A container for consensus elements. More...

#include <OpenMS/KERNEL/ConsensusMap.h>

Inheritance diagram for ConsensusMap:

Classes
struct	FileDescription
	Source file description for input files. More...
Public Types
Type definitions

typedef std::vector < ConsensusFeature >	Base
typedef RangeManager< 2 >	RangeManagerType
typedef Map< UInt64, FileDescription >	FileDescriptions
typedef std::vector < ConsensusFeature >::iterator	Iterator
	Mutable iterator.
typedef std::vector < ConsensusFeature > ::const_iterator	ConstIterator
	Non-mutable iterator.
typedef std::vector < ConsensusFeature > ::reverse_iterator	ReverseIterator
	Mutable reverse iterator.
typedef std::vector < ConsensusFeature > ::const_reverse_iterator	ConstReverseIterator
	Non-mutable reverse iterator.
Public Member Functions
	ConsensusMap ()
	Default constructor.
	ConsensusMap (const ConsensusMap &source)
	Copy constructor.
	~ConsensusMap ()
	Destructor.
	ConsensusMap (Base::size_type n)
	Creates a ConsensusMap with n elements.
ConsensusMap &	operator= (const ConsensusMap &source)
	Assignment operator.
ConsensusMap &	operator+= (const ConsensusMap &rhs)
	Add one consensus map to another.
void	clear (bool clear_meta_data=true)
	Clears all data and meta data.
const FileDescriptions &	getFileDescriptions () const
	Non-mutable access to the file descriptions.
FileDescriptions &	getFileDescriptions ()
	Mutable access to the file descriptions.
const String &	getExperimentType () const
	Non-mutable access to the experiment type.
void	setExperimentType (const String &experiment_type)
	Mutable access to the experiment type.
void	updateRanges ()
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
const std::vector < PeptideIdentification > &	getUnassignedPeptideIdentifications () const
	non-mutable access to the unassigned peptide identifications
std::vector < PeptideIdentification > &	getUnassignedPeptideIdentifications ()
	mutable access to the unassigned peptide identifications
void	setUnassignedPeptideIdentifications (const std::vector< PeptideIdentification > &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
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.
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).
Static Public Member Functions
template<typename FeatureT >
static void	convert (UInt64 const input_map_index, FeatureMap< FeatureT > const &input_map, ConsensusMap &output_map, Size n=-1)
	Convert a FeatureMap (of any feature type) to a ConsensusMap.
static void	convert (UInt64 const input_map_index, MSExperiment<> &input_map, ConsensusMap &output_map, Size n=-1)
	Similar to `convert` for FeatureMaps.
static void	convert (UInt64 const input_map_index, std::vector< Peak2D > &input_map, ConsensusMap &output_map, Size n=-1)
	Convert a vector of 2D Peaks (Peak2D) into a ConsensusMap.
template<typename FeatureT >
static void	convert (ConsensusMap const &input_map, const bool keep_uids, FeatureMap< FeatureT > &output_map)
	Convert a ConsensusMap to a FeatureMap (of any feature type).
Protected Attributes
FileDescriptions	file_description_
	Map from index to file description.
String	experiment_type_
	type of experiment (label-free, itraq, ...); see xsd schema
std::vector < ProteinIdentification >	protein_identifications_
	protein identifications
std::vector < PeptideIdentification >	unassigned_peptide_identifications_
	protein identifications
std::vector< DataProcessing >	data_processing_
	applied data processing

Detailed Description

A container for consensus elements.

A ConsensusMap is a container holding 2-dimensional consensus elements (ConsensusFeature) which in turn represent combined elements of 2-dimensional experiments. The map is implemented as a vector of elements.

The map indices used in the consensus features should be registered in this class.

Member Typedef Documentation

typedef std::vector<ConsensusFeature> Base

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

Non-mutable iterator.

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

Non-mutable reverse iterator.

typedef Map<UInt64, FileDescription> FileDescriptions

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

Mutable iterator.

typedef RangeManager<2> RangeManagerType

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

Mutable reverse iterator.

Constructor & Destructor Documentation

ConsensusMap ( )

Default constructor.

ConsensusMap ( const ConsensusMap & source )

Copy constructor.

~ConsensusMap ( )

Destructor.

ConsensusMap ( Base::size_type n ) [explicit]

Creates a ConsensusMap with n elements.

Member Function Documentation

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.

Size applyMemberFunction ( Size(Type::*)() const member_function ) const [inline]

The "const" variant.

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.

Referenced by ConsensusMap::convert().

static void convert	(	UInt64 const	input_map_index,
		MSExperiment<> &	input_map,
		ConsensusMap &	output_map,
		Size	n = `-1`
	)			`[inline, static]`

Similar to convert for FeatureMaps.

Only the n most intense elements are copied.

Currently MSExperiment<> does not have a unique id but ConsensusMap has one, so we assign a new one here.

Parameters:

	input_map_index	The index of the input map.
	input_map	The input map to be converted.
	output_map	The resulting ConsensusMap.
	n	The maximum number of elements to be copied.

References ConsensusMap::clear(), MSExperiment< PeakT, ChromatogramPeakT >::get2DData(), ConsensusMap::getFileDescriptions(), MSExperiment< PeakT, ChromatogramPeakT >::getSize(), OpenMS::reverseComparator(), UniqueIdInterface::setUniqueId(), ConsensusMap::updateRanges(), and MSExperiment< PeakT, ChromatogramPeakT >::updateRanges().

static void convert	(	UInt64 const	input_map_index,
		std::vector< Peak2D > &	input_map,
		ConsensusMap &	output_map,
		Size	n = `-1`
	)			`[inline, static]`

Convert a vector of 2D Peaks (Peak2D) into a ConsensusMap.

Only the n most intense elements are copied.

Note: a new unique ID is generated for the consensus map.

Parameters:

	input_map_index	The index of the input map.
	input_map	The input map to be converted.
	output_map	The resulting ConsensusMap.
	n	The maximum number of elements to be copied.

References ConsensusMap::clear(), ConsensusMap::getFileDescriptions(), OpenMS::reverseComparator(), UniqueIdInterface::setUniqueId(), and ConsensusMap::updateRanges().

static void convert	(	ConsensusMap const &	input_map,
		const bool	keep_uids,
		FeatureMap< FeatureT > &	output_map
	)			`[inline, static]`

Convert a ConsensusMap to a FeatureMap (of any feature type).

The previous content of output_map is cleared. UID's of the elements and the container is copied if the keep_uids flag is set.

Parameters:

	input_map	The container to be converted.
	keep_uids	Shall the UID's of the elements and the container be kept or created anew
	output_map	The resulting ConsensusMap.

References OpenMS::Constants::c, FeatureMap< FeatureT >::clear(), ConsensusMap::getProteinIdentifications(), ConsensusMap::getUnassignedPeptideIdentifications(), FeatureMap< FeatureT >::setProteinIdentifications(), FeatureMap< FeatureT >::setUnassignedPeptideIdentifications(), and UniqueIdInterface::setUniqueId().

static void convert	(	UInt64 const	input_map_index,
		FeatureMap< FeatureT > const &	input_map,
		ConsensusMap &	output_map,
		Size	n = `-1`
	)			`[inline, static]`

Convert a FeatureMap (of any feature type) to a ConsensusMap.

Each ConsensusFeature contains a map index, so this has to be given as well. The previous content of output_map is cleared. An arguable design decision is that the unique id of the FeatureMap is copied (!) to the ConsensusMap, because that is the way it is meant to be used in the algorithms.

Only the first (!) n elements are copied. (This parameter exists mainly for compatibility with convert for MSExperiments. To use it in a meaningful way, apply one of the sorting methods to input_map beforehand.)

Parameters:

	input_map_index	The index of the input map.
	input_map	The container to be converted.
	output_map	The resulting ConsensusMap.
	n	The maximum number of elements to be copied.

References ConsensusMap::clear(), ConsensusMap::getFileDescriptions(), FeatureMap< FeatureT >::getProteinIdentifications(), FeatureMap< FeatureT >::getUnassignedPeptideIdentifications(), UniqueIdInterface::getUniqueId(), ConsensusMap::setProteinIdentifications(), ConsensusMap::setUnassignedPeptideIdentifications(), UniqueIdInterface::setUniqueId(), and ConsensusMap::updateRanges().

Referenced by MapAlignmentAlgorithmPoseClustering::setReference().

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

const String& getExperimentType ( ) const

Non-mutable access to the experiment type.

const FileDescriptions& getFileDescriptions ( ) const

Non-mutable access to the file descriptions.

Referenced by ConsensusMap::convert().

FileDescriptions& getFileDescriptions ( )

Mutable access to the file descriptions.

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

non-mutable access to the protein identifications

Referenced by ConsensusMap::convert().

std::vector<ProteinIdentification>& getProteinIdentifications ( )

mutable access to the protein identifications

std::vector<PeptideIdentification>& getUnassignedPeptideIdentifications ( )

mutable access to the unassigned peptide identifications

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

non-mutable access to the unassigned peptide identifications

Referenced by ConsensusMap::convert().

bool operator!= ( const ConsensusMap & rhs ) const

Equality operator.

ConsensusMap& operator+= ( const ConsensusMap & rhs )

Add one consensus map to another.

Consensus elements are merged into one container, simply by appending. ConsensusElementLists are appended. Information on map lists ......

Parameters:

rhs

The consensus map.

ConsensusMap& operator= ( const ConsensusMap & source )

Assignment operator.

bool operator== ( const ConsensusMap & rhs ) const

Equality operator.

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

sets the description of the applied data processing

void setExperimentType ( const String & experiment_type )

Mutable access to the experiment type.

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

sets the protein identifications

Referenced by ConsensusMap::convert().

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

sets the unassigned peptide identifications

Referenced by ConsensusMap::convert().

void sortByIntensity ( bool reverse = false )

Sorts the peaks according to ascending intensity.

void sortByMaps ( )

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

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 sortByRT ( )

Sorts the peaks to RT position.

void sortBySize ( )

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

void swap ( ConsensusMap & from )

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

void updateRanges ( )

Referenced by ConsensusMap::convert().

Member Data Documentation

std::vector<DataProcessing> data_processing_ [protected]

applied data processing

String experiment_type_ [protected]

type of experiment (label-free, itraq, ...); see xsd schema

FileDescriptions file_description_ [protected]

Map from index to file description.

std::vector<ProteinIdentification> protein_identifications_ [protected]

protein identifications

std::vector<PeptideIdentification> unassigned_peptide_identifications_ [protected]

protein identifications

OpenMS / TOPP release 1.10.0

Documentation generated on Thu Mar 7 2013 09:42:54 using doxygen 1.7.1

ConsensusMap Class Reference [Kernel]

Classes

Public Types

Public Member Functions

Static Public Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

ConsensusMap Class Reference
[Kernel]