OpenMS
FeatureFinderMultiplexAlgorithm.h
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31 // $Maintainer: Lars Nilse $
32 // $Authors: Lars Nilse $
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34 
35 #pragma once
36 
42 
48 
49 #include <vector>
50 #include <fstream>
51 #include <map>
52 
53 namespace OpenMS
54 {
55 
56 class OPENMS_DLLAPI FeatureFinderMultiplexAlgorithm :
57  public DefaultParamHandler, public ProgressLogger
58 {
59 public:
62 
64  void run(MSExperiment& exp, bool progress);
65 
70 
71 protected:
72 
73  // experimental data
76 
78 
80 
81  bool progress_;
82 
83  unsigned charge_min_;
84  unsigned charge_max_;
85 
88 
89 
90  // mass shift names and their values
91  std::map<String, double> label_mass_shift_;
92 
93  // final results, maps of detected features
96 
97  // blacklist
99 
110  std::vector<MultiplexIsotopicPeakPattern> generatePeakPatterns_(int charge_min, int charge_max, int peaks_per_peptide_max, const std::vector<MultiplexDeltaMasses>& mass_pattern_list);
111 
121  void correctPeptideIntensities_(const MultiplexIsotopicPeakPattern& pattern, std::map<size_t, SplinePackage>& spline_chromatograms, const std::vector<double>& rt_peptide, std::vector<double>& intensity_peptide) const;
122 
131  std::vector<double> determinePeptideIntensitiesCentroided_(const MultiplexIsotopicPeakPattern& pattern, const std::multimap<size_t, MultiplexSatelliteCentroided >& satellites);
132 
141  std::vector<double> determinePeptideIntensitiesProfile_(const MultiplexIsotopicPeakPattern& pattern, const std::multimap<size_t, MultiplexSatelliteProfile >& satellites);
142 
150  void generateMapsCentroided_(const std::vector<MultiplexIsotopicPeakPattern>& patterns, const std::vector<MultiplexFilteredMSExperiment>& filter_results, std::vector<std::map<int, GridBasedCluster> >& cluster_results);
151 
159  void generateMapsProfile_(const std::vector<MultiplexIsotopicPeakPattern>& patterns, const std::vector<MultiplexFilteredMSExperiment>& filter_results, const std::vector<std::map<int, GridBasedCluster> >& cluster_results);
160 
161 };
162 
163 }
A container for consensus elements.
Definition: ConsensusMap.h:92
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
Definition: FeatureFinderMultiplexAlgorithm.h:58
std::vector< MultiplexIsotopicPeakPattern > generatePeakPatterns_(int charge_min, int charge_max, int peaks_per_peptide_max, const std::vector< MultiplexDeltaMasses > &mass_pattern_list)
generate list of m/z shifts
FeatureMap & getFeatureMap()
get methods
FeatureMap feature_map_
Definition: FeatureFinderMultiplexAlgorithm.h:94
std::map< String, double > label_mass_shift_
Definition: FeatureFinderMultiplexAlgorithm.h:91
FeatureFinderMultiplexAlgorithm()
default constructor
unsigned isotopes_per_peptide_max_
Definition: FeatureFinderMultiplexAlgorithm.h:87
void run(MSExperiment &exp, bool progress)
main method for feature detection
std::vector< double > determinePeptideIntensitiesCentroided_(const MultiplexIsotopicPeakPattern &pattern, const std::multimap< size_t, MultiplexSatelliteCentroided > &satellites)
calculate peptide intensities
bool centroided_
Definition: FeatureFinderMultiplexAlgorithm.h:77
unsigned isotopes_per_peptide_min_
Definition: FeatureFinderMultiplexAlgorithm.h:86
ProgressLogger prog_log_
Definition: FeatureFinderMultiplexAlgorithm.h:79
void generateMapsProfile_(const std::vector< MultiplexIsotopicPeakPattern > &patterns, const std::vector< MultiplexFilteredMSExperiment > &filter_results, const std::vector< std::map< int, GridBasedCluster > > &cluster_results)
generates consensus and feature maps containing all peptide multiplets
unsigned charge_min_
Definition: FeatureFinderMultiplexAlgorithm.h:83
ConsensusMap consensus_map_
Definition: FeatureFinderMultiplexAlgorithm.h:95
void generateMapsCentroided_(const std::vector< MultiplexIsotopicPeakPattern > &patterns, const std::vector< MultiplexFilteredMSExperiment > &filter_results, std::vector< std::map< int, GridBasedCluster > > &cluster_results)
generates consensus and feature maps containing all peptide multiplets
std::vector< double > determinePeptideIntensitiesProfile_(const MultiplexIsotopicPeakPattern &pattern, const std::multimap< size_t, MultiplexSatelliteProfile > &satellites)
calculate peptide intensities
unsigned charge_max_
Definition: FeatureFinderMultiplexAlgorithm.h:84
void correctPeptideIntensities_(const MultiplexIsotopicPeakPattern &pattern, std::map< size_t, SplinePackage > &spline_chromatograms, const std::vector< double > &rt_peptide, std::vector< double > &intensity_peptide) const
determine ratios through linear regression and correct peptide intensities
MSExperiment exp_centroid_
Definition: FeatureFinderMultiplexAlgorithm.h:75
bool progress_
Definition: FeatureFinderMultiplexAlgorithm.h:81
MSExperiment exp_blacklist_
Definition: FeatureFinderMultiplexAlgorithm.h:98
MSExperiment exp_profile_
Definition: FeatureFinderMultiplexAlgorithm.h:74
A container for features.
Definition: FeatureMap.h:106
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:72
data structure for pattern of isotopic peaks
Definition: MultiplexIsotopicPeakPattern.h:55
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:53
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48