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SILACFiltering.h
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31 // $Maintainer: Lars Nilse $
32 // $Authors: Steffen Sass, Holger Plattfaut, Bastian Blank $
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34 
35 #ifndef OPENMS_FILTERING_DATAREDUCTION_SILACFILTERING_H
36 #define OPENMS_FILTERING_DATAREDUCTION_SILACFILTERING_H
37 
43 
44 #include <gsl/gsl_interp.h>
45 #include <gsl/gsl_spline.h>
46 #include <list>
47 #include <map>
48 #include <vector>
49 
50 namespace OpenMS
51 {
52  class SILACFilter;
53 
62  class OPENMS_DLLAPI SILACFiltering :
63  public ProgressLogger
64  {
65 public:
66  typedef std::vector<SILACFilter> Filters;
67 
72 
76  class OPENMS_DLLAPI SpectrumInterpolation
77  {
78 private:
79  gsl_interp_accel * current_;
80  gsl_spline * spline_;
81 
82 public:
85 
87  {
88  return gsl_spline_eval(spline_, mz, current_);
89  }
90 
91  };
92 
93 private:
98 
103 
108 
113 
118 
122  void pickSeeds_();
123 
127  void filterSeeds_();
128 
129 public:
130 
133 
139  SILACFiltering(MSExperiment<Peak1D> & exp, const PeakWidthEstimator::Result &, const DoubleReal intensity_cutoff, const String debug_filebase_ = "");
140 
145  void addFilter(SILACFilter & filter);
146 
150  void filterDataPoints();
151 
160  {
163  std::vector<DoubleReal> mass_separations;
165  };
166 
170  std::multimap<DoubleReal, BlacklistEntry> blacklist;
171  };
172 }
173 
174 #endif /* SILACFILTERING_H_ */
std::vector< DoubleReal > mass_separations
Definition: SILACFiltering.h:163
A more convenient string class.
Definition: String.h:56
DoubleReal operator()(DoubleReal mz) const
Definition: SILACFiltering.h:86
DRange< 2 > range
Definition: SILACFiltering.h:161
Filter to use for SILACFiltering.
Definition: SILACFilter.h:58
Int charge
Definition: SILACFiltering.h:162
std::vector< SILACFilter > Filters
Definition: SILACFiltering.h:66
const PeakWidthEstimator::Result peak_width
peak-width equation
Definition: SILACFiltering.h:132
gsl_spline * spline_
Definition: SILACFiltering.h:80
Filters filters_
holds all filters used in the filtering
Definition: SILACFiltering.h:71
DoubleReal intensity_cutoff_
minimal intensity of SILAC features
Definition: SILACFiltering.h:97
Definition: PeakWidthEstimator.h:60
std::multimap< DoubleReal, BlacklistEntry > blacklist
holds the range that is blacklisted for other filters and the filter that generated the blacklist ent...
Definition: SILACFiltering.h:170
Wrapper class for spectrum interpolation.
Definition: SILACFiltering.h:76
structure for blacklist
Definition: SILACFiltering.h:159
MSExperiment< Peak1D > & exp_
raw data
Definition: SILACFiltering.h:102
MSExperiment< Peak1D > picked_exp_
picked data
Definition: SILACFiltering.h:107
Base class for all classes that want to report their progess.
Definition: ProgressLogger.h:56
DoubleReal relative_peak_position
Definition: SILACFiltering.h:164
const String debug_filebase_
Definition: SILACFiltering.h:117
MSExperiment< Peak1D > picked_exp_seeds_
picked data seeds
Definition: SILACFiltering.h:112
int Int
Signed integer type.
Definition: Types.h:100
Filtering for SILAC data.
Definition: SILACFiltering.h:62
gsl_interp_accel * current_
Definition: SILACFiltering.h:79

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:20 using doxygen 1.8.5