| OpenMS 2.5.0

Protected Attributes | List of all members
MRMFeature Class Reference

A multi-chromatogram MRM feature. More...

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

Inheritance diagram for MRMFeature:

## Public Types

typedef std::vector< Feature > | FeatureListType
| Type definitions. More...
Public Types inherited from Feature
typedef QualityLess | OverallQualityLess
| Compare by quality. More...
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
| MRMFeature ()
| Default constructor. More...
| MRMFeature (const MRMFeature &rhs)
| Copy constructor. More...
| MRMFeature (MRMFeature &&rhs)=default
| Move constructor. More...
MRMFeature & | operator= (const MRMFeature &rhs)
| Assignment operator. More...
MRMFeature & | operator= (MRMFeature &&) &=default
| Move assignment operator. More...
| ~MRMFeature () override
| Destructor. More...
Accessors
const OpenSwath_Scores & | getScores () const
| get all peakgroup scores More...
OpenSwath_Scores & | getScores ()
| get all peakgroup scores More...
Feature & | getFeature (const String &key)
| get a specified feature More...
const Feature & | getFeature (const String &key) const
| get a specified feature (const) More...
void | setScores (const OpenSwath_Scores &scores)
| set all peakgroup scores More...
void | addScore (const String &score_name, double score)
| set a single peakgroup score More...
void | addFeature (const Feature &feature, const String &key)
| Adds an feature from a single chromatogram into the feature. More...
void | addFeature (Feature &&feature, const String &key)
const std::vector< Feature > & | getFeatures () const
| get a list of features More...
void | getFeatureIDs (std::vector< String > &result) const
| get a list of IDs of available features More...
void | addPrecursorFeature (const Feature &feature, const String &key)
| Adds a precursor feature from a single chromatogram into the feature. More...
void | addPrecursorFeature (Feature &&feature, const String &key)
void | getPrecursorFeatureIDs (std::vector< String > &result) const
| get a list of IDs of available precursor features More...
Feature & | getPrecursorFeature (String key)
| get a specified precursor feature More...
const Feature & | getPrecursorFeature (String key) const
| get a specified precursor feature (const) More...
void | IDScoresAsMetaValue (bool decoy, const OpenSwath_Ind_Scores &idscores)
Public Member Functions inherited from Feature
Feature & | operator= (const Feature &rhs)
| Assignment operator. More...
Feature & | operator= (Feature &&) &noexcept
| Move assignment operator. More...
bool | operator== (const Feature &rhs) const
| Equality operator. More...
const std::vector< Feature > & | getSubordinates () const
| immutable access to subordinate features More...
std::vector< Feature > & | getSubordinates ()
| mutable access to subordinate features More...
void | setSubordinates (const std::vector< Feature > &rhs)
| mutable access to subordinate features More...
template<typename Type >
Size | applyMemberFunction (Size(Type::*member_function)())
| Applies a member function of Type to the feature (including subordinates). The returned values are accumulated. More...
template<typename Type >
Size | applyMemberFunction (Size(Type::*member_function)() const) const
| The "const" variant. More...
| Feature ()
| Default constructor. More...
| Feature (const Feature &feature)
| Copy constructor. More...
| Feature (Feature &&) noexcept
| Move constructor. More...
| ~Feature () override
| Destructor. More...
const std::vector< ConvexHull2D > & | getConvexHulls () const
| Non-mutable access to the convex hulls. More...
std::vector< ConvexHull2D > & | getConvexHulls ()
| Mutable access to the convex hulls of single mass traces. More...
void | setConvexHulls (const std::vector< ConvexHull2D > &hulls)
| Set the convex hulls of single mass traces. More...
ConvexHull2D & | getConvexHull () const
| Returns the overall convex hull of the feature (calculated from the convex hulls of the mass traces) More...
bool | encloses (double rt, double mz) const
| Returns if the mass trace convex hulls of the feature enclose the position specified by `rt` and `mz`. More...
QualityType | getOverallQuality () const
| Non-mutable access to the overall quality. More...
void | setOverallQuality (QualityType q)
| Set the overall quality. More...
QualityType | getQuality (Size index) const
| Non-mutable access to the quality in dimension c. More...
void | setQuality (Size index, QualityType q)
| Set the quality in dimension c. More...
Public Member Functions inherited from BaseFeature
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...
| 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...
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

FeatureListType | features_
FeatureListType | precursor_features_
OpenSwath_Scores | pg_scores_
| peak group scores More...
std::map< String, int > | feature_map_
| map native ids to the features More...
std::map< String, int > | precursor_feature_map_
| map native ids to the precursor features More...
Protected Attributes inherited from Feature
QualityType | qualities_ [2]
| Quality measures for each dimension. More...
std::vector< ConvexHull2D > | convex_hulls_
| Array of convex hulls (one for each mass trace) More...
bool | convex_hulls_modified_
| Flag that indicates if the overall convex hull needs to be recomputed (i.e. mass trace convex hulls were modified) More...
ConvexHull2D | convex_hull_
| Overall convex hull of the feature. More...
std::vector< Feature > | subordinates_
| subordinate features (e.g. features that represent alternative explanations, usually with lower quality) 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< 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...

## 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 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...
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...
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 multi-chromatogram MRM feature.

An MRM feature contains corresponding features in multiple chromatograms, it is thus a representation of a peak group. The individual features in each chromatogram are represented by OpenMS Features.

## Member Typedef Documentation

## ◆ FeatureListType

typedef std::vector<Feature> FeatureListType

Type definitions.

Feature list type

## Constructor & Destructor Documentation

## ◆ MRMFeature() [1/3]

MRMFeature | ( |  | ) |

Default constructor.

## ◆ MRMFeature() [2/3]

MRMFeature | ( | const MRMFeature & | rhs | ) |

Copy constructor.

## ◆ MRMFeature() [3/3]

MRMFeature | ( | MRMFeature && | rhs | ) |

default

Move constructor.

## ◆ ~MRMFeature()

~MRMFeature | ( |  | ) |

override

Destructor.

## Member Function Documentation

## ◆ addFeature() [1/2]

void addFeature | ( | const Feature & | feature,
|  | const String & | key
| ) |  |

Adds an feature from a single chromatogram into the feature.

Referenced by MRMTransitionGroupPicker::pickFragmentChromatograms(), and MRMTransitionGroup< SpectrumT, TransitionT >::subset().

## ◆ addFeature() [2/2]

void addFeature | ( | Feature && | feature,
|  | const String & | key
| ) |  |

## ◆ addPrecursorFeature() [1/2]

void addPrecursorFeature | ( | const Feature & | feature,
|  | const String & | key
| ) |  |

Adds a precursor feature from a single chromatogram into the feature.

Referenced by MRMTransitionGroupPicker::pickPrecursorChromatograms(), and MRMTransitionGroup< SpectrumT, TransitionT >::subset().

## ◆ addPrecursorFeature() [2/2]

void addPrecursorFeature | ( | Feature && | feature,
|  | const String & | key
| ) |  |

## ◆ addScore()

void addScore | ( | const String & | score_name,
|  | double | score
| ) |  |

set a single peakgroup score

## ◆ getFeature() [1/2]

Feature& getFeature | ( | const String & | key | ) |

get a specified feature

Referenced by EmgScoring::calcElutionFitScore().

## ◆ getFeature() [2/2]

const Feature& getFeature | ( | const String & | key | ) | const

get a specified feature (const)

## ◆ getFeatureIDs()

void getFeatureIDs | ( | std::vector< String > & | result | ) | const

get a list of IDs of available features

## ◆ getFeatures()

const std::vector<Feature>& getFeatures | ( |  | ) | const

get a list of features

## ◆ getPrecursorFeature() [1/2]

Feature& getPrecursorFeature | ( | String | key | ) |

get a specified precursor feature

## ◆ getPrecursorFeature() [2/2]

const Feature& getPrecursorFeature | ( | String | key | ) | const

get a specified precursor feature (const)

## ◆ getPrecursorFeatureIDs()

void getPrecursorFeatureIDs | ( | std::vector< String > & | result | ) | const

get a list of IDs of available precursor features

## ◆ getScores() [1/2]

const OpenSwath_Scores& getScores | ( |  | ) | const

get all peakgroup scores

## ◆ getScores() [2/2]

OpenSwath_Scores& getScores | ( |  | ) |

get all peakgroup scores

## ◆ IDScoresAsMetaValue()

void IDScoresAsMetaValue | ( | bool | decoy,
|  | const OpenSwath_Ind_Scores & | idscores
| ) |  |

## ◆ operator=() [1/2]

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

Assignment operator.

## ◆ operator=() [2/2]

MRMFeature& operator= | ( | MRMFeature && |  | ) | &

default

Move assignment operator.

## ◆ setScores()

void setScores | ( | const OpenSwath_Scores & | scores | ) |

set all peakgroup scores

## Member Data Documentation

## ◆ feature_map_

std::map<String, int> feature_map_

protected

map native ids to the features

## ◆ features_

FeatureListType features_

protected

## ◆ pg_scores_

OpenSwath_Scores pg_scores_

protected

peak group scores

## ◆ precursor_feature_map_

std::map<String, int> precursor_feature_map_

protected

map native ids to the precursor features

## ◆ precursor_features_

FeatureListType precursor_features_

protected