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>

Include dependency graph for FeatureFinderIdentificationAlgorithm.h:

This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

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
	OpenMS
	Main OpenMS namespace.

---

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	Maximum IM value (upper bound of IM distribution)
double	median	Median IM value (robust central tendency, used for extraction)
double	min	Minimum IM value (lower bound of IM distribution)