An algorithm to decharge features (i.e. as found by FeatureFinder).
More...
#include <OpenMS/ANALYSIS/DECHARGING/FeatureDeconvolution.h>
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MassExplainer::AdductsType | potential_adducts_ |
| List of adducts used to explain mass differences. More...
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Map< Size, String > | map_label_ |
| labeling table More...
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Map< String, Size > | map_label_inverse_ |
| labeling table inverse More...
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bool | enable_intensity_filter_ |
| status of intensity filter for edges More...
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CHARGEMODE | q_try_ |
| status of charge discovery More...
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Int | verbose_level_ |
| amount of debug information displayed More...
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| FeatureDeconvolution () |
| default constructor More...
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| FeatureDeconvolution (const FeatureDeconvolution &source) |
| Copy constructor. More...
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FeatureDeconvolution & | operator= (const FeatureDeconvolution &source) |
| Assignment operator. More...
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| ~FeatureDeconvolution () override |
| destructor More...
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void | compute (const FeatureMapType &fm_in, FeatureMapType &fm_out, ConsensusMap &cons_map, ConsensusMap &cons_map_p) |
| Compute a zero-charge feature map from a set of charged features. More...
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void | updateMembers_ () override |
| This method is used to update extra member variables at the end of the setParameters() method. More...
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void | checkSolution_ (const ConsensusMap &cons_map) const |
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void | inferMoreEdges_ (PairsType &edges, Map< Size, std::set< CmpInfo_ > > &feature_adducts) |
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void | printEdgesOfConnectedFeatures_ (Size idx_1, Size idx_2, const PairsType &feature_relation) |
| A function mostly for debugging. More...
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bool | intensityFilterPassed_ (const Int q1, const Int q2, const Compomer &cmp, const FeatureType &f1, const FeatureType &f2) |
| returns true if the intensity filter was passed or switched off More...
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bool | chargeTestworthy_ (const Int feature_charge, const Int putative_charge, const bool other_unchanged) const |
| determines if we should test a putative feature charge More...
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An algorithm to decharge features (i.e. as found by FeatureFinder).
◆ ClusterPointType
◆ CoordinateType
◆ FeatureMapType
◆ FeatureType
◆ PairsType
◆ CHARGEMODE
Enumerator |
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QFROMFEATURE | |
QHEURISTIC | |
QALL | |
◆ FeatureDeconvolution() [1/2]
◆ FeatureDeconvolution() [2/2]
◆ ~FeatureDeconvolution()
◆ chargeTestworthy_()
bool chargeTestworthy_ |
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const Int |
feature_charge, |
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const Int |
putative_charge, |
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const bool |
other_unchanged |
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determines if we should test a putative feature charge
Answer query given the internal status of q_try. Features with q<=0 always return true.
◆ checkSolution_()
◆ compute()
Compute a zero-charge feature map from a set of charged features.
Find putative ChargePairs, then score them and hand over to ILP.
- Parameters
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fm_in | Input feature-map |
fm_out | Output feature-map (sorted by position and augmented with user params) |
cons_map | [out] Output of grouped features belonging to a charge group |
cons_map_p | [out] Output of paired features connected by an edge |
◆ inferMoreEdges_()
void inferMoreEdges_ |
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PairsType & |
edges, |
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Map< Size, std::set< CmpInfo_ > > & |
feature_adducts |
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test if "simple" edges have alternative (more difficult explanation) supported by neighboring edges e.g. (.) -> (H+) might be augmented to (Na+) -> (H+Na+)
◆ intensityFilterPassed_()
returns true if the intensity filter was passed or switched off
Filter for adding an edge only when the two features connected by it, fulfill the intensity criterion.
◆ operator=()
◆ printEdgesOfConnectedFeatures_()
void printEdgesOfConnectedFeatures_ |
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Size |
idx_1, |
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Size |
idx_2, |
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const PairsType & |
feature_relation |
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A function mostly for debugging.
◆ updateMembers_()
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.
◆ enable_intensity_filter_
bool enable_intensity_filter_ |
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protected |
status of intensity filter for edges
◆ map_label_
◆ map_label_inverse_
◆ potential_adducts_
List of adducts used to explain mass differences.
◆ q_try_
status of charge discovery
◆ verbose_level_
amount of debug information displayed