OpenMS
SeedListGenerator Class Reference

Generate seed lists for feature detection. More...

#include <OpenMS/TRANSFORMATIONS/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 FeatureFinderAlgorithmPicked) supports custom seed lists (in featureXML format).

Experimental classes:
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()

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.