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FeatureFinderMultiplexAlgorithm.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Lars Nilse $
32 // $Authors: Lars Nilse $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
38 #include <OpenMS/KERNEL/MSExperiment.h>
39 #include <OpenMS/KERNEL/ConsensusMap.h>
40 #include <OpenMS/KERNEL/FeatureMap.h>
41 #include <OpenMS/CONCEPT/ProgressLogger.h>
42
43 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexDeltaMasses.h>
44 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexIsotopicPeakPattern.h>
45 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexFilteredMSExperiment.h>
46 #include <OpenMS/FILTERING/DATAREDUCTION/SplinePackage.h>
47 #include <OpenMS/COMPARISON/CLUSTERING/GridBasedCluster.h>
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:
61 FeatureFinderMultiplexAlgorithm();
62
64 void run(MSExperiment& exp, bool progress);
65
67 FeatureMap& getFeatureMap();
68 ConsensusMap& getConsensusMap();
69 MSExperiment& getBlacklist();
70
71 protected:
72
73 // experimental data
74 MSExperiment exp_profile_;
75 MSExperiment exp_centroid_;
76
77 bool centroided_;
78
79 ProgressLogger prog_log_;
80
81 bool progress_;
82
83 unsigned charge_min_;
84 unsigned charge_max_;
85
86 unsigned isotopes_per_peptide_min_;
87 unsigned isotopes_per_peptide_max_;
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
94 FeatureMap feature_map_;
95 ConsensusMap consensus_map_;
96
97 // blacklist
98 MSExperiment exp_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);
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 }
OpenMS::FeatureFinderMultiplexAlgorithm::centroided_
bool centroided_
Definition: FeatureFinderMultiplexAlgorithm.h:77
OpenMS::FeatureFinderMultiplexAlgorithm::exp_profile_
MSExperiment exp_profile_
Definition: FeatureFinderMultiplexAlgorithm.h:74
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::FeatureFinderMultiplexAlgorithm::feature_map_
FeatureMap feature_map_
Definition: FeatureFinderMultiplexAlgorithm.h:94
MultiplexDeltaMasses.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::FeatureFinderMultiplexAlgorithm::exp_blacklist_
MSExperiment exp_blacklist_
Definition: FeatureFinderMultiplexAlgorithm.h:98
OpenMS::FeatureFinderMultiplexAlgorithm::prog_log_
ProgressLogger prog_log_
Definition: FeatureFinderMultiplexAlgorithm.h:79
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
OpenMS::FeatureFinderMultiplexAlgorithm
Definition: FeatureFinderMultiplexAlgorithm.h:56
OpenMS::FeatureFinderMultiplexAlgorithm::exp_centroid_
MSExperiment exp_centroid_
Definition: FeatureFinderMultiplexAlgorithm.h:75
ConsensusMap.h
FeatureMap.h
OpenMS::FeatureFinderMultiplexAlgorithm::consensus_map_
ConsensusMap consensus_map_
Definition: FeatureFinderMultiplexAlgorithm.h:95
ProgressLogger.h
OpenMS::FeatureFinderMultiplexAlgorithm::isotopes_per_peptide_min_
unsigned isotopes_per_peptide_min_
Definition: FeatureFinderMultiplexAlgorithm.h:86
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MSExperiment.h
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
DefaultParamHandler.h
OpenMS::FeatureFinderMultiplexAlgorithm::progress_
bool progress_
Definition: FeatureFinderMultiplexAlgorithm.h:81
OpenMS::FeatureFinderMultiplexAlgorithm::label_mass_shift_
std::map< String, double > label_mass_shift_
Definition: FeatureFinderMultiplexAlgorithm.h:91
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:79
MultiplexFilteredMSExperiment.h
OpenMS::FeatureFinderMultiplexAlgorithm::isotopes_per_peptide_max_
unsigned isotopes_per_peptide_max_
Definition: FeatureFinderMultiplexAlgorithm.h:87
SplinePackage.h
MultiplexIsotopicPeakPattern.h
OpenMS::FeatureFinderMultiplexAlgorithm::charge_max_
unsigned charge_max_
Definition: FeatureFinderMultiplexAlgorithm.h:84
OpenMS::MultiplexIsotopicPeakPattern
data structure for pattern of isotopic peaks
Definition: MultiplexIsotopicPeakPattern.h:54
GridBasedCluster.h
OpenMS::FeatureFinderMultiplexAlgorithm::charge_min_
unsigned charge_min_
Definition: FeatureFinderMultiplexAlgorithm.h:83