MRMFeature#

class pyopenms.MRMFeature#

Bases: object

Cython implementation of _MRMFeature

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1MRMFeature.html: – Inherits from [‘Feature’]

__init__()#

Cython signature: void MRMFeature()
Cython signature: void MRMFeature(MRMFeature &)

Methods

`__init__`	Cython signature: void MRMFeature()
`addFeature`	Cython signature: void addFeature(Feature & f, String key) Adds an feature from a single chromatogram into the feature
`addPrecursorFeature`	Cython signature: void addPrecursorFeature(Feature & f, String key) Adds a precursor feature from a single chromatogram into the feature
`clearMetaInfo`	Cython signature: void clearMetaInfo() Removes all meta values
`clearUniqueId`	Cython signature: size_t clearUniqueId() Clear the unique id.
`encloses`	Cython signature: bool encloses(double rt, double mz)
`ensureUniqueId`	Cython signature: size_t ensureUniqueId() Assigns a valid unique id, but only if the present one is invalid.
`getAnnotationState`	Cython signature: AnnotationState getAnnotationState()
`getCharge`	Cython signature: int getCharge()
`getConvexHull`	Cython signature: ConvexHull2D getConvexHull()
`getConvexHulls`	Cython signature: libcpp_vector[ConvexHull2D] getConvexHulls()
`getFeature`	Cython signature: Feature getFeature(String key) Returns a specified feature
`getFeatureIDs`	Cython signature: void getFeatureIDs(libcpp_vector[String] & result) Returns a list of IDs of available features
`getFeatures`	Cython signature: libcpp_vector[Feature] getFeatures() Returns all the features
`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
`getOverallQuality`	Cython signature: float getOverallQuality() Model and quality methods
`getPeptideIdentifications`	Cython signature: libcpp_vector[PeptideIdentification] getPeptideIdentifications() Returns a reference to the PeptideIdentification vector
`getPrecursorFeature`	Cython signature: Feature getPrecursorFeature(String key) Returns a specified precursor feature
`getPrecursorFeatureIDs`	Cython signature: void getPrecursorFeatureIDs(libcpp_vector[String] & result) Returns a list of IDs of available precursor features
`getQuality`	Cython signature: float getQuality(size_t index) Returns the quality in dimension c
`getRT`	Cython signature: double getRT() Returns the RT coordinate (index 0)
`getScores`	Cython signature: OpenSwath_Scores getScores() Returns all peakgroup scores
`getSubordinates`	Cython signature: libcpp_vector[Feature] getSubordinates() Returns the subordinate features
`getUniqueId`	Cython signature: size_t getUniqueId() Returns the unique id
`getWidth`	Cython signature: float getWidth()
`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.
`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)
`setConvexHulls`	Cython signature: void setConvexHulls(libcpp_vector[ConvexHull2D])
`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
`setOverallQuality`	Cython signature: void setOverallQuality(float q) Sets the overall quality
`setPeptideIdentifications`	Cython signature: void setPeptideIdentifications(libcpp_vector[PeptideIdentification] & peptides) Sets the PeptideIdentification vector
`setQuality`	Cython signature: void setQuality(size_t index, float q) Sets the quality in dimension c
`setRT`	Cython signature: void setRT(double) Returns the RT coordinate (index 0)
`setScores`	Cython signature: void setScores(OpenSwath_Scores s) Sets all peakgroup scores
`setSubordinates`	Cython signature: void setSubordinates(libcpp_vector[Feature]) Returns the subordinate features
`setUniqueId`	Cython signature: void setUniqueId(uint64_t rhs) Assigns a new, valid unique id.
`setWidth`	Cython signature: void setWidth(float q)

addFeature()#: Cython signature: void addFeature(Feature & f, String key) Adds an feature from a single chromatogram into the feature

addPrecursorFeature()#: Cython signature: void addPrecursorFeature(Feature & f, String key) Adds a precursor feature from a single chromatogram into the feature

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

encloses()#

Cython signature: bool encloses(double rt, double mz)

Parameters

rt – Sequence to digest
mz – Digestion products

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()

getCharge()#: Cython signature: int getCharge()

getConvexHull()#: Cython signature: ConvexHull2D getConvexHull()

getConvexHulls()#: Cython signature: libcpp_vector[ConvexHull2D] getConvexHulls()

getFeature()#: Cython signature: Feature getFeature(String key) Returns a specified feature

getFeatureIDs()#: Cython signature: void getFeatureIDs(libcpp_vector[String] & result) Returns a list of IDs of available features

getFeatures()#: Cython signature: libcpp_vector[Feature] getFeatures() Returns all the features

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

getOverallQuality()#: Cython signature: float getOverallQuality() Model and quality methods

getPeptideIdentifications()#: Cython signature: libcpp_vector[PeptideIdentification] getPeptideIdentifications() Returns a reference to the PeptideIdentification vector

getPrecursorFeature()#: Cython signature: Feature getPrecursorFeature(String key) Returns a specified precursor feature

getPrecursorFeatureIDs()#: Cython signature: void getPrecursorFeatureIDs(libcpp_vector[String] & result) Returns a list of IDs of available precursor features

getQuality()#: Cython signature: float getQuality(size_t index) Returns the quality in dimension c

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

getScores()#: Cython signature: OpenSwath_Scores getScores() Returns all peakgroup scores

getSubordinates()#: Cython signature: libcpp_vector[Feature] getSubordinates() Returns the subordinate features

getUniqueId()#: Cython signature: size_t getUniqueId() Returns the unique id

getWidth()#: Cython signature: float getWidth()

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

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)

setConvexHulls()#: Cython signature: void setConvexHulls(libcpp_vector[ConvexHull2D])

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

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

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

setQuality()#: Cython signature: void setQuality(size_t index, float q) Sets the quality in dimension c

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

setScores()#: Cython signature: void setScores(OpenSwath_Scores s) Sets all peakgroup scores

setSubordinates()#: Cython signature: void setSubordinates(libcpp_vector[Feature]) Returns the subordinate features

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

setWidth()#: Cython signature: void setWidth(float q)