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: Union[bytes, str, String]) → Union[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: Union[bytes, str, String]) → bool

Returns whether an entry with the given name exists

removeMetaValue(self, in_0: Union[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: Union[bytes, str, String], in_1: Union[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