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| ConsensusFeature () |
| Default constructor. More...
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| ConsensusFeature (const ConsensusFeature &rhs)=default |
| Copy constructor. More...
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| ConsensusFeature (ConsensusFeature &&rhs)=default |
| Move constructor. More...
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| ConsensusFeature (const BaseFeature &feature) |
| Constructor from basic feature. More...
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| ConsensusFeature (UInt64 map_index, const Peak2D &element, UInt64 element_index) |
| Constructor with map and element index for a singleton consensus feature. More...
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| ConsensusFeature (UInt64 map_index, const BaseFeature &element) |
| Constructor with map index for a singleton consensus feature. More...
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ConsensusFeature & | operator= (const ConsensusFeature &rhs)=default |
| Assignment operator. More...
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ConsensusFeature & | operator= (ConsensusFeature &&rhs)=default |
| Move Assignment operator. More...
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| ~ConsensusFeature () override |
| Destructor. More...
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void | insert (const ConsensusFeature &cf) |
| Adds all feature handles (of the CF) into the consensus feature. More...
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void | insert (ConsensusFeature &&cf) |
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void | insert (const FeatureHandle &handle) |
| Adds an feature handle into the consensus feature. More...
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void | insert (FeatureHandle &&handle) |
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void | insert (const HandleSetType &handle_set) |
| Adds all feature handles in handle_set to this consensus feature. More...
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void | insert (HandleSetType &&handle_set) |
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void | insert (UInt64 map_index, const Peak2D &element, UInt64 element_index) |
| Creates a FeatureHandle and adds it. More...
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void | insert (UInt64 map_index, const BaseFeature &element) |
| Creates a FeatureHandle and adds it. More...
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const HandleSetType & | getFeatures () const |
| Non-mutable access to the contained feature handles. More...
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std::vector< FeatureHandle > | getFeatureList () const |
| Mutable access to a copy of the contained feature handles. More...
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void | setFeatures (HandleSetType h) |
| Set the feature set to a new one. More...
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DRange< 2 > | getPositionRange () const |
| Returns the position range of the contained elements. More...
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DRange< 1 > | getIntensityRange () const |
| Returns the intensity range of the contained elements. More...
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void | computeConsensus () |
| Computes and updates the consensus position, intensity, and charge. More...
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void | computeMonoisotopicConsensus () |
| Computes and updates the consensus position, intensity, and charge. More...
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void | computeDechargeConsensus (const FeatureMap &fm, bool intensity_weighted_averaging=false) |
| Computes the uncharged parent RT & mass, assuming the handles are charge variants. More...
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void | addRatio (const Ratio &r) |
| Add a ratio. More...
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void | setRatios (std::vector< Ratio > &rs) |
| Add a ratio vector. More...
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std::vector< Ratio > | getRatios () const |
| Get the ratio vector. More...
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std::vector< Ratio > & | getRatios () |
| Get the ratio vector. More...
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WidthType | getWidth () const |
| Non-mutable access to the features width (full width at half max, FWHM) More...
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void | setWidth (WidthType fwhm) |
| Set the width of the feature (FWHM) More...
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const ChargeType & | getCharge () const |
| Non-mutable access to charge state. More...
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void | setCharge (const ChargeType &ch) |
| Set charge state. More...
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BaseFeature & | operator= (const BaseFeature &rhs)=default |
| Assignment operator. More...
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BaseFeature & | operator= (BaseFeature &&rhs) &=default |
| Move Assignment operator. More...
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bool | operator== (const BaseFeature &rhs) const |
| Equality operator. More...
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bool | operator!= (const BaseFeature &rhs) const |
| Inequality operator. More...
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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...
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| BaseFeature () |
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| BaseFeature (const BaseFeature &feature)=default |
| Copy constructor. More...
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| BaseFeature (BaseFeature &&feature) noexcept |
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| BaseFeature (const BaseFeature &rhs, UInt64 map_index) |
| Copy constructor with a new map_index. More...
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| BaseFeature (const Peak2D &point) |
| Constructor from raw data point. More...
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| BaseFeature (const RichPeak2D &point) |
| Constructor from raw data point with meta information. More...
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| BaseFeature (const FeatureHandle &fh) |
| Constructor from a featurehandle. More...
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| ~BaseFeature () override |
| Destructor. More...
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QualityType | getQuality () const |
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void | setQuality (QualityType q) |
| Set the overall quality. More...
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const std::vector< PeptideIdentification > & | getPeptideIdentifications () const |
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std::vector< PeptideIdentification > & | getPeptideIdentifications () |
| returns a mutable reference to the PeptideIdentification vector More...
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void | setPeptideIdentifications (const std::vector< PeptideIdentification > &peptides) |
| sets the PeptideIdentification vector More...
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void | sortPeptideIdentifications () |
| sorts PeptideIdentifications, assuming they have the same scoreType. More...
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bool | hasPrimaryID () const |
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const IdentificationData::IdentifiedMolecule & | getPrimaryID () const |
| Return the primary ID (peptide, RNA, compound) assigned to this feature. More...
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void | clearPrimaryID () |
| clear any primary ID that was assigned More...
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void | setPrimaryID (const IdentificationData::IdentifiedMolecule &id) |
| set the primary ID (peptide, RNA, compound) for this feature More...
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const std::set< IdentificationData::ObservationMatchRef > & | getIDMatches () const |
| immutable access to the set of matches (e.g. PSMs) with IDs for this feature More...
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std::set< IdentificationData::ObservationMatchRef > & | getIDMatches () |
| mutable access to the set of matches (e.g. PSMs) with IDs for this feature More...
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void | addIDMatch (IdentificationData::ObservationMatchRef ref) |
| add an ID match (e.g. PSM) for this feature More...
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void | updateIDReferences (const IdentificationData::RefTranslator &trans) |
| Update ID references (primary ID, matches) for this feature. More...
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| RichPeak2D () |
| Default constructor. More...
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| RichPeak2D (const RichPeak2D &p)=default |
| Copy constructor. More...
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| RichPeak2D (const Peak2D &p) |
| Constructor from Peak2D. More...
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| RichPeak2D (const PositionType &pos, const IntensityType in) |
| Member constructor. More...
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| RichPeak2D (RichPeak2D &&p)=default |
| Move constructor. More...
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| ~RichPeak2D () override |
| Destructor. More...
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RichPeak2D & | operator= (const RichPeak2D &rhs)=default |
| Assignment operator. More...
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RichPeak2D & | operator= (RichPeak2D &&rhs) &=default |
| Move Assignment operator. More...
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RichPeak2D & | operator= (const Peak2D &rhs) |
| Assignment operator. More...
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bool | operator== (const RichPeak2D &rhs) const |
| Equality operator. More...
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bool | operator!= (const RichPeak2D &rhs) const |
| Equality operator. More...
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Peak2D & | operator= (const Peak2D &rhs)=default |
| Assignment operator. More...
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Peak2D & | operator= (Peak2D &&) &=default |
| Move assignment operator. More...
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bool | operator== (const Peak2D &rhs) const |
| Equality operator. More...
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bool | operator!= (const Peak2D &rhs) const |
| Equality operator. More...
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| Peak2D () |
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| Peak2D (const PositionType &pos, const IntensityType in) |
| Member constructor. More...
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| Peak2D (const Peak2D &p)=default |
| Copy constructor. More...
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| Peak2D (Peak2D &&)=default |
| Move constructor. More...
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| ~Peak2D () |
| Destructor. More...
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IntensityType | getIntensity () const |
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void | setIntensity (IntensityType intensity) |
| Sets data point intensity (height) More...
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PositionType const & | getPosition () const |
| Non-mutable access to the position. More...
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PositionType & | getPosition () |
| Mutable access to the position. More...
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void | setPosition (const PositionType &position) |
| Mutable access to the position. More...
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CoordinateType | getMZ () const |
| Returns the m/z coordinate (index 1) More...
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void | setMZ (CoordinateType coordinate) |
| Mutable access to the m/z coordinate (index 1) More...
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CoordinateType | getRT () const |
| Returns the RT coordinate (index 0) More...
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void | setRT (CoordinateType coordinate) |
| Mutable access to the RT coordinate (index 0) More...
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| MetaInfoInterface () |
| Constructor. More...
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| MetaInfoInterface (const MetaInfoInterface &rhs) |
| Copy constructor. More...
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| MetaInfoInterface (MetaInfoInterface &&) noexcept |
| Move constructor. More...
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| ~MetaInfoInterface () |
| Destructor. More...
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MetaInfoInterface & | operator= (const MetaInfoInterface &rhs) |
| Assignment operator. More...
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MetaInfoInterface & | operator= (MetaInfoInterface &&) noexcept |
| Move assignment operator. More...
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void | swap (MetaInfoInterface &rhs) |
| Swap contents. More...
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bool | operator== (const MetaInfoInterface &rhs) const |
| Equality operator. More...
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bool | operator!= (const MetaInfoInterface &rhs) const |
| Equality operator. More...
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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...
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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...
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bool | metaValueExists (const String &name) const |
| Returns whether an entry with the given name exists. More...
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bool | metaValueExists (UInt index) const |
| Returns whether an entry with the given index exists. More...
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void | setMetaValue (const String &name, const DataValue &value) |
| Sets the DataValue corresponding to a name. More...
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void | setMetaValue (UInt index, const DataValue &value) |
| Sets the DataValue corresponding to an index. More...
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void | removeMetaValue (const String &name) |
| Removes the DataValue corresponding to name if it exists. More...
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void | removeMetaValue (UInt index) |
| Removes the DataValue corresponding to index if it exists. More...
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void | addMetaValues (const MetaInfoInterface &from) |
| function to copy all meta values from one object to this one More...
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void | getKeys (std::vector< String > &keys) const |
| Fills the given vector with a list of all keys for which a value is set. More...
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void | getKeys (std::vector< UInt > &keys) const |
| Fills the given vector with a list of all keys for which a value is set. More...
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bool | isMetaEmpty () const |
| Returns if the MetaInfo is empty. More...
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void | clearMetaInfo () |
| Removes all meta values. More...
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| UniqueIdInterface () |
| Default constructor - the unique id will be invalid More...
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| UniqueIdInterface (const UniqueIdInterface &rhs)=default |
| Copy constructor - copies the unique id. More...
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| UniqueIdInterface (UniqueIdInterface &&rhs)=default |
| Move constructor. More...
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UniqueIdInterface & | operator= (UniqueIdInterface const &rhs)=default |
| Assignment operator - copies the unique id. More...
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UniqueIdInterface & | operator= (UniqueIdInterface &&) &=default |
| Move Assignment operator - copies the unique id. More...
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virtual | ~UniqueIdInterface ()=default |
| Destructor. More...
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bool | operator== (UniqueIdInterface const &rhs) const |
| Equality comparison operator - the unique ids must be equal (!) More...
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UInt64 | getUniqueId () const |
| Non-mutable access to unique id - returns the unique id. More...
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Size | clearUniqueId () |
| Clear the unique id. The new unique id will be invalid. Returns 1 if the unique id was changed, 0 otherwise. More...
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void | swap (UniqueIdInterface &from) |
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Size | hasValidUniqueId () const |
| Returns whether the unique id is valid. Returns 1 if the unique id is valid, 0 otherwise. More...
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Size | hasInvalidUniqueId () const |
| Returns whether the unique id is invalid. Returns 1 if the unique id is invalid, 0 otherwise. More...
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Size | setUniqueId () |
| Assigns a new, valid unique id. Always returns 1. More...
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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...
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void | setUniqueId (UInt64 rhs) |
| Assigns the given unique id. More...
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void | setUniqueId (const String &rhs) |
| Mutable access to unique id. More...
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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