| OpenMS 2.5.0

MultiplexFilteringProfile.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/KERNEL/BaseFeature.h>
38 #include <OpenMS/KERNEL/StandardTypes.h>
39 #include <OpenMS/CONCEPT/ProgressLogger.h>
40 #include <OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakPickerHiRes.h>
41 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexIsotopicPeakPattern.h>
42 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexFiltering.h>
43 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexFilteredPeak.h>
44 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexFilteredMSExperiment.h>
45 #include <OpenMS/MATH/MISC/CubicSpline2d.h>
46 #include <OpenMS/FILTERING/DATAREDUCTION/SplineInterpolatedPeaks.h>
47
48 #include <vector>
49 #include <algorithm>
50 #include <iostream>
51
52 namespace OpenMS
53 {
67 class OPENMS_DLLAPI MultiplexFilteringProfile :
68 public MultiplexFiltering
69 {
70 public:
92 MultiplexFilteringProfile(MSExperiment& exp_profile, const MSExperiment& exp_centroided, const std::vector<std::vector<PeakPickerHiRes::PeakBoundary> >& boundaries,
93 const std::vector<MultiplexIsotopicPeakPattern>& patterns, int isotopes_per_peptide_min, int isotopes_per_peptide_max, double intensity_cutoff, double rt_band,
94 double mz_tolerance, bool mz_tolerance_unit, double peptide_similarity, double averagine_similarity, double averagine_similarity_scaling, String averagine_type="peptide");
95
105 std::vector<MultiplexFilteredMSExperiment> filter();
106
110 std::vector<std::vector<PeakPickerHiRes::PeakBoundary> >& getPeakBoundaries();
111
112 private:
122 bool filterAveragineModel_(const MultiplexIsotopicPeakPattern& pattern, const MultiplexFilteredPeak& peak, const std::multimap<size_t, MultiplexSatelliteProfile >& satellites_profile) const;
123
132 bool filterPeptideCorrelation_(const MultiplexIsotopicPeakPattern& pattern, const std::multimap<size_t, MultiplexSatelliteProfile >& satellites_profile) const;
133
137 std::vector<SplineInterpolatedPeaks> exp_spline_profile_;
138 std::vector<std::vector<PeakPickerHiRes::PeakBoundary> > boundaries_;
139
140 };
141
142 }
143
MultiplexFiltering.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
MultiplexFilteredPeak.h
OpenMS::MultiplexFiltering
base class for filtering centroided and profile data for peak patterns
Definition: MultiplexFiltering.h:73
CubicSpline2d.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::MultiplexFilteringProfile
filters centroided and profile data for peak patterns
Definition: MultiplexFilteringProfile.h:67
OpenMS::MultiplexFilteredPeak
data structure storing a single peak that passed all filters
Definition: MultiplexFilteredPeak.h:70
StandardTypes.h
PeakPickerHiRes.h
ProgressLogger.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::MultiplexFilteringProfile::boundaries_
std::vector< std::vector< PeakPickerHiRes::PeakBoundary > > boundaries_
Definition: MultiplexFilteringProfile.h:138
SplineInterpolatedPeaks.h
BaseFeature.h
MultiplexFilteredMSExperiment.h
MultiplexIsotopicPeakPattern.h
OpenMS::MultiplexFilteringProfile::exp_spline_profile_
std::vector< SplineInterpolatedPeaks > exp_spline_profile_
spline interpolated profile data and peak boundaries
Definition: MultiplexFilteringProfile.h:137
OpenMS::MultiplexIsotopicPeakPattern
data structure for pattern of isotopic peaks
Definition: MultiplexIsotopicPeakPattern.h:54