OpenMS  2.7.0
Classes | Public Types | List of all members
ConsensusFeature Class Reference

A consensus feature spanning multiple LC-MS/MS experiments. More...

#include <OpenMS/KERNEL/ConsensusFeature.h>

Inheritance diagram for ConsensusFeature:
[legend]
Collaboration diagram for ConsensusFeature:
[legend]

Classes

struct  MapsLess
 Compare by the sets of consensus elements (lexicographically) More...
 
struct  Ratio
 slim struct to feed the need for systematically storing of ratios ( More...
 
struct  SizeLess
 Compare by size(), the number of consensus elements. More...
 

Public Types

typedef std::set< FeatureHandle, FeatureHandle::IndexLessHandleSetType
 Type definitions. More...
 
typedef HandleSetType::const_iterator const_iterator
 
typedef HandleSetType::iterator iterator
 
typedef HandleSetType::const_reverse_iterator const_reverse_iterator
 
typedef HandleSetType::reverse_iterator reverse_iterator
 
- Public Types inherited from BaseFeature
enum  AnnotationState {
  FEATURE_ID_NONE , FEATURE_ID_SINGLE , FEATURE_ID_MULTIPLE_SAME , FEATURE_ID_MULTIPLE_DIVERGENT ,
  SIZE_OF_ANNOTATIONSTATE
}
 state of identification, use getIDState() to query it More...
 
typedef float QualityType
 Type of quality values. More...
 
typedef Int ChargeType
 Type of charge values. More...
 
typedef float WidthType
 Type of feature width/FWHM (RT) More...
 
- Public Types inherited from Peak2D
typedef float IntensityType
 Intensity type. More...
 
typedef double CoordinateType
 Coordinate type (of the position) More...
 
typedef DPosition< 2 > PositionType
 Position type. More...
 
enum  DimensionDescription { RT = 0 , MZ = 1 , DIMENSION = 2 }
 This enum maps the symbolic names of the dimensions to numbers. 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 Member Functions

Constructors and Destructor
 ConsensusFeature ()
 Default constructor. More...
 
 ConsensusFeature (const ConsensusFeature &rhs)=default
 Copy constructor. More...
 
 ConsensusFeature (ConsensusFeature &&rhs)=default
 Move constructor. More...
 
 ConsensusFeature (const BaseFeature &feature)
 Constructor from basic feature. More...
 
 ConsensusFeature (UInt64 map_index, const Peak2D &element, UInt64 element_index)
 Constructor with map and element index for a singleton consensus feature. More...
 
 ConsensusFeature (UInt64 map_index, const BaseFeature &element)
 Constructor with map index for a singleton consensus feature. More...
 
ConsensusFeatureoperator= (const ConsensusFeature &rhs)=default
 Assignment operator. More...
 
ConsensusFeatureoperator= (ConsensusFeature &&rhs)=default
 Move Assignment operator. More...
 
 ~ConsensusFeature () override
 Destructor. More...
 
Management of feature handles
void insert (const ConsensusFeature &cf)
 Adds all feature handles (of the CF) into the consensus feature. More...
 
void insert (const FeatureHandle &handle)
 Adds an feature handle into the consensus feature. More...
 
void insert (const HandleSetType &handle_set)
 Adds all feature handles in handle_set to this consensus feature. More...
 
void insert (UInt64 map_index, const Peak2D &element, UInt64 element_index)
 Creates a FeatureHandle and adds it. More...
 
void insert (UInt64 map_index, const BaseFeature &element)
 Creates a FeatureHandle and adds it. More...
 
const HandleSetTypegetFeatures () const
 Non-mutable access to the contained feature handles. More...
 
std::vector< FeatureHandlegetFeatureList () const
 Mutable access to a copy of the contained feature handles. More...
 
void setFeatures (HandleSetType h)
 Set the feature set to a new one. More...
 
Accessors
DRange< 2 > getPositionRange () const
 Returns the position range of the contained elements. More...
 
DRange< 1 > getIntensityRange () const
 Returns the intensity range of the contained elements. More...
 
void computeConsensus ()
 Computes and updates the consensus position, intensity, and charge. More...
 
void computeMonoisotopicConsensus ()
 Computes and updates the consensus position, intensity, and charge. More...
 
void computeDechargeConsensus (const FeatureMap &fm, bool intensity_weighted_averaging=false)
 Computes the uncharged parent RT & mass, assuming the handles are charge variants. More...
 
void addRatio (const Ratio &r)
 Add a ratio. More...
 
void setRatios (std::vector< Ratio > &rs)
 Add a ratio vector. More...
 
std::vector< RatiogetRatios () const
 Get the ratio vector. More...
 
std::vector< Ratio > & getRatios ()
 Get the ratio vector. More...
 
- Public Member Functions inherited from BaseFeature
 BaseFeature ()
 Default constructor. More...
 
 BaseFeature (const BaseFeature &feature)=default
 Copy constructor. More...
 
 BaseFeature (BaseFeature &&feature)=default
 Move constructor. More...
 
 BaseFeature (const BaseFeature &rhs, UInt64 map_index)
 Copy constructor with a new map_index. More...
 
 BaseFeature (const Peak2D &point)
 Constructor from raw data point. More...
 
 BaseFeature (const RichPeak2D &point)
 Constructor from raw data point with meta information. More...
 
 BaseFeature (const FeatureHandle &fh)
 Constructor from a featurehandle. More...
 
 ~BaseFeature () override
 Destructor. More...
 
QualityType getQuality () const
 Non-mutable access to the overall quality. More...
 
void setQuality (QualityType q)
 Set the overall quality. More...
 
WidthType getWidth () const
 Non-mutable access to the features width (full width at half max, FWHM) More...
 
void setWidth (WidthType fwhm)
 Set the width of the feature (FWHM) More...
 
const ChargeTypegetCharge () const
 Non-mutable access to charge state. More...
 
void setCharge (const ChargeType &ch)
 Set charge state. More...
 
BaseFeatureoperator= (const BaseFeature &rhs)=default
 Assignment operator. More...
 
BaseFeatureoperator= (BaseFeature &&rhs) &=default
 Move Assignment operator. More...
 
bool operator== (const BaseFeature &rhs) const
 Equality operator. More...
 
bool operator!= (const BaseFeature &rhs) const
 Inequality operator. More...
 
const std::vector< PeptideIdentification > & getPeptideIdentifications () const
 returns a const reference to the PeptideIdentification vector More...
 
std::vector< PeptideIdentification > & getPeptideIdentifications ()
 returns a mutable reference to the PeptideIdentification vector More...
 
void setPeptideIdentifications (const std::vector< PeptideIdentification > &peptides)
 sets the PeptideIdentification vector More...
 
void sortPeptideIdentifications ()
 sorts PeptideIdentifications, assuming they have the same scoreType. More...
 
AnnotationState getAnnotationState () const
 state of peptide identifications attached to this feature. If one ID has multiple hits, the output depends on the top-hit only More...
 
- Public Member Functions inherited from RichPeak2D
 RichPeak2D ()
 Default constructor. More...
 
 RichPeak2D (const RichPeak2D &p)=default
 Copy constructor. More...
 
 RichPeak2D (const Peak2D &p)
 Constructor from Peak2D. More...
 
 RichPeak2D (const PositionType &pos, const IntensityType in)
 Member constructor. More...
 
 RichPeak2D (RichPeak2D &&p)=default
 Move constructor. More...
 
 ~RichPeak2D () override
 Destructor. More...
 
RichPeak2Doperator= (const RichPeak2D &rhs)=default
 Assignment operator. More...
 
RichPeak2Doperator= (RichPeak2D &&rhs) &=default
 Move Assignment operator. More...
 
RichPeak2Doperator= (const Peak2D &rhs)
 Assignment operator. More...
 
bool operator== (const RichPeak2D &rhs) const
 Equality operator. More...
 
bool operator!= (const RichPeak2D &rhs) const
 Equality operator. More...
 
- Public Member Functions inherited from Peak2D
Peak2Doperator= (const Peak2D &rhs)=default
 Assignment operator. More...
 
Peak2Doperator= (Peak2D &&) &=default
 Move assignment operator. More...
 
bool operator== (const Peak2D &rhs) const
 Equality operator. More...
 
bool operator!= (const Peak2D &rhs) const
 Equality operator. More...
 
 Peak2D ()
 
 Peak2D (const PositionType &pos, const IntensityType in)
 Member constructor. More...
 
 Peak2D (const Peak2D &p)=default
 Copy constructor. More...
 
 Peak2D (Peak2D &&)=default
 Move constructor. More...
 
 ~Peak2D ()
 Destructor. More...
 
IntensityType getIntensity () const
 
void setIntensity (IntensityType intensity)
 Non-mutable access to the data point intensity (height) More...
 
PositionType const & getPosition () const
 Non-mutable access to the position. More...
 
PositionTypegetPosition ()
 Mutable access to the position. More...
 
void setPosition (const PositionType &position)
 Mutable access to the position. More...
 
CoordinateType getMZ () const
 Returns the m/z coordinate (index 1) More...
 
void setMZ (CoordinateType coordinate)
 Mutable access to the m/z coordinate (index 1) More...
 
CoordinateType getRT () const
 Returns the RT coordinate (index 0) More...
 
void setRT (CoordinateType coordinate)
 Mutable access to the RT coordinate (index 0) 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...
 
MetaInfoInterfaceoperator= (const MetaInfoInterface &rhs)
 Assignment operator. More...
 
MetaInfoInterfaceoperator= (MetaInfoInterface &&) noexcept
 Move assignment operator. More...
 
bool operator== (const MetaInfoInterface &rhs) const
 Equality operator. More...
 
bool operator!= (const MetaInfoInterface &rhs) const
 Equality operator. More...
 
const DataValuegetMetaValue (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 DataValuegetMetaValue (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 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...
 
UniqueIdInterfaceoperator= (UniqueIdInterface const &rhs)=default
 Assignment operator - copies the unique id. More...
 
UniqueIdInterfaceoperator= (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...
 

Accessors for set of FeatureHandles

HandleSetType handles_
 
std::vector< Ratioratios_
 
Size size () const
 
const_iterator begin () const
 
iterator begin ()
 
const_iterator end () const
 
iterator end ()
 
const_reverse_iterator rbegin () const
 
reverse_iterator rbegin ()
 
const_reverse_iterator rend () const
 
reverse_iterator rend ()
 
void clear ()
 
bool empty () const
 

Additional Inherited Members

- Static Public Member Functions inherited from Peak2D
static char const * shortDimensionName (UInt const dim)
 Short name of the dimension (abbreviated form) More...
 
static char const * shortDimensionNameRT ()
 Short name of the dimension (abbreviated form) More...
 
static char const * shortDimensionNameMZ ()
 Short name of the dimension (abbreviated form) More...
 
static char const * fullDimensionName (UInt const dim)
 Full name of the dimension (self-explanatory form) More...
 
static char const * fullDimensionNameRT ()
 Full name of the dimension (self-explanatory form) More...
 
static char const * fullDimensionNameMZ ()
 Full name of the dimension (self-explanatory form) More...
 
static char const * shortDimensionUnit (UInt const dim)
 Unit of measurement (abbreviated form) More...
 
static char const * shortDimensionUnitRT ()
 Unit of measurement (abbreviated form) More...
 
static char const * shortDimensionUnitMZ ()
 Unit of measurement (abbreviated form) More...
 
static char const * fullDimensionUnit (UInt const dim)
 Unit of measurement (self-explanatory form) More...
 
static char const * fullDimensionUnitRT ()
 Unit of measurement (self-explanatory form) More...
 
static char const * fullDimensionUnitMZ ()
 Unit of measurement (self-explanatory form) More...
 
- Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistrymetaRegistry ()
 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...
 
- Static Public Attributes inherited from BaseFeature
static const std::string NamesOfAnnotationState [SIZE_OF_ANNOTATIONSTATE]
 
- Protected Member Functions inherited from MetaInfoInterface
void createIfNotExists_ ()
 Creates the MetaInfo object if it does not exist. More...
 
- Protected Attributes inherited from BaseFeature
QualityType quality_
 Overall quality measure of the feature. More...
 
ChargeType charge_
 Charge of the peptide represented by this feature. The default value is 0, which represents an unknown charge state. More...
 
WidthType width_
 Width (FWHM) for the feature. The default value is 0.0, a feature finding algorithm can compute this form the model. More...
 
std::vector< PeptideIdentificationpeptides_
 PeptideIdentifications belonging to the feature. More...
 
- Protected Attributes inherited from Peak2D
PositionType position_
 The data point position. More...
 
IntensityType intensity_
 The data point intensity. More...
 
- Protected Attributes inherited from MetaInfoInterface
MetaInfometa_
 Pointer to the MetaInfo object (0 by default) More...
 
- Protected Attributes inherited from UniqueIdInterface
UInt64 unique_id_
 the unique id More...
 
- Static Protected Attributes inherited from Peak2D
static char const *const dimension_name_short_ [DIMENSION]
 Short name of the dimension (abbreviated form) More...
 
static char const *const dimension_name_full_ [DIMENSION]
 Full name of the dimension (self-explanatory form) More...
 
static char const *const dimension_unit_short_ [DIMENSION]
 Unit of measurement (abbreviated form) More...
 
static char const *const dimension_unit_full_ [DIMENSION]
 Unit of measurement (self-explanatory form) More...
 

Detailed Description

A consensus feature spanning multiple LC-MS/MS experiments.

A ConsensusFeature represents 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 through a unique identifier.

A consensus feature represents corresponding features in multiple feature maps. The corresponding features are represented a set of FeatureHandle instances. Each ConsensusFeature "contains" zero or more FeatureHandles.

See also
ConsensusMap

Member Typedef Documentation

◆ const_iterator

typedef HandleSetType::const_iterator const_iterator

◆ const_reverse_iterator

typedef HandleSetType::const_reverse_iterator const_reverse_iterator

◆ HandleSetType

Type definitions.

◆ iterator

typedef HandleSetType::iterator iterator

◆ reverse_iterator

typedef HandleSetType::reverse_iterator reverse_iterator

Constructor & Destructor Documentation

◆ ConsensusFeature() [1/6]

Default constructor.

◆ ConsensusFeature() [2/6]

ConsensusFeature ( const ConsensusFeature rhs)
default

Copy constructor.

◆ ConsensusFeature() [3/6]

ConsensusFeature ( ConsensusFeature &&  rhs)
default

Move constructor.

◆ ConsensusFeature() [4/6]

ConsensusFeature ( const BaseFeature feature)
explicit

Constructor from basic feature.

◆ ConsensusFeature() [5/6]

ConsensusFeature ( UInt64  map_index,
const Peak2D element,
UInt64  element_index 
)

Constructor with map and element index for a singleton consensus feature.

Sets the consensus feature position and intensity to the values of element as well.

◆ ConsensusFeature() [6/6]

ConsensusFeature ( UInt64  map_index,
const BaseFeature element 
)

Constructor with map index for a singleton consensus feature.

Sets the consensus feature position, intensity, charge, quality, and peptide identifications to the values of element as well.

◆ ~ConsensusFeature()

~ConsensusFeature ( )
override

Destructor.

Member Function Documentation

◆ addRatio()

void addRatio ( const Ratio r)

Add a ratio.

Connects a ratio to the ConsensusFeature.

Note
still experimental. consensusfeaturehandler will ignore it.

◆ begin() [1/2]

iterator begin ( )

◆ begin() [2/2]

const_iterator begin ( ) const

◆ clear()

void clear ( )

◆ computeConsensus()

void computeConsensus ( )

Computes and updates the consensus position, intensity, and charge.

The position and intensity of the contained feature handles is averaged. The most frequent charge state wins, while the tie breaking prefers smaller (absolute) charges.

Note
This method has to be called explicitly, after adding the feature handles.

◆ computeDechargeConsensus()

void computeDechargeConsensus ( const FeatureMap fm,
bool  intensity_weighted_averaging = false 
)

Computes the uncharged parent RT & mass, assuming the handles are charge variants.

The position of the feature handles (decharged) is averaged (using intensity as weights if intensity_weighted_averaging is true). Intensities are summed up. Charge is set to 0. Mass calculation: If the given features contain a metavalue "dc_charge_adduct_mass" then this will be used as adduct mass instead of weight(H+) * charge.

Note
This method has to be called explicitly, after adding the feature handles.
Parameters
fmInput feature map, which provides additional information on the features
intensity_weighted_averagingUse unweighted averaging (default) or weighted by intensity

◆ computeMonoisotopicConsensus()

void computeMonoisotopicConsensus ( )

Computes and updates the consensus position, intensity, and charge.

The m/z position is the lowest m/z value of the feature handles. The RT position and intensity of the contained feature handles is averaged. The most frequent charge state wins, while the tie breaking prefers smaller (absolute) charges.

Note
This method has to be called explicitly, after adding the feature handles.

◆ empty()

bool empty ( ) const

◆ end() [1/2]

iterator end ( )

◆ end() [2/2]

const_iterator end ( ) const

◆ getFeatureList()

std::vector<FeatureHandle> getFeatureList ( ) const

Mutable access to a copy of the contained feature handles.

◆ getFeatures()

const HandleSetType& getFeatures ( ) const

Non-mutable access to the contained feature handles.

◆ getIntensityRange()

DRange<1> getIntensityRange ( ) const

Returns the intensity range of the contained elements.

◆ getPositionRange()

DRange<2> getPositionRange ( ) const

Returns the position range of the contained elements.

◆ getRatios() [1/2]

std::vector<Ratio>& getRatios ( )

Get the ratio vector.

◆ getRatios() [2/2]

std::vector<Ratio> getRatios ( ) const

Get the ratio vector.

◆ insert() [1/5]

void insert ( const ConsensusFeature cf)

Adds all feature handles (of the CF) into the consensus feature.

◆ insert() [2/5]

void insert ( const FeatureHandle handle)

Adds an feature handle into the consensus feature.

Exceptions
Exception::InvalidValueis thrown if a handle with the same map index and unique id already exists.

◆ insert() [3/5]

void insert ( const HandleSetType handle_set)

Adds all feature handles in handle_set to this consensus feature.

◆ insert() [4/5]

void insert ( UInt64  map_index,
const BaseFeature element 
)

Creates a FeatureHandle and adds it.

Exceptions
Exception::InvalidValueis thrown if a handle with the same map index and unique id already exists.

◆ insert() [5/5]

void insert ( UInt64  map_index,
const Peak2D element,
UInt64  element_index 
)

Creates a FeatureHandle and adds it.

Exceptions
Exception::InvalidValueis thrown if a handle with the same map index and unique id already exists.

◆ operator=() [1/2]

ConsensusFeature& operator= ( ConsensusFeature &&  rhs)
default

Move Assignment operator.

◆ operator=() [2/2]

ConsensusFeature& operator= ( const ConsensusFeature rhs)
default

Assignment operator.

◆ rbegin() [1/2]

reverse_iterator rbegin ( )

◆ rbegin() [2/2]

const_reverse_iterator rbegin ( ) const

◆ rend() [1/2]

reverse_iterator rend ( )

◆ rend() [2/2]

const_reverse_iterator rend ( ) const

◆ setFeatures()

void setFeatures ( HandleSetType  h)

Set the feature set to a new one.

◆ setRatios()

void setRatios ( std::vector< Ratio > &  rs)

Add a ratio vector.

Connects the ratios to the ConsensusFeature.

Note
still experimental. consensusfeaturehandler will ignore it.

◆ size()

Size size ( ) const

Member Data Documentation

◆ handles_

HandleSetType handles_
private

◆ ratios_

std::vector<Ratio> ratios_
private