A container for features. More...

#include <OpenMS/KERNEL/FeatureMap.h>

Inheritance diagram for FeatureMap< FeatureT >:

Public Types
Type definitions

typedef FeatureT	FeatureType
typedef RangeManager< 2 >	RangeManagerType
typedef std::vector< FeatureType >	Base
typedef Base::iterator	Iterator
typedef Base::const_iterator	ConstIterator
typedef Base::reverse_iterator	ReverseIterator
typedef Base::const_reverse_iterator	ConstReverseIterator
typedef FeatureType &	Reference
typedef const FeatureType &	ConstReference
Public Member Functions
FeatureMap &	operator= (const FeatureMap &rhs)
	Assignment operator.
bool	operator== (const FeatureMap &rhs) const
	Equality operator.
bool	operator!= (const FeatureMap &rhs) const
	Equality operator.
FeatureMap	operator+ (const FeatureMap &rhs) const
	Joins two feature maps.
FeatureMap &	operator+= (const FeatureMap &rhs)
	Add one feature map to another.
void	updateRanges ()
void	swap (FeatureMap &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
void	clear (bool clear_meta_data=true)
	Clears all data and meta data.
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.
template<typename Type >
Size	applyMemberFunction (Size(Type::*member_function)() const) const
	The "const" variant.
Constructors and Destructor

	FeatureMap ()
	Default constructor.
	FeatureMap (const FeatureMap &source)
	Copy constructor.
virtual	~FeatureMap ()
	Destructor.
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.
void	sortByPosition ()
	Sort features by position. Lexicographical comparison (first RT then m/z) is done.
void	sortByRT ()
	Sort features by RT position.
void	sortByMZ ()
	Sort features by m/z position.
void	sortByOverallQuality (bool reverse=false)
	Sort features by ascending overall quality.
Protected Attributes
std::vector < ProteinIdentification >	protein_identifications_
	protein identifications
std::vector < PeptideIdentification >	unassigned_peptide_identifications_
	peptide identifications not matched to a specific feature
std::vector< DataProcessing >	data_processing_
	applied data processing

Detailed Description

template<typename FeatureT = Feature>
class OpenMS::FeatureMap< FeatureT >

A container for features.

A map is a container holding 2-dimensional features, which in turn represent chemical entities (peptides, proteins, etc.) found in a 2-dimensional 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

typedef std::vector<FeatureType> Base

typedef Base::const_iterator ConstIterator

typedef const FeatureType& ConstReference

typedef Base::const_reverse_iterator ConstReverseIterator

typedef FeatureT FeatureType

typedef Base::iterator Iterator

typedef RangeManager<2> RangeManagerType

typedef FeatureType& Reference

typedef Base::reverse_iterator ReverseIterator

Constructor & Destructor Documentation

FeatureMap ( ) [inline]

Default constructor.

FeatureMap ( const FeatureMap< FeatureT > & source ) [inline]

Copy constructor.

virtual ~FeatureMap ( ) [inline, virtual]

Destructor.

Member Function Documentation

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.

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

The "const" variant.

void clear ( bool clear_meta_data = true ) [inline]

Clears all data and meta data.

Parameters:

clear_meta_data

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

Referenced by FeatureMap< Feature >::clear(), ConsensusMap::convert(), and FeatureFinder::run().

const std::vector<DataProcessing>& getDataProcessing ( ) const [inline]

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

Referenced by TOPPBase::addDataProcessing_(), and IDMapper::annotate().

std::vector<DataProcessing>& getDataProcessing ( ) [inline]

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

const std::vector<ProteinIdentification>& getProteinIdentifications ( ) const [inline]

non-mutable access to the protein identifications

Referenced by MetaDataBrowser::add(), IDMapper::annotate(), ConsensusMap::convert(), and MRMFeatureFinderScoring::pickExperiment().

std::vector<ProteinIdentification>& getProteinIdentifications ( ) [inline]

mutable access to the protein identifications

const std::vector<PeptideIdentification>& getUnassignedPeptideIdentifications ( ) const [inline]

non-mutable access to the unassigned peptide identifications

Referenced by MetaDataBrowser::add(), IDMapper::annotate(), and ConsensusMap::convert().

std::vector<PeptideIdentification>& getUnassignedPeptideIdentifications ( ) [inline]

mutable access to the unassigned peptide identifications

bool operator!= ( const FeatureMap< FeatureT > & rhs ) const [inline]

Equality operator.

FeatureMap operator+ ( const FeatureMap< FeatureT > & rhs ) const [inline]

Joins two feature maps.

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

FeatureMap& operator+= ( const FeatureMap< FeatureT > & rhs ) [inline]

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.

FeatureMap& operator= ( const FeatureMap< FeatureT > & rhs ) [inline]