KDTreeFeatureMaps

class pyopenms.KDTreeFeatureMaps

Bases: object

Cython implementation of _KDTreeFeatureMaps

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1KDTreeFeatureMaps.html

– Inherits from [‘DefaultParamHandler’]

__init__()

  • Cython signature: void KDTreeFeatureMaps() Stores a set of features, together with a 2D tree for fast search

  • Cython signature: void KDTreeFeatureMaps(libcpp_vector[FeatureMap] & maps, Param & param)

  • Cython signature: void KDTreeFeatureMaps(libcpp_vector[ConsensusMap] & maps, Param & param)

Methods

__init__

  • Cython signature: void KDTreeFeatureMaps()

addMaps

  • Cython signature: void addMaps(libcpp_vector[FeatureMap] & maps)

charge

Cython signature: int charge(size_t i)

clear

Cython signature: void clear()

getDefaults

Cython signature: Param getDefaults() Returns the default parameters

getName

Cython signature: String getName() Returns the name

getNeighborhood

Cython signature: void getNeighborhood(size_t index, libcpp_vector[size_t] & result_indices, double rt_tol, double mz_tol, bool mz_ppm, bool include_features_from_same_map, double max_pairwise_log_fc) Fill result with indices of all features compatible (wrt.

getParameters

Cython signature: Param getParameters() Returns the parameters

getSubsections

Cython signature: libcpp_vector[String] getSubsections()

intensity

Cython signature: float intensity(size_t i)

mapIndex

Cython signature: size_t mapIndex(size_t i)

mz

Cython signature: double mz(size_t i)

numMaps

Cython signature: size_t numMaps()

optimizeTree

Cython signature: void optimizeTree()

queryRegion

Cython signature: void queryRegion(double rt_low, double rt_high, double mz_low, double mz_high, libcpp_vector[size_t] & result_indices, size_t ignored_map_index)

rt

Cython signature: double rt(size_t i)

setName

Cython signature: void setName(const String &) Sets the name

setParameters

Cython signature: void setParameters(Param & param) Sets the parameters

size

Cython signature: size_t size()

treeSize

Cython signature: size_t treeSize()
addMaps()

  • Cython signature: void addMaps(libcpp_vector[FeatureMap] & maps) Add maps and balance kd-tree

  • Cython signature: void addMaps(libcpp_vector[ConsensusMap] & maps)

charge()

Cython signature: int charge(size_t i)

clear()

Cython signature: void clear()

getDefaults()

Cython signature: Param getDefaults() Returns the default parameters

getName()

Cython signature: String getName() Returns the name

getNeighborhood()

Cython signature: void getNeighborhood(size_t index, libcpp_vector[size_t] & result_indices, double rt_tol, double mz_tol, bool mz_ppm, bool include_features_from_same_map, double max_pairwise_log_fc) Fill result with indices of all features compatible (wrt. RT, m/z, map index) to the feature with index

getParameters()

Cython signature: Param getParameters() Returns the parameters

getSubsections()

Cython signature: libcpp_vector[String] getSubsections()

intensity()

Cython signature: float intensity(size_t i)

mapIndex()

Cython signature: size_t mapIndex(size_t i)

mz()

Cython signature: double mz(size_t i)

numMaps()

Cython signature: size_t numMaps()

optimizeTree()

Cython signature: void optimizeTree()

queryRegion()

Cython signature: void queryRegion(double rt_low, double rt_high, double mz_low, double mz_high, libcpp_vector[size_t] & result_indices, size_t ignored_map_index)

rt()

Cython signature: double rt(size_t i)

setName()

Cython signature: void setName(const String &) Sets the name

setParameters()

Cython signature: void setParameters(Param & param) Sets the parameters

size()

Cython signature: size_t size()

treeSize()

Cython signature: size_t treeSize()