Feature
- class pyopenms.Feature
Bases:
objectCython implementation of _Feature
- Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1Feature.html
– Inherits from [‘UniqueIdInterface’, ‘RichPeak2D’]
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__()
Cython signature: void Feature()
Cython signature: void Feature(Feature &)
Methods
Cython signature: void Feature()
Cython signature: void clearMetaInfo() Removes all meta values
Cython signature: size_t clearUniqueId() Clear the unique id.
Cython signature: bool encloses(double rt, double mz)
Cython signature: size_t ensureUniqueId() Assigns a valid unique id, but only if the present one is invalid.
Cython signature: AnnotationState getAnnotationState()
Cython signature: int getCharge()
Cython signature: ConvexHull2D getConvexHull()
Cython signature: libcpp_vector[ConvexHull2D] getConvexHulls()
Cython signature: float getIntensity() Returns the data point intensity (height)
Cython signature: void getKeys(libcpp_vector[String] & keys) Fills the given vector with a list of all keys for which a value is set
Cython signature: double getMZ() Returns the m/z coordinate (index 1)
Cython signature: DataValue getMetaValue(String) Returns the value corresponding to a string, or
Cython signature: float getOverallQuality() Model and quality methods
Cython signature: libcpp_vector[PeptideIdentification] getPeptideIdentifications() Returns a reference to the PeptideIdentification vector
Cython signature: float getQuality(size_t index) Returns the quality in dimension c
Cython signature: double getRT() Returns the RT coordinate (index 0)
Cython signature: libcpp_vector[Feature] getSubordinates() Returns the subordinate features
Cython signature: size_t getUniqueId() Returns the unique id
Cython signature: float getWidth()
Cython signature: size_t hasInvalidUniqueId() Returns whether the unique id is invalid.
Cython signature: size_t hasValidUniqueId() Returns whether the unique id is valid.
Cython signature: bool isMetaEmpty() Returns if the MetaInfo is empty
Cython signature: bool isValid(uint64_t unique_id) Returns true if the unique_id is valid, false otherwise
Cython signature: MetaInfoRegistry metaRegistry() Returns a reference to the MetaInfoRegistry
Cython signature: bool metaValueExists(String) Returns whether an entry with the given name exists
Cython signature: void removeMetaValue(String) Removes the DataValue corresponding to name if it exists
Cython signature: void setCharge(int q)
Cython signature: void setConvexHulls(libcpp_vector[ConvexHull2D])
Cython signature: void setIntensity(float) Returns the data point intensity (height)
Cython signature: void setMZ(double) Returns the m/z coordinate (index 1)
Cython signature: void setMetaValue(String, DataValue) Sets the DataValue corresponding to a name
Cython signature: void setOverallQuality(float q) Sets the overall quality
Cython signature: void setPeptideIdentifications(libcpp_vector[PeptideIdentification] & peptides) Sets the PeptideIdentification vector
Cython signature: void setQuality(size_t index, float q) Sets the quality in dimension c
Cython signature: void setRT(double) Returns the RT coordinate (index 0)
Cython signature: void setSubordinates(libcpp_vector[Feature]) Returns the subordinate features
Cython signature: void setUniqueId(uint64_t rhs) Assigns a new, valid unique id.
Cython signature: void setWidth(float q)
- 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()
- 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
- 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)
- 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)
- 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)