| OpenMS 2.5.0

MasstraceCorrelator.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
38 #include <OpenMS/CONCEPT/ProgressLogger.h>
39 #include <OpenMS/KERNEL/ConsensusMap.h>
40 #include <OpenMS/KERNEL/MSExperiment.h>
41
42 namespace OpenMS
43 {
44
53 class OPENMS_DLLAPI MasstraceCorrelator :
54 public DefaultParamHandler,
55 public ProgressLogger
56 {
57
58 public:
59
60 MasstraceCorrelator();
61
62 ~MasstraceCorrelator() override;
63
64 // a mass trace is a vector of pairs in (RT, Intensity)
65 typedef std::vector<std::pair<double, double> > MasstracePointsType;
66
80 void createPseudoSpectra(const ConsensusMap& map, MSExperiment& pseudo_spectra,
81 Size min_peak_nr, double min_correlation, int max_lag,
82 double max_rt_apex_difference);
83
84 /* Score two mass traces against each other
85 *
86 * This function scores two mass traces (vector of <RT,Intensity>) against each other:
87 *
88 * - The algorithm first creates 2 arrays that contain matched intensities
89 * in RT-space (accounting for missing data points and unequal length)
90 * - Next, these arrays are scored using cross-correlation scores and
91 * pearson coefficients.
92 *
93 * @note The pairs need to be sorted by the first entry (RT)
94 *
95 * @param hull_points1 The first input masstrace
96 * @param hull_points2 The second input masstrace
97 * @param lag The computed lag (output coelution score)
98 * @param lag_intensity The computed intensity at the lag (output shape score)
99 * @param pearson_score The computed pearson score (output)
100 * @param min_corr Minimal correlation needed to proceed computing the cross-correlations
101 * @param max_lag Currently unused
102 * @param mindiff Minimal differences for matching up the two mass traces
103 *
104 */
105 void scoreHullpoints(const MasstracePointsType& hull_points1,
106 const MasstracePointsType& hull_points2,
107 int& lag,
108 double& lag_intensity,
109 double& pearson_score,
110 const double min_corr,
111 const int max_lag,
112 const double mindiff = 0.1);
113
114 /* Create a cache of the features in a consensus map
115 *
116 * This creates a cache of the input consensus map by creating the
117 * following data structures:
118 * - a vector of mass traces (each mass trace is simply a vector of <RT,Intensity>
119 * - a vector of maximal intensities (max_rt, max_int)
120 * - a vector of retention times of the feature
121 *
122 * @param map The input consensus map
123 * @param feature_points The list of all mass traces
124 * @param max_intensities The list of maximal intensities
125 * @param rt_cache The list of retention times of all features
126 */
127 void createConsensusMapCache(const ConsensusMap& map,
128 std::vector<MasstracePointsType>& feature_points,
129 std::vector<std::pair<double, double> >& max_intensities,
130 std::vector<double>& rt_cache);
131
132 protected:
133
155 void matchMassTraces_(const MasstracePointsType& hull_points1,
156 const MasstracePointsType& hull_points2,
157 std::vector<double>& vec1,
158 std::vector<double>& vec2,
159 double mindiff,
160 double padEnds = true);
161 };
162 }
163
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
ConsensusMap.h
OpenMS::MasstraceCorrelator::MasstracePointsType
std::vector< std::pair< double, double > > MasstracePointsType
Definition: MasstraceCorrelator.h:65
OpenMS::MasstraceCorrelator
Correlates individual masstraces found in mass spectrometric maps.
Definition: MasstraceCorrelator.h:53
ProgressLogger.h
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::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:79
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127