|
|
| 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...
|
|
ConsensusFeature & | operator= (const ConsensusFeature &rhs)=default |
| Assignment operator. More...
|
|
ConsensusFeature & | operator= (ConsensusFeature &&rhs)=default |
| Move Assignment operator. More...
|
|
| ~ConsensusFeature () override |
| Destructor. More...
|
|
|
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 HandleSetType & | getFeatures () const |
| Non-mutable access to the contained feature handles. More...
|
|
std::vector< FeatureHandle > | getFeatureList () 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...
|
|
|
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< Ratio > | getRatios () const |
| Get the ratio vector. More...
|
|
std::vector< Ratio > & | getRatios () |
| Get the ratio vector. 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...
|
|
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...
|
|
| 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...
|
|
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...
|
|
const PositionType & | 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...
|
|
| 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...
|
|
| 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...
|
|
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