OpenMS
2.5.0
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A functor class for the calculation of distances between features or consensus features. More...
#include <OpenMS/ANALYSIS/MAPMATCHING/FeatureDistance.h>
Classes | |
struct | DistanceParams_ |
Structure for storing distance parameters. More... | |
Public Member Functions | |
FeatureDistance (double max_intensity=1.0, bool force_constraints=false) | |
Constructor. More... | |
~FeatureDistance () override | |
Destructor. More... | |
FeatureDistance & | operator= (const FeatureDistance &other) |
Assignment operator. More... | |
std::pair< bool, double > | operator() (const BaseFeature &left, const BaseFeature &right) |
Evaluation operator - checks constraints and computes the distance between two features. 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 ¶m) |
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... | |
Static Public Attributes | |
static const double | infinity |
Value to return if max. difference is exceeded or if charge states don't match. More... | |
Protected Member Functions | |
void | updateMembers_ () override |
Docu in base class. More... | |
double | distance_ (double diff, const DistanceParams_ ¶ms) const |
Computes a distance component given absolute difference and parameters. More... | |
Protected Member Functions inherited from DefaultParamHandler | |
void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
Protected Attributes | |
DistanceParams_ | params_rt_ |
Storage of parameters for the individual distance components. More... | |
DistanceParams_ | params_mz_ |
DistanceParams_ | params_intensity_ |
double | total_weight_reciprocal_ |
Reciprocal value of the total weight in the distance function. More... | |
double | max_intensity_ |
Maximum intensity of features (for normalization) More... | |
bool | ignore_charge_ |
Compute a distance even if charge states don't match? More... | |
bool | ignore_adduct_ |
Compute a distance even if adducts don't match? More... | |
bool | force_constraints_ |
Always return infinity if "max. difference" constraints are not met? More... | |
bool | log_transform_ |
Log-transform intensities when computing intensity distance? 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... | |
A functor class for the calculation of distances between features or consensus features.
It implements a customizable distance function of the following form:
This function returns a normalized distance between zero and one (unless constraints are violated, see below).
, , and are the RT, m/z, and intensity values of the respective feature.
Constraints are: and . If an absolute difference exceeds the specified maximum, the behavior depends on the value used for check_constraints
in the constructor: If "false" (i.e., no constraints), the distance in that dimension may become greater than 1; if "true", infinity is returned as overall distance.
and are the maximum allowed differences in RT and m/z, respectively. They are specified by the parameters distance_RT:max_difference
and distance_MZ:max_difference
, and are used for normalization, i.e., the observed RT or m/z differences of the feature pair are scaled relative to this value.
is the intensity which yields a normalized intensity of 1. This parameter is not settable via user params, but is set in the constructor (via parameter max_intensity
), since it depends on the data at hand.
is the exponent for the distance in dimension X, specified by the parameter distance_X:exponent
. Normalized differences (between (0, 1) unless unconstrained) are taken to this power. This makes it possible to compare values using linear, quadratic, etc. distance.
is the weight of final distance in dimension X, specified by the parameter distance_X:weight
. The weights can be used to increase or decrease the contribution of RT, m/z, or intensity in the distance function. (The default weight for the intensity dimension is zero, i.e. intensity is not considered by default. However, is still a constraint and should be set sensibly in the c'tor.)
By default, two features are paired only if they have the same charge state (or at least one unknown charge '0') - otherwise, infinity is returned. This behavior can be changed by the ignore_charge
parameter.
Name | Type | Default | Restrictions | Description |
---|---|---|---|---|
ignore_charge | string | false | true, false | false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state |
ignore_adduct | string | true | true, false | true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts |
distance_RT:max_difference | float | 100.0 | min: 0.0 | Never pair features with a larger RT distance (in seconds). |
distance_RT:exponent | float | 1.0 | min: 0.0 | Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow) |
distance_RT:weight | float | 1.0 | min: 0.0 | Final RT distances are weighted by this factor |
distance_MZ:max_difference | float | 0.3 | min: 0.0 | Never pair features with larger m/z distance (unit defined by 'unit') |
distance_MZ:unit | string | Da | Da, ppm | Unit of the 'max_difference' parameter |
distance_MZ:exponent | float | 2.0 | min: 0.0 | Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow) |
distance_MZ:weight | float | 1.0 | min: 0.0 | Final m/z distances are weighted by this factor |
distance_intensity:exponent | float | 1.0 | min: 0.0 | Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow) |
distance_intensity:weight | float | 0.0 | min: 0.0 | Final intensity distances are weighted by this factor |
distance_intensity:log_transform | string | disabled | enabled, disabled | Log-transform intensities? If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1)) |
FeatureDistance | ( | double | max_intensity = 1.0 , |
bool | force_constraints = false |
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Constructor.
max_intensity | Maximum intensity of features (for normalization) |
force_constraints | Check "max. difference" constraints given in the parameters and return infinity if violated? |
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override |
Destructor.
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inlineprotected |
Computes a distance component given absolute difference and parameters.
std::pair<bool, double> operator() | ( | const BaseFeature & | left, |
const BaseFeature & | right | ||
) |
Evaluation operator - checks constraints and computes the distance between two features.
FeatureDistance& operator= | ( | const FeatureDistance & | other | ) |
Assignment operator.
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overrideprotectedvirtual |
Docu in base class.
Reimplemented from DefaultParamHandler.
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protected |
Always return infinity if "max. difference" constraints are not met?
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Compute a distance even if adducts don't match?
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protected |
Compute a distance even if charge states don't match?
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static |
Value to return if max. difference is exceeded or if charge states don't match.
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Log-transform intensities when computing intensity distance?
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protected |
Maximum intensity of features (for normalization)
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Storage of parameters for the individual distance components.
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Reciprocal value of the total weight in the distance function.