ConsensusFeature

class pyopenms.dataframes.ConsensusFeature

Bases: object

Cython implementation of _ConsensusFeature

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1ConsensusFeature.html

– Inherits from [‘UniqueIdInterface’, ‘BaseFeature’]

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. —– Get access to the underlying features through getFeatureList()

__init__()

• Cython signature: void ConsensusFeature()

• Cython signature: void ConsensusFeature(ConsensusFeature &)

• Cython signature: void ConsensusFeature(uint64_t, Peak2D, uint64_t)

• Cython signature: void ConsensusFeature(uint64_t, BaseFeature)

• Cython signature: void ConsensusFeature(uint64_t, ConsensusFeature)

Methods

__init__	Cython signature: void ConsensusFeature()
addRatio	Cython signature: void addRatio(Ratio r) Connects a ratio to the ConsensusFeature.
clear	Cython signature: void clear()
clearMetaInfo	Cython signature: void clearMetaInfo() Removes all meta values
clearUniqueId	Cython signature: size_t clearUniqueId() Clear the unique id.
computeConsensus	Cython signature: void computeConsensus() Computes and updates the consensus position, intensity, and charge
computeDechargeConsensus	Cython signature: void computeDechargeConsensus(FeatureMap, bool) Computes the uncharged parent RT & mass, assuming the handles are charge variants
computeMonoisotopicConsensus	Cython signature: void computeMonoisotopicConsensus() Computes and updates the consensus position, intensity, and charge
empty	Cython signature: bool empty()
ensureUniqueId	Cython signature: size_t ensureUniqueId() Assigns a valid unique id, but only if the present one is invalid.
getAnnotationState	Cython signature: AnnotationState getAnnotationState() State of peptide identifications attached to this feature.
getCharge	Cython signature: int getCharge() Returns the charge state
getFeatureList	Cython signature: libcpp_vector[FeatureHandle] getFeatureList()
getIntensity	Cython signature: float getIntensity() Returns the data point intensity (height)
getKeys	Cython signature: void getKeys(libcpp_vector[String] & keys) Fills the given vector with a list of all keys for which a value is set
getMZ	Cython signature: double getMZ() Returns the m/z coordinate (index 1)
getMetaValue	Cython signature: DataValue getMetaValue(String) Returns the value corresponding to a string, or
getPeptideIdentifications	Cython signature: libcpp_vector[PeptideIdentification] getPeptideIdentifications() Returns the PeptideIdentification vector
getQuality	Cython signature: float getQuality() Returns the overall quality
getRT	Cython signature: double getRT() Returns the RT coordinate (index 0)
getRatios	Cython signature: libcpp_vector[Ratio] getRatios() Get the ratio vector.
getUniqueId	Cython signature: size_t getUniqueId() Returns the unique id
getWidth	Cython signature: float getWidth() Returns the features width (full width at half max, FWHM)
hasInvalidUniqueId	Cython signature: size_t hasInvalidUniqueId() Returns whether the unique id is invalid.
hasValidUniqueId	Cython signature: size_t hasValidUniqueId() Returns whether the unique id is valid.
insert	Cython signature: void insert(uint64_t map_idx, Peak2D, uint64_t element_idx)
isMetaEmpty	Cython signature: bool isMetaEmpty() Returns if the MetaInfo is empty
isValid	Cython signature: bool isValid(uint64_t unique_id) Returns true if the unique_id is valid, false otherwise
metaRegistry	Cython signature: MetaInfoRegistry metaRegistry() Returns a reference to the MetaInfoRegistry
metaValueExists	Cython signature: bool metaValueExists(String) Returns whether an entry with the given name exists
removeMetaValue	Cython signature: void removeMetaValue(String) Removes the DataValue corresponding to name if it exists
setCharge	Cython signature: void setCharge(int q) Sets the charge state
setIntensity	Cython signature: void setIntensity(float) Returns the data point intensity (height)
setMZ	Cython signature: void setMZ(double) Returns the m/z coordinate (index 1)
setMetaValue	Cython signature: void setMetaValue(String, DataValue) Sets the DataValue corresponding to a name
setPeptideIdentifications	Cython signature: void setPeptideIdentifications(libcpp_vector[PeptideIdentification] & peptides) Sets the PeptideIdentification vector
setQuality	Cython signature: void setQuality(float q) Sets the overall quality
setRT	Cython signature: void setRT(double) Returns the RT coordinate (index 0)
setRatios	Cython signature: void setRatios(libcpp_vector[Ratio] rs) Connects the ratios to the ConsensusFeature.
setUniqueId	Cython signature: void setUniqueId(uint64_t rhs) Assigns a new, valid unique id.
setWidth	Cython signature: void setWidth(float q) Sets the width of the feature (FWHM)
size	Cython signature: size_t size()

addRatio()

Cython signature: void addRatio(Ratio r) Connects a ratio to the ConsensusFeature.

clear()

Cython signature: void clear()

clearMetaInfo()

Cython signature: void clearMetaInfo() Removes all meta values

clearUniqueId()

Cython signature: size_t clearUniqueId() Clear the unique id. The new unique id will be invalid. Returns 1 if the unique id was changed, 0 otherwise

computeConsensus()

Cython signature: void computeConsensus() Computes and updates the consensus position, intensity, and charge

computeDechargeConsensus()

Cython signature: void computeDechargeConsensus(FeatureMap, bool) Computes the uncharged parent RT & mass, assuming the handles are charge variants

computeMonoisotopicConsensus()

Cython signature: void computeMonoisotopicConsensus() Computes and updates the consensus position, intensity, and charge

empty()

Cython signature: bool empty()

ensureUniqueId()

Cython signature: size_t ensureUniqueId() Assigns a valid unique id, but only if the present one is invalid. Returns 1 if the unique id was changed, 0 otherwise

getAnnotationState()

Cython signature: AnnotationState getAnnotationState() State of peptide identifications attached to this feature. If one ID has multiple hits, the output depends on the top-hit only

getCharge()

Cython signature: int getCharge() Returns the charge state

getFeatureList()

Cython signature: libcpp_vector[FeatureHandle] getFeatureList()

getIntensity()

Cython signature: float getIntensity() Returns the data point intensity (height)

getKeys()

Cython signature: void getKeys(libcpp_vector[String] & keys) Fills the given vector with a list of all keys for which a value is set

getMZ()

Cython signature: double getMZ() Returns the m/z coordinate (index 1)

getMetaValue()

Cython signature: DataValue getMetaValue(String) Returns the value corresponding to a string, or

getPeptideIdentifications()

Cython signature: libcpp_vector[PeptideIdentification] getPeptideIdentifications() Returns the PeptideIdentification vector

getQuality()

Cython signature: float getQuality() Returns the overall quality

getRT()

Cython signature: double getRT() Returns the RT coordinate (index 0)

getRatios()

Cython signature: libcpp_vector[Ratio] getRatios() Get the ratio vector.

getUniqueId()

Cython signature: size_t getUniqueId() Returns the unique id

getWidth()

Cython signature: float getWidth() Returns the features width (full width at half max, FWHM)

hasInvalidUniqueId()

Cython signature: size_t hasInvalidUniqueId() Returns whether the unique id is invalid. Returns 1 if the unique id is invalid, 0 otherwise

hasValidUniqueId()

Cython signature: size_t hasValidUniqueId() Returns whether the unique id is valid. Returns 1 if the unique id is valid, 0 otherwise

insert()

• Cython signature: void insert(uint64_t map_idx, Peak2D, uint64_t element_idx)

• Cython signature: void insert(uint64_t map_idx, BaseFeature)

• Cython signature: void insert(uint64_t map_idx, ConsensusFeature)

isMetaEmpty()

Cython signature: bool isMetaEmpty() Returns if the MetaInfo is empty

isValid()

Cython signature: bool isValid(uint64_t unique_id) Returns true if the unique_id is valid, false otherwise

metaRegistry()

Cython signature: MetaInfoRegistry metaRegistry() Returns a reference to the MetaInfoRegistry

metaValueExists()

Cython signature: bool metaValueExists(String) Returns whether an entry with the given name exists

removeMetaValue()

Cython signature: void removeMetaValue(String) Removes the DataValue corresponding to name if it exists

setCharge()

Cython signature: void setCharge(int q) Sets the charge state

setIntensity()

Cython signature: void setIntensity(float) Returns the data point intensity (height)

setMZ()

Cython signature: void setMZ(double) Returns the m/z coordinate (index 1)

setMetaValue()

Cython signature: void setMetaValue(String, DataValue) Sets the DataValue corresponding to a name

setPeptideIdentifications()

Cython signature: void setPeptideIdentifications(libcpp_vector[PeptideIdentification] & peptides) Sets the PeptideIdentification vector

setQuality()

Cython signature: void setQuality(float q) Sets the overall quality

setRT()

Cython signature: void setRT(double) Returns the RT coordinate (index 0)

setRatios()

Cython signature: void setRatios(libcpp_vector[Ratio] rs) Connects the ratios to the ConsensusFeature.

setUniqueId()

Cython signature: void setUniqueId(uint64_t rhs) Assigns a new, valid unique id. Always returns 1

setWidth()

Cython signature: void setWidth(float q) Sets the width of the feature (FWHM)

size()

Cython signature: size_t size()