FeatureFinderIdentificationAlgorithm.h File Reference

#include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h>
#include <OpenMS/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/FEATUREFINDER/FeatureFinderAlgorithmPickedHelperStructs.h>
#include <OpenMS/FEATUREFINDER/FFIDAlgoExternalIDHandler.h>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
#include <vector>
#include <fstream>
#include <map>

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Classes
class	FeatureFinderIdentificationAlgorithm
struct	FeatureFinderIdentificationAlgorithm::RTRegion
	region in RT in which a peptide elutes: More...
struct	FeatureFinderIdentificationAlgorithm::IMStats
	Ion mobility statistics for a peptide in a specific RT region and charge state. More...
struct	FeatureFinderIdentificationAlgorithm::FeatureFilterQuality
	predicate for filtering features by overall quality: More...
struct	FeatureFinderIdentificationAlgorithm::FeatureFilterPeptides
	predicate for filtering features by assigned peptides: More...
struct	FeatureFinderIdentificationAlgorithm::PeptideCompare
	comparison functor for (unassigned) peptide IDs More...
struct	FeatureFinderIdentificationAlgorithm::FeatureCompare
	comparison functor for features More...

Namespaces
namespace	OpenMS
	Main OpenMS namespace.

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Class Documentation

OpenMS::FeatureFinderIdentificationAlgorithm::RTRegion

struct OpenMS::FeatureFinderIdentificationAlgorithm::RTRegion

region in RT in which a peptide elutes:

Collaboration diagram for FeatureFinderIdentificationAlgorithm::RTRegion:

Class Members
double	end
ChargeMap	ids	internal/external peptide IDs (per charge) in this region
double	start

OpenMS::FeatureFinderIdentificationAlgorithm::IMStats

struct OpenMS::FeatureFinderIdentificationAlgorithm::IMStats

Ion mobility statistics for a peptide in a specific RT region and charge state.

This structure stores statistical measures of ion mobility values collected from peptide identifications within a single RT region. These statistics are used for:

• Chromatogram extraction with appropriate IM windows (using median)
• Feature annotation for quality control (all three values)
• Detecting potential mis-identifications (large min-max spread may indicate issues)

All values default to -1.0 to indicate missing/unavailable IM data.

Collaboration diagram for FeatureFinderIdentificationAlgorithm::IMStats:

Class Members
double	max = -1.0	Maximum IM value (upper bound of IM distribution)
double	median = -1.0	Median IM value (robust central tendency, used for extraction)
double	min = -1.0	Minimum IM value (lower bound of IM distribution)