MRMFeature

class pyopenms.MRMFeature

Bases: object

Cython implementation of _MRMFeature

Original C++ documentation is available here

– Inherits from [‘Feature’]

__init__()

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: MRMFeature) → None

Methods

__init__	Overload:
addFeature(self, f, key)	Adds an feature from a single chromatogram into the feature
addPrecursorFeature(self, f, key)	Adds a precursor feature from a single chromatogram into the feature
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)
getFeature(self, key)	Returns a specified feature
getFeatureIDs(self, result)	Returns a list of IDs of available features
getFeatures(self)	Returns all the features
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
getPrecursorFeature(self, key)	Returns a specified precursor feature
getPrecursorFeatureIDs(self, result)	Returns a list of IDs of available precursor features
getQuality(self, index)	Returns the quality in dimension c
getRT(self)	Returns the RT coordinate (index 0)
getScores(self)	Returns all peakgroup scores
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)
setScores(self, s)	Sets all peakgroup scores
setSubordinates(self, in_0)	Returns the subordinate features
setUniqueId(self, rhs)	Assigns a new, valid unique id.
setWidth(self, q)

addFeature(self, f: Feature, key: Union[bytes, str, String]) → None

Adds an feature from a single chromatogram into the feature

addPrecursorFeature(self, f: Feature, key: Union[bytes, str, String]) → None

Adds a precursor feature from a single chromatogram into the feature

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]

getFeature(self, key: Union[bytes, str, String]) → Feature

Returns a specified feature

getFeatureIDs(self, result: List[bytes]) → None

Returns a list of IDs of available features

getFeatures(self) → List[Feature]

Returns all the features

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

getOverallQuality(self) → float

Model and quality methods

getPeptideIdentifications(self) → List[PeptideIdentification]

Returns a reference to the PeptideIdentification vector

getPrecursorFeature(self, key: Union[bytes, str, String]) → Feature

Returns a specified precursor feature

getPrecursorFeatureIDs(self, result: List[bytes]) → None

Returns a list of IDs of available precursor features

getQuality(self, index: int) → float

Returns the quality in dimension c

getRT(self) → float

Returns the RT coordinate (index 0)

getScores(self) → OpenSwath_Scores

Returns all peakgroup scores

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: 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

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: 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

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)

setScores(self, s: OpenSwath_Scores) → None

Sets all peakgroup scores

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