Generate seed lists for feature detection. More...

#include <OpenMS/FEATUREFINDER/SeedListGenerator.h>

Public Types
typedef std::vector< DPosition< 2 > >	SeedList
	List of seed positions. More...

Public Member Functions
	SeedListGenerator ()
	Default constructor. More...

void	generateSeedList (const PeakMap &experiment, SeedList &seeds)
	Generate a seed list based on an MS experiment. More...

void	generateSeedList (std::vector< PeptideIdentification > &peptides, SeedList &seeds, bool use_peptide_mass=false)
	Generate a seed list based on a list of peptide identifications. More...

void	generateSeedLists (const ConsensusMap &consensus, std::map< UInt64, SeedList > &seed_lists)
	Generate seed lists based on a consensus map. More...

void	convertSeedList (const SeedList &seeds, FeatureMap &features)
	Convert a list of seed positions to a feature map (expected format for FeatureFinder) More...

void	convertSeedList (const FeatureMap &features, SeedList &seeds)
	Convert a feature map with seed positions back to a simple list. More...

Detailed Description

Generate seed lists for feature detection.

Seed lists specify locations in an MS experiment where features are expected. Currently, only the "centroided" FeatureFinder algorithm (class @p FeatureFinderAlgorithmPicked) supports custom seed lists (in featureXML format).

\xrefitem experimental "Experimental classes" "Experimental List" This is a new class that still needs to be tested.

Member Typedef Documentation

◆ SeedList

typedef std::vector<DPosition<2> > SeedList

List of seed positions.

Constructor & Destructor Documentation

◆ SeedListGenerator()

SeedListGenerator ( )

Default constructor.

Member Function Documentation

◆ convertSeedList() [1/2]

void convertSeedList	(	const FeatureMap &	features,
		SeedList &	seeds
	)

Convert a feature map with seed positions back to a simple list.

◆ convertSeedList() [2/2]

void convertSeedList	(	const SeedList &	seeds,
		FeatureMap &	features
	)

Convert a list of seed positions to a feature map (expected format for FeatureFinder)

◆ generateSeedList() [1/2]

void generateSeedList	(	const PeakMap &	experiment,
		SeedList &	seeds
	)

Generate a seed list based on an MS experiment.

This uses the locations of MS2 precursors as seed positions.

◆ generateSeedList() [2/2]

void generateSeedList	(	std::vector< PeptideIdentification > &	peptides,
		SeedList &	seeds,
		bool	use_peptide_mass = `false`
	)

Generate a seed list based on a list of peptide identifications.

This uses the retention time of the MS2 precursor ("RT" MetaInfo entry) together with either the precursor m/z value ("MZ" MetaInfo entry) or - if use_peptide_mass is true - the monoisotopic mass and charge of the best peptide hit to define the seed position for a peptide identification.

The peptide hits in peptides will be sorted if use_peptide_mass is true.

◆ generateSeedLists()

void generateSeedLists	(	const ConsensusMap &	consensus,
		std::map< UInt64, SeedList > &	seed_lists
	)

Generate seed lists based on a consensus map.

This creates one seed list per constituent map of the consensus map. For each constituent map, a seed is generated at the position of each consensus feature that does not contain a sub-feature from this map. (The idea is to fill "holes" in the consensus map by looking for features explicitly at the positions of the "holes".) The seed lists are indexed by the IDs of the constituent maps in the consensus map.

Note that the resulting seed lists use the retention time scale of the consensus map, which might be different from the original time scales of the experiments if e.g. the MapAligner tool was used to perform retention time correction as part of the alignment process.

Public Types

Public Member Functions