not found)

getColumnHeaders() [1/2]

ColumnHeaders & getColumnHeaders

(

)

Mutable access to the file descriptions.

getColumnHeaders() [2/2]

const ColumnHeaders & getColumnHeaders

(

)

const

Non-mutable access to the file descriptions.

Referenced by MS1LabeledFAIMS::append_(), and MS1LabeledRatioQuantifier::run().

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

getExperimentType()

const std::string & getExperimentType

(

)

const

Non-mutable access to the experiment type.

Referenced by MS1LabeledRatioQuantifier::run().

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

returns the MS run path (stored in ColumnHeaders)

getProteinIdentifications() [1/2]

std::vector< ProteinIdentification > & getProteinIdentifications

(

)

mutable access to the protein identifications

getProteinIdentifications() [2/2]

const std::vector< ProteinIdentification > & getProteinIdentifications

(

)

const

non-mutable access to the protein identifications

Referenced by FeatureGroupingAlgorithm::postprocess_().

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]

PeptideIdentificationList & getUnassignedPeptideIdentifications

(

)

mutable access to the unassigned peptide identifications

getUnassignedPeptideIdentifications() [2/2]

const PeptideIdentificationList & getUnassignedPeptideIdentifications

(

)

const

non-mutable access to the unassigned peptide identifications

Referenced by MS1LabeledFAIMS::append_(), IDScoreSwitcherAlgorithm::determineScoreNameOrientationAndType(), FeatureGroupingAlgorithm::postprocess_(), and MS1LabeledRatioQuantifier::run().

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.

Note

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=() [1/2]

ConsensusMap & operator= ( ConsensusMap &&  source )

default

MoveAssignment operator.

operator=() [2/2]

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 std::string &

experiment_type

)

Mutable access to the experiment type.

setPrimaryMSRunPath() [1/2]

void setPrimaryMSRunPath

(

const StringList &

s

)

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

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

Parameters

[in]	s	Fallback if e does not have a primary MS runpath
[in,out]	e	Use primary MS runpath from this mzML file

setProteinIdentifications() [1/2]

void setProteinIdentifications

(

const std::vector< ProteinIdentification > &

protein_identifications

)

sets the protein identifications

setProteinIdentifications() [2/2]

void setProteinIdentifications

(

std::vector< ProteinIdentification > &&

protein_identifications

)

sets the protein identifications by moving

setUnassignedPeptideIdentifications()

void setUnassignedPeptideIdentifications

(

const PeptideIdentificationList &

unassigned_peptide_identifications

)

sets the unassigned peptide identifications

Referenced by MS1LabeledFAIMS::annotate().

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).

Referenced by FeatureGroupingAlgorithm::postprocess_().

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).

Referenced by MS1LabeledFAIMS::annotate().

sortByQuality()

void sortByQuality

(

bool

reverse = false

)

Sorts the peaks according to ascending quality.

Referenced by FeatureGroupingAlgorithm::postprocess_().

sortByRT()

void sortByRT

(

)

Sorts the peaks to RT position.

sortBySize()

void sortBySize

(

)

Sorts with respect to the size (number of elements)

Referenced by FeatureGroupingAlgorithm::postprocess_().

sortPeptideIdentificationsByMapIndex()

void sortPeptideIdentificationsByMapIndex

(

)

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

split()

std::vector< FeatureMap > split

(

SplitMeta

mode = SplitMeta::DISCARD

)

const

splits ConsensusMap into its original FeatureMaps

If the ConsensusMap originated from some number of FeatureMaps, those are reconstructed with the information provided by the map index. If the ConsensusMap originated from the IsobaricAnalyzer, only Features are separated. All PeptideIdentifications (assigned and unassigned) are added to the first FeatureMap.

MetaValues of ConsensusFeatures can be copied to all FeatureMaps, just to the first or they can be ignored.

The result holds one FeatureMap per column header (see getColumnHeaders()), ordered by map index: the k-th FeatureMap corresponds to the k-th column header in key order. Map indices do not have to be contiguous, e.g. for the column headers {0, 3} the second FeatureMap (position 1) holds the features of map index 3. For the usual contiguous map indices 0..n-1 the position equals the map index.

Parameters

[in]

mode

Decide what to do with the MetaValues annotated at the ConsensusFeatures.

Returns

FeatureMaps, one per column header, in key order of the column headers

Exceptions

Exception::ElementNotFound	if a FeatureHandle or the 'map_index' meta value of a PeptideIdentification refers to a map index which is not a column header of this ConsensusMap (see isMapConsistent()). Also thrown if there is no feature (or no column) with map index 0 although the data was processed by the IsobaricAnalyzer or mode is SplitMeta::COPY_FIRST.
Exception::MissingInformation	if the data was not processed by the IsobaricAnalyzer and a PeptideIdentification has no 'map_index' meta value

swap()

void swap

(

ConsensusMap &

from

)

Swaps the content 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 >.

Referenced by MS1LabeledFAIMS::annotate(), and MS1LabeledFAIMS::group().

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_

std::string experiment_type_ = "label-free"

protected

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

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_

PeptideIdentificationList unassigned_peptide_identifications_

protected

unassigned peptide identifications (without feature)