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BaseFeature Class Reference

A basic LC-MS feature. More...

#include <OpenMS/KERNEL/BaseFeature.h>

Inheritance diagram for BaseFeature:
RichPeak2D Peak2D MetaInfoInterface UniqueIdInterface ConsensusFeature Feature MRMFeature

Classes

struct  QualityLess
 Compare by quality. More...
 

Public Member Functions

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)
 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...
 
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...
 
Constructors and Destructor
 BaseFeature ()
 Default constructor. More...
 
 BaseFeature (const BaseFeature &feature)
 Copy constructor. 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 ()
 Destructor. More...
 
Quality methods
QualityType getQuality () const
 Non-mutable access to the overall quality. More...
 
void setQuality (QualityType q)
 Set the overall quality. More...
 
- Public Member Functions inherited from RichPeak2D
 RichPeak2D ()
 Default constructor. More...
 
 RichPeak2D (const RichPeak2D &p)
 Copy constructor. More...
 
 RichPeak2D (const Peak2D &p)
 Constructor from Peak2D. More...
 
 ~RichPeak2D ()
 Destructor. More...
 
RichPeak2Doperator= (const RichPeak2D &rhs)
 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)
 Assignment operator. More...
 
bool operator== (const Peak2D &rhs) const
 Equality operator. More...
 
bool operator!= (const Peak2D &rhs) const
 Equality operator. More...
 
 Peak2D ()
 
 Peak2D (const Peak2D &p)
 Copy 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 ()
 destructor More...
 
MetaInfoInterfaceoperator= (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 DataValuegetMetaValue (const String &name) const
 returns the value corresponding to a string More...
 
const DataValuegetMetaValue (UInt index) const
 returns the value corresponding to an index More...
 
bool metaValueExists (const String &name) const
 returns if this MetaInfo is set More...
 
bool metaValueExists (UInt index) const
 returns if this MetaInfo is set 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 UniqueIdInterface
 UniqueIdInterface ()
 Default constructor - the unique id will be invalid More...
 
 UniqueIdInterface (const UniqueIdInterface &rhs)
 Copy constructor - copies the unique id. More...
 
UniqueIdInterfaceoperator= (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...
 

Protected Attributes

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_
 Peptide 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...
 

Type definitions

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...
 
static const std::string NamesOfAnnotationState [SIZE_OF_ANNOTATIONSTATE]
 

Additional Inherited Members

- 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...
 
- 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...
 
- Protected Member Functions inherited from MetaInfoInterface
void createIfNotExists_ ()
 creates the MetaInfo object if it does not exist 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 basic LC-MS feature.

This class represents a "minimal" feature, defined by a position in RT and m/z, intensity, charge, quality, and annotated peptides. Most classes dealing with features will use the subclasses Feature or ConsensusFeature directly. However, algorithms that rely on very general characteristics of features can use this class to provide a unified solution for both "normal" features and consensus features.

Constructor & Destructor Documentation

Default constructor.

BaseFeature ( const BaseFeature feature)

Copy constructor.

BaseFeature ( const Peak2D point)
explicit

Constructor from raw data point.

BaseFeature ( const RichPeak2D point)
explicit

Constructor from raw data point with meta information.

Destructor.

Member Function Documentation

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

const ChargeType& getCharge ( ) const

Non-mutable access to charge state.

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

returns a const reference to the PeptideIdentification vector

std::vector<PeptideIdentification>& getPeptideIdentifications ( )

returns a mutable reference to the PeptideIdentification vector

QualityType getQuality ( ) const

Non-mutable access to the overall quality.

Referenced by BaseFeature::QualityLess::operator()().

WidthType getWidth ( ) const

Non-mutable access to the features width (full width at half max, FWHM)

bool operator!= ( const BaseFeature rhs) const

Inequality operator.

BaseFeature& operator= ( const BaseFeature rhs)

Assignment operator.

bool operator== ( const BaseFeature rhs) const

Equality operator.

void setCharge ( const ChargeType ch)
void setPeptideIdentifications ( const std::vector< PeptideIdentification > &  peptides)

sets the PeptideIdentification vector

void setQuality ( QualityType  q)

Set the overall quality.

void setWidth ( WidthType  fwhm)

Set the width of the feature (FWHM)

Member Data Documentation

ChargeType charge_
protected

Charge of the peptide represented by this feature. The default value is 0, which represents an unknown charge state.

std::vector<PeptideIdentification> peptides_
protected

Peptide PeptideIdentifications belonging to the feature.

QualityType quality_
protected

Overall quality measure of the feature.

WidthType width_
protected

Width (FWHM) for the feature. The default value is 0.0, a feature finding algorithm can compute this form the model.


OpenMS / TOPP release 2.0.0 Documentation generated on Sat May 16 2015 16:13:45 using doxygen 1.8.9.1