Feature#

class pyopenms.Feature#

Bases: object

Cython implementation of _Feature

Original C++ documentation is available here

– Inherits from [‘UniqueIdInterface’, ‘RichPeak2D’]

An LC-MS feature

The Feature class is used to describe the two-dimensional signal caused by an analyte. It can store a charge state and a list of peptide identifications (for peptides). The area occupied by the Feature in the LC-MS data set is represented by a list of convex hulls (one for each isotopic peak). There is also a convex hull for the entire Feature. The model description can store the parameters of a two-dimensional theoretical model of the underlying signal in LC-MS. Currently, non-peptide compounds are also represented as features

__init__()#

Overload:

__init__(self) None

Overload:

__init__(self, in_0: Feature) None

Methods

__init__

Overload:

clearMetaInfo(self)

Removes all meta values

clearUniqueId(self)

Clear the unique id.

encloses(self, rt, mz)

Returns if the mass trace convex hulls of the feature enclose the position specified by rt and mz

ensureUniqueId(self)

Assigns a valid unique id, but only if the present one is invalid.

getAnnotationState(self)

getCharge(self)

getConvexHull(self)

getConvexHulls(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

getOverallQuality(self)

Model and quality methods

getPeptideIdentifications(self)

Returns a reference to the PeptideIdentification vector

getQuality(self, index)

Returns the quality in dimension c

getRT(self)

Returns the RT coordinate (index 0)

getSubordinates(self)

Returns the subordinate features

getUniqueId(self)

Returns the unique id

getWidth(self)

hasInvalidUniqueId(self)

Returns whether the unique id is invalid.

hasValidUniqueId(self)

Returns whether the unique id is valid.

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)

setConvexHulls(self, in_0)

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

setOverallQuality(self, q)

Sets the overall quality

setPeptideIdentifications(self, peptides)

Sets the PeptideIdentification vector

setQuality(self, index, q)

Sets the quality in dimension c

setRT(self, in_0)

Returns the RT coordinate (index 0)

setSubordinates(self, in_0)

Returns the subordinate features

setUniqueId(self, rhs)

Assigns a new, valid unique id.

setWidth(self, q)

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

encloses(self, rt: float, mz: float) bool#

Returns if the mass trace convex hulls of the feature enclose the position specified by rt and mz

Parameters:
  • rt – Sequence to digest

  • mz – Digestion products

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#
getCharge(self) int#
getConvexHull(self) ConvexHull2D#
getConvexHulls(self) List[ConvexHull2D]#
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

getOverallQuality(self) float#

Model and quality methods

getPeptideIdentifications(self) List[PeptideIdentification]#

Returns a reference to the PeptideIdentification vector

getQuality(self, index: int) float#

Returns the quality in dimension c

getRT(self) float#

Returns the RT coordinate (index 0)

getSubordinates(self) List[Feature]#

Returns the subordinate features

getUniqueId(self) int#

Returns the unique id

getWidth(self) float#
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

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#
setConvexHulls(self, in_0: List[ConvexHull2D]) None#
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

setOverallQuality(self, q: float) None#

Sets the overall quality

setPeptideIdentifications(self, peptides: List[PeptideIdentification]) None#

Sets the PeptideIdentification vector

setQuality(self, index: int, q: float) None#

Sets the quality in dimension c

setRT(self, in_0: float) None#

Returns the RT coordinate (index 0)

setSubordinates(self, in_0: List[Feature]) None#

Returns the subordinate features

setUniqueId(self, rhs: int) None#

Assigns a new, valid unique id. Always returns 1

setWidth(self, q: float) None#