OpenMS  2.5.0
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 
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 
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 
OpenMS::MultiplexClustering::MultiplexDistance
scaled Euclidean distance for clustering
Definition: MultiplexClustering.h:111
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
BSpline2d.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
ProgressLogger.h
OpenMS::MultiplexClustering::rt_minimum_
double rt_minimum_
minimum retention time
Definition: MultiplexClustering.h:160
OpenMS::MultiplexClustering::rt_scaling_
double rt_scaling_
scaling in y-direction for clustering
Definition: MultiplexClustering.h:150
GridBasedCluster.h
OpenMS::DPosition< 2 >
MultiplexFilteredMSExperiment.h
OpenMS::MultiplexClustering::rt_typical_
double rt_typical_
typical retention time
Definition: MultiplexClustering.h:155
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:145
OpenMS::MultiplexClustering::grid_spacing_mz_
std::vector< double > grid_spacing_mz_
grid spacing for clustering
Definition: MultiplexClustering.h:144
PeakPickerHiRes.h
MultiplexFiltering.h
StandardTypes.h
OpenMS::MultiplexClustering::MultiplexDistance::rt_scaling_
double rt_scaling_
Definition: MultiplexClustering.h:136