ConsensusFeature#

class pyopenms.ConsensusFeature#

Bases: object

Cython implementation of _ConsensusFeature

Original C++ documentation is available here: – Inherits from [‘UniqueIdInterface’, ‘BaseFeature’]

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.

Get access to the underlying features through getFeatureList()

__init__()#

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: ConsensusFeature) → None

Overload:

__init__(self, in_0: int, in_1: Peak2D, in_2: int) → None

Overload:

__init__(self, in_0: int, in_1: BaseFeature) → None

Overload:

__init__(self, in_0: int, in_1: ConsensusFeature) → None

Methods

`__init__`	Overload:
`addRatio`(self, r)	Connects a ratio to the ConsensusFeature.
`clear`(self)
`clearMetaInfo`(self)	Removes all meta values
`clearUniqueId`(self)	Clear the unique id.
`computeConsensus`(self)	Computes and updates the consensus position, intensity, and charge
`computeDechargeConsensus`(self, in_0, in_1)	Computes the uncharged parent RT & mass, assuming the handles are charge variants
`computeMonoisotopicConsensus`(self)	Computes and updates the consensus position, intensity, and charge
`empty`(self)
`ensureUniqueId`(self)	Assigns a valid unique id, but only if the present one is invalid.
`getAnnotationState`(self)	State of peptide identifications attached to this feature.
`getCharge`(self)	Returns the charge state
`getFeatureList`(self)
`getIntensity`(self)	Returns the data point intensity (height)
`getKeys`(self, keys)	Fills the given vector with a list of all keys for which a value is set
`getMZ`(self)	Returns the m/z coordinate (index 1)
`getMetaValue`(self, in_0)	Returns the value corresponding to a string, or
`getPeptideIdentifications`(self)	Returns the PeptideIdentification vector
`getQuality`(self)	Returns the overall quality
`getRT`(self)	Returns the RT coordinate (index 0)
`getRatios`(self)	Get the ratio vector.
`getUniqueId`(self)	Returns the unique id
`getWidth`(self)	Returns the features width (full width at half max, FWHM)
`hasInvalidUniqueId`(self)	Returns whether the unique id is invalid.
`hasValidUniqueId`(self)	Returns whether the unique id is valid.
`insert`	Overload:
`isMetaEmpty`(self)	Returns if the MetaInfo is empty
`isValid`(self, unique_id)	Returns true if the unique_id is valid, false otherwise
`metaRegistry`(self)	Returns a reference to the MetaInfoRegistry
`metaValueExists`(self, in_0)	Returns whether an entry with the given name exists
`removeMetaValue`(self, in_0)	Removes the DataValue corresponding to name if it exists
`setCharge`(self, q)	Sets the charge state
`setIntensity`(self, in_0)	Returns the data point intensity (height)
`setMZ`(self, in_0)	Returns the m/z coordinate (index 1)
`setMetaValue`(self, in_0, in_1)	Sets the DataValue corresponding to a name
`setPeptideIdentifications`(self, peptides)	Sets the PeptideIdentification vector
`setQuality`(self, q)	Sets the overall quality
`setRT`(self, in_0)	Returns the RT coordinate (index 0)
`setRatios`(self, rs)	Connects the ratios to the ConsensusFeature.
`setUniqueId`(self, rhs)	Assigns a new, valid unique id.
`setWidth`(self, q)	Sets the width of the feature (FWHM)
`size`(self)

addRatio(self, r: Ratio) → None#: Connects a ratio to the ConsensusFeature.

clear(self) → None#

clearMetaInfo(self) → None#: Removes all meta values

clearUniqueId(self) → int#: Clear the unique id. The new unique id will be invalid. Returns 1 if the unique id was changed, 0 otherwise

computeConsensus(self) → None#: Computes and updates the consensus position, intensity, and charge

computeDechargeConsensus(self, in_0: FeatureMap, in_1: bool) → None#: Computes the uncharged parent RT & mass, assuming the handles are charge variants

computeMonoisotopicConsensus(self) → None#: Computes and updates the consensus position, intensity, and charge

empty(self) → bool#

ensureUniqueId(self) → int#: Assigns a valid unique id, but only if the present one is invalid. Returns 1 if the unique id was changed, 0 otherwise

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

getCharge(self) → int#: Returns the charge state

getFeatureList(self) → List[FeatureHandle]#

getIntensity(self) → float#: Returns the data point intensity (height)

getKeys(self, keys: List[bytes]) → None#: Fills the given vector with a list of all keys for which a value is set

getMZ(self) → float#: Returns the m/z coordinate (index 1)

getMetaValue(self, in_0: bytes | str | String) → int | float | bytes | str | List[int] | List[float] | List[bytes]#: Returns the value corresponding to a string, or

getPeptideIdentifications(self) → List[PeptideIdentification]#: Returns the PeptideIdentification vector

getQuality(self) → float#: Returns the overall quality

getRT(self) → float#: Returns the RT coordinate (index 0)

getRatios(self) → List[Ratio]#: Get the ratio vector.

getUniqueId(self) → int#: Returns the unique id

getWidth(self) → float#: Returns the features width (full width at half max, FWHM)

hasInvalidUniqueId(self) → int#: Returns whether the unique id is invalid. Returns 1 if the unique id is invalid, 0 otherwise

hasValidUniqueId(self) → int#: Returns whether the unique id is valid. Returns 1 if the unique id is valid, 0 otherwise

insert()#

Overload:

insert(self, map_idx: int, in_1: Peak2D, element_idx: int) → None

Overload:

insert(self, map_idx: int, in_1: BaseFeature) → None

Overload:

insert(self, map_idx: int, in_1: ConsensusFeature) → None

isMetaEmpty(self) → bool#: Returns if the MetaInfo is empty

isValid(self, unique_id: int) → bool#: Returns true if the unique_id is valid, false otherwise

metaRegistry(self) → MetaInfoRegistry#: Returns a reference to the MetaInfoRegistry

metaValueExists(self, in_0: bytes | str | String) → bool#: Returns whether an entry with the given name exists

removeMetaValue(self, in_0: bytes | str | String) → None#: Removes the DataValue corresponding to name if it exists

setCharge(self, q: int) → None#: Sets the charge state

setIntensity(self, in_0: float) → None#: Returns the data point intensity (height)

setMZ(self, in_0: float) → None#: Returns the m/z coordinate (index 1)

setMetaValue(self, in_0: bytes | str | String, in_1: int | float | bytes | str | List[int] | List[float] | List[bytes]) → None#: Sets the DataValue corresponding to a name

setPeptideIdentifications(self, peptides: List[PeptideIdentification]) → None#: Sets the PeptideIdentification vector

setQuality(self, q: float) → None#: Sets the overall quality

setRT(self, in_0: float) → None#: Returns the RT coordinate (index 0)

setRatios(self, rs: List[Ratio]) → None#: Connects the ratios to the ConsensusFeature.

setUniqueId(self, rhs: int) → None#: Assigns a new, valid unique id. Always returns 1

setWidth(self, q: float) → None#: Sets the width of the feature (FWHM)

size(self) → int#