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MultiplexClustering.h
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Lars Nilse $
32 // $Authors: Lars Nilse $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/StandardTypes.h>
38 #include <OpenMS/CONCEPT/ProgressLogger.h>
39 #include <OpenMS/MATH/MISC/BSpline2d.h>
40 #include <OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakPickerHiRes.h>
41 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexFilteredMSExperiment.h>
42 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexFiltering.h>
43 #include <OpenMS/COMPARISON/CLUSTERING/GridBasedCluster.h>
44
45 #include <vector>
46 #include <algorithm>
47 #include <iostream>
48
49 namespace OpenMS
50 {
63 class OPENMS_DLLAPI MultiplexClustering :
64 public ProgressLogger
65 {
66 public:
70 typedef GridBasedCluster::Point Point;
71
83 MultiplexClustering(const MSExperiment& exp_profile, const MSExperiment& exp_picked, const std::vector<std::vector<PeakPickerHiRes::PeakBoundary> >& boundaries, double rt_typical, double rt_minimum);
84
96 MultiplexClustering(const MSExperiment& exp, double mz_tolerance, bool mz_tolerance_unit, double rt_typical, double rt_minimum);
97
106 std::vector<std::map<int,GridBasedCluster> > cluster(const std::vector<MultiplexFilteredMSExperiment>& filter_results);
107
111 class OPENMS_DLLAPI MultiplexDistance
112 {
113 public:
119 MultiplexDistance(double rt_scaling);
120
124 MultiplexDistance();
125
133 double operator()(Point p1, Point p2);
134
135 private:
136 double rt_scaling_;
137
138 };
139
140 private:
144 std::vector<double> grid_spacing_mz_;
145 std::vector<double> grid_spacing_rt_;
146
150 double rt_scaling_;
151
155 double rt_typical_;
156
160 double rt_minimum_;
161
162 };
163
164 }
165
MultiplexFiltering.h
OpenMS::MultiplexClustering::rt_scaling_
double rt_scaling_
scaling in y-direction for clustering
Definition: MultiplexClustering.h:150
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::MultiplexClustering::MultiplexDistance::rt_scaling_
double rt_scaling_
Definition: MultiplexClustering.h:136
OpenMS::MultiplexClustering::MultiplexDistance
scaled Euclidean distance for clustering
Definition: MultiplexClustering.h:111
StandardTypes.h
PeakPickerHiRes.h
OpenMS::MultiplexClustering::Point
GridBasedCluster::Point Point
cluster centre, cluster bounding box, grid index
Definition: MultiplexClustering.h:70
ProgressLogger.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::MultiplexClustering
clusters results from multiplex filtering
Definition: MultiplexClustering.h:63
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
OpenMS::MultiplexClustering::rt_minimum_
double rt_minimum_
minimum retention time
Definition: MultiplexClustering.h:160
OpenMS::MultiplexClustering::grid_spacing_rt_
std::vector< double > grid_spacing_rt_
Definition: MultiplexClustering.h:145
OpenMS::DPosition< 2 >
OpenMS::MultiplexClustering::grid_spacing_mz_
std::vector< double > grid_spacing_mz_
grid spacing for clustering
Definition: MultiplexClustering.h:144
OpenMS::MultiplexClustering::rt_typical_
double rt_typical_
typical retention time
Definition: MultiplexClustering.h:155
MultiplexFilteredMSExperiment.h
GridBasedCluster.h
BSpline2d.h