| OpenMS 2.5.0

Classes | Public Member Functions | Protected Attributes | List of all members
BaseFeature Class Reference
Kernel

A basic LC-MS feature. More...

`#include <OpenMS/KERNEL/BaseFeature.h>`

Inheritance diagram for BaseFeature:

## 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 ChargeType & | getCharge () const
| Non-mutable access to charge state. More...
void | setCharge (const ChargeType &ch)
| Set charge state. More...
BaseFeature & | operator= (const BaseFeature &rhs)=default
| Assignment operator. More...
BaseFeature & | operator= (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...
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)=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 () override
| 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)=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...
RichPeak2D & | operator= (const RichPeak2D &rhs)=default
| Assignment operator. More...
RichPeak2D & | operator= (RichPeak2D &&rhs) &=default
| Move Assignment operator. More...
RichPeak2D & | operator= (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
Peak2D & | operator= (const Peak2D &rhs)=default
| Assignment operator. More...
Peak2D & | operator= (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...
PositionType & | getPosition ()
| 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...
MetaInfoInterface & | operator= (const MetaInfoInterface &rhs)
| Assignment operator. More...
MetaInfoInterface & | operator= (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 DataValue & | getMetaValue (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 DataValue & | getMetaValue (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 | 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...
UniqueIdInterface & | operator= (UniqueIdInterface const &rhs)=default
| Assignment operator - copies the unique id. More...
UniqueIdInterface & | operator= (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...

## 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< PeptideIdentification > | peptides_
| 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
MetaInfo * | meta_
| 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 MetaInfoRegistry & | metaRegistry ()
| 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.

## Member Typedef Documentation

## ◆ ChargeType

typedef Int ChargeType

Type of charge values.

## ◆ QualityType

typedef float QualityType

Type of quality values.

## ◆ WidthType

typedef float WidthType

Type of feature width/FWHM (RT)

## Member Enumeration Documentation

## ◆ AnnotationState

enum AnnotationState

state of identification, use getIDState() to query it

Enumerator
FEATURE_ID_NONE |
FEATURE_ID_SINGLE |
FEATURE_ID_MULTIPLE_SAME |
FEATURE_ID_MULTIPLE_DIVERGENT |
SIZE_OF_ANNOTATIONSTATE |

## Constructor & Destructor Documentation

## ◆ BaseFeature() [1/6]

BaseFeature | ( |  | ) |

Default constructor.

## ◆ BaseFeature() [2/6]

BaseFeature | ( | const BaseFeature & | feature | ) |

default

Copy constructor.

## ◆ BaseFeature() [3/6]

BaseFeature | ( | BaseFeature && | feature | ) |

default

Move constructor.

## ◆ BaseFeature() [4/6]

BaseFeature | ( | const BaseFeature & | rhs,
|  | UInt64 | map_index
| ) |  |

Copy constructor with a new map_index.

## ◆ BaseFeature() [5/6]

BaseFeature | ( | const Peak2D & | point | ) |

explicit

Constructor from raw data point.

## ◆ BaseFeature() [6/6]

BaseFeature | ( | const RichPeak2D & | point | ) |

explicit

Constructor from raw data point with meta information.

## ◆ ~BaseFeature()

~BaseFeature | ( |  | ) |

override

Destructor.

## Member Function Documentation

## ◆ getAnnotationState()

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

## ◆ getCharge()

const ChargeType& getCharge | ( |  | ) | const

Non-mutable access to charge state.

Referenced by TOPPGNPSExport::main_().

## ◆ getPeptideIdentifications() [1/2]

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

returns a const reference to the PeptideIdentification vector

Referenced by TOPPGNPSExport::main_(), and FeatureFinderIdentificationAlgorithm::FeatureFilterPeptides::operator()().

## ◆ getPeptideIdentifications() [2/2]

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

returns a mutable reference to the PeptideIdentification vector

## ◆ getQuality()

QualityType getQuality | ( |  | ) | const

Non-mutable access to the overall quality.

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

## ◆ getWidth()

WidthType getWidth | ( |  | ) | const

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

## ◆ operator!=()

bool operator!= | ( | const BaseFeature & | rhs | ) | const

Inequality operator.

## ◆ operator=() [1/2]

BaseFeature& operator= | ( | const BaseFeature & | rhs | ) |

default

Assignment operator.

## ◆ operator=() [2/2]

BaseFeature& operator= | ( | BaseFeature && | rhs | ) | &

default

Move Assignment operator.

## ◆ operator==()

bool operator== | ( | const BaseFeature & | rhs | ) | const

Equality operator.

## ◆ setCharge()

void setCharge | ( | const ChargeType & | ch | ) |

Set charge state.

Referenced by MsInspectFile::load(), SpecArrayFile::load(), and IsotopeWaveletTransform< PeakType >::mapSeeds2Features().

## ◆ setPeptideIdentifications()

void setPeptideIdentifications | ( | const std::vector< PeptideIdentification > & | peptides | ) |

sets the PeptideIdentification vector

## ◆ setQuality()

void setQuality | ( | QualityType | q | ) |

Set the overall quality.

## ◆ setWidth()

void setWidth | ( | WidthType | fwhm | ) |

Set the width of the feature (FWHM)

## Member Data Documentation

## ◆ charge_

ChargeType charge_

protected

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

## ◆ NamesOfAnnotationState

const std::string NamesOfAnnotationState[SIZE_OF_ANNOTATIONSTATE]

static

## ◆ peptides_

std::vector<PeptideIdentification> peptides_

protected

Peptide PeptideIdentifications belonging to the feature.

## ◆ quality_

QualityType quality_

protected

Overall quality measure of the feature.

## ◆ width_

WidthType width_

protected

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