OpenMS  3.0.0
MultiplexClustering.h
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31 // $Maintainer: Lars Nilse $
32 // $Authors: Lars Nilse $
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34 
35 #pragma once
36 
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:
71 
82  MultiplexClustering(const MSExperiment& exp_profile, const MSExperiment& exp_picked, const std::vector<std::vector<PeakPickerHiRes::PeakBoundary> >& boundaries, double rt_typical);
83 
94  MultiplexClustering(const MSExperiment& exp, double mz_tolerance, bool mz_tolerance_unit, double rt_typical);
95 
104  std::vector<std::map<int,GridBasedCluster> > cluster(const std::vector<MultiplexFilteredMSExperiment>& filter_results);
105 
109  class OPENMS_DLLAPI MultiplexDistance
110  {
111  public:
117  MultiplexDistance(double rt_scaling);
118 
123 
131  double operator()(const Point& p1, const Point& p2) const;
132 
133  private:
134  double rt_scaling_;
135 
136  };
137 
138  private:
142  std::vector<double> grid_spacing_mz_;
143  std::vector<double> grid_spacing_rt_;
144 
148  double rt_scaling_;
149 
153  double rt_typical_;
154 
158  //unused
159  //double rt_minimum_;
160 
161  };
162 
163 }
164 
OpenMS::MultiplexClustering::MultiplexDistance
scaled Euclidean distance for clustering
Definition: MultiplexClustering.h:109
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
BSpline2d.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
ProgressLogger.h
OpenMS::MultiplexClustering::rt_scaling_
double rt_scaling_
scaling in y-direction for clustering
Definition: MultiplexClustering.h:148
GridBasedCluster.h
OpenMS::DPosition< 2 >
MultiplexFilteredMSExperiment.h
OpenMS::MultiplexClustering::rt_typical_
double rt_typical_
typical retention time
Definition: MultiplexClustering.h:153
OpenMS::MultiplexClustering
clusters results from multiplex filtering
Definition: MultiplexClustering.h:63
OpenMS::MultiplexClustering::Point
GridBasedCluster::Point Point
cluster centre, cluster bounding box, grid index
Definition: MultiplexClustering.h:70
OpenMS::MultiplexClustering::grid_spacing_rt_
std::vector< double > grid_spacing_rt_
Definition: MultiplexClustering.h:143
OpenMS::MultiplexClustering::grid_spacing_mz_
std::vector< double > grid_spacing_mz_
grid spacing for clustering
Definition: MultiplexClustering.h:142
PeakPickerHiRes.h
MultiplexFiltering.h
StandardTypes.h
OpenMS::MultiplexClustering::MultiplexDistance::rt_scaling_
double rt_scaling_
Definition: MultiplexClustering.h:134