| OpenMS 2.5.0

Public Types | Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
KDTreeFeatureMaps Class Reference

Stores a set of features, together with a 2D tree for fast search. More...

`#include <OpenMS/ANALYSIS/QUANTITATION/KDTreeFeatureMaps.h>`

Inheritance diagram for KDTreeFeatureMaps:

## Public Types

typedef KDTree::KDTree< 2, KDTreeFeatureNode > | FeatureKDTree
| 2D tree on features More...

## Public Member Functions

| KDTreeFeatureMaps ()
| Default constructor. More...
template<typename MapType >
| KDTreeFeatureMaps (const std::vector< MapType > &maps, const Param &param)
| Constructor. More...
| ~KDTreeFeatureMaps () override
| Destructor. More...
template<typename MapType >
void | addMaps (const std::vector< MapType > &maps)
| Add `maps` and balance kd-tree. More...
void | addFeature (Size mt_map_index, const BaseFeature *feature)
| Add feature. More...
const BaseFeature * | feature (Size i) const
| Return pointer to feature i. More...
double | rt (Size i) const
| RT. More...
double | mz (Size i) const
| m/z More...
float | intensity (Size i) const
| Intensity. More...
Int | charge (Size i) const
| Charge. More...
Size | mapIndex (Size i) const
| Map index. More...
Size | size () const
| Number of features stored. More...
Size | treeSize () const
| Number of points in the tree. More...
Size | numMaps () const
| Number of maps. More...
void | clear ()
| Clear all data. More...
void | optimizeTree ()
| Optimize the kD tree. More...
void | getNeighborhood (Size index, std::vector< Size > &result_indices, double rt_tol, double mz_tol, bool mz_ppm, bool include_features_from_same_map=false, double max_pairwise_log_fc=-1.0) const
| Fill `result` with indices of all features compatible (wrt. RT, m/z, map index) to the feature with `index`. More...
void | queryRegion (double rt_low, double rt_high, double mz_low, double mz_high, std::vector< Size > &result_indices, Size ignored_map_index=std::numeric_limits< Size >::max()) const
| Fill `result` with indices of all features within the specified boundaries. More...
void | applyTransformations (const std::vector< TransformationModelLowess *> &trafos)
| Apply RT transformations. More...
Public Member Functions inherited from DefaultParamHandler
| DefaultParamHandler (const String &name)
| Constructor with name that is displayed in error messages. More...
| DefaultParamHandler (const DefaultParamHandler &rhs)
| Copy constructor. More...
virtual | ~DefaultParamHandler ()
| Destructor. More...
virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs)
| Assignment operator. More...
virtual bool | operator== (const DefaultParamHandler &rhs) const
| Equality operator. More...
void | setParameters (const Param &param)
| Sets the parameters. More...
const Param & | getParameters () const
| Non-mutable access to the parameters. More...
const Param & | getDefaults () const
| Non-mutable access to the default parameters. More...
const String & | getName () const
| Non-mutable access to the name. More...
void | setName (const String &name)
| Mutable access to the name. More...
const std::vector< String > & | getSubsections () const
| Non-mutable access to the registered subsections. More...

## Protected Member Functions

void | updateMembers_ () override
| This method is used to update extra member variables at the end of the setParameters() method. More...
Protected Member Functions inherited from DefaultParamHandler
void | defaultsToParam_ ()
| Updates the parameters after the defaults have been set in the constructor. More...

## Protected Attributes

std::vector< const BaseFeature * > | features_
| Feature data. More...
std::vector< Size > | map_index_
| Map indices. More...
std::vector< double > | rt_
| (Potentially transformed) retention times More...
Size | num_maps_
| Number of maps. More...
FeatureKDTree | kd_tree_
| 2D tree on features from all input maps. More...
Protected Attributes inherited from DefaultParamHandler
Param | param_
| Container for current parameters. More...
Param | defaults_
| Container for default parameters. This member should be filled in the constructor of derived classes! More...
std::vector< String > | subsections_
| Container for registered subsections. This member should be filled in the constructor of derived classes! More...
String | error_name_
| Name that is displayed in error messages during the parameter checking. More...
bool | check_defaults_
| If this member is set to false no checking if parameters in done;. More...
bool | warn_empty_defaults_
| If this member is set to false no warning is emitted when defaults are empty;. More...

## Detailed Description

Stores a set of features, together with a 2D tree for fast search.

## Member Typedef Documentation

## ◆ FeatureKDTree

typedef KDTree::KDTree<2,KDTreeFeatureNode> FeatureKDTree

2D tree on features

## Constructor & Destructor Documentation

## ◆ KDTreeFeatureMaps() [1/2]

KDTreeFeatureMaps | ( |  | ) |

inline

Default constructor.

## ◆ KDTreeFeatureMaps() [2/2]

KDTreeFeatureMaps | ( | const std::vector< MapType > & | maps,
|  | const Param & | param
| ) |  |

inline

Constructor.

## ◆ ~KDTreeFeatureMaps()

~KDTreeFeatureMaps | ( |  | ) |

inline override

Destructor.

## Member Function Documentation

## ◆ addFeature()

void addFeature | ( | Size | mt_map_index,
|  | const BaseFeature * | feature
| ) |  |

Add feature.

## ◆ addMaps()

void addMaps | ( | const std::vector< MapType > & | maps | ) |

inline

Add `maps` and balance kd-tree.

References MSExperiment::begin(), and MSExperiment::end().

## ◆ applyTransformations()

void applyTransformations | ( | const std::vector< TransformationModelLowess *> & | trafos | ) |

Apply RT transformations.

## ◆ charge()

Int charge | ( | Size | i | ) | const

Charge.

## ◆ clear()

void clear | ( |  | ) |

Clear all data.

## ◆ feature()

const BaseFeature* feature | ( | Size | i | ) | const

Return pointer to feature i.

## ◆ getNeighborhood()

void getNeighborhood | ( | Size | index,
|  | std::vector< Size > & | result_indices,
|  | double | rt_tol,
|  | double | mz_tol,
|  | bool | mz_ppm,
|  | bool | include_features_from_same_map = `false`,
|  | double | max_pairwise_log_fc = `-1.0`
| ) |  | const

Fill `result` with indices of all features compatible (wrt. RT, m/z, map index) to the feature with `index`.

## ◆ intensity()

float intensity | ( | Size | i | ) | const

Intensity.

## ◆ mapIndex()

Size mapIndex | ( | Size | i | ) | const

Map index.

## ◆ mz()

double mz | ( | Size | i | ) | const

m/z

## ◆ numMaps()

Size numMaps | ( |  | ) | const

Number of maps.

## ◆ optimizeTree()

void optimizeTree | ( |  | ) |

Optimize the kD tree.

## ◆ queryRegion()

void queryRegion | ( | double | rt_low,
|  | double | rt_high,
|  | double | mz_low,
|  | double | mz_high,
|  | std::vector< Size > & | result_indices,
|  | Size | ignored_map_index = `std::numeric_limits< Size >::max()`
| ) |  | const

Fill `result` with indices of all features within the specified boundaries.

## ◆ rt()

double rt | ( | Size | i | ) | const

RT.

## ◆ size()

Size size | ( |  | ) | const

Number of features stored.

## ◆ treeSize()

Size treeSize | ( |  | ) | const

Number of points in the tree.

## ◆ updateMembers_()

void updateMembers_ | ( |  | ) |

override protected virtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

## Member Data Documentation

## ◆ features_

std::vector<const BaseFeature*> features_

protected

Feature data.

## ◆ kd_tree_

FeatureKDTree kd_tree_

protected

2D tree on features from all input maps.

## ◆ map_index_

std::vector<Size> map_index_

protected

Map indices.

## ◆ num_maps_

Size num_maps_

protected

Number of maps.

## ◆ rt_

std::vector<double> rt_

protected

(Potentially transformed) retention times