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SILACFilter.h
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34 
35 #ifndef OPENMS_FILTERING_DATAREDUCTION_SILACFILTER_H
36 #define OPENMS_FILTERING_DATAREDUCTION_SILACFILTER_H
37 
42 #include <gsl/gsl_interp.h>
43 #include <gsl/gsl_spline.h>
44 #include <queue>
45 #include <list>
46 
47 namespace OpenMS
48 {
58  class OPENMS_DLLAPI SILACFilter
59  {
60 private:
61  friend class SILACFiltering;
62 
64 
68  std::vector<DoubleReal> mass_separations_;
69 
74 
79 
84 
89 
94 
99 
104 
109 
113  std::vector<DoubleReal> peak_positions_;
114 
118  std::vector<DoubleReal> mz_peptide_separations_;
119 
123  std::vector<DoubleReal> expected_mz_shifts_;
124 
129 
133  std::vector<SILACPattern> elements_;
134 
139 
143  std::vector<std::vector<DoubleReal> > exact_shifts_;
144 
148  std::vector<std::vector<DoubleReal> > exact_mz_positions_;
149 
153  std::vector<std::vector<DoubleReal> > exact_intensities_;
154 
158  std::vector<std::vector<DoubleReal> > expected_shifts_;
159 
165  bool isSILACPattern_(const MSSpectrum<Peak1D> &, const SILACFiltering::SpectrumInterpolation &, DoubleReal mz, DoubleReal picked_mz, const SILACFiltering &, MSSpectrum<Peak1D> & debug, SILACPattern & pattern);
166 
170  bool isSILACPatternPicked_(const MSSpectrum<Peak1D> &, DoubleReal mz, const SILACFiltering &, MSSpectrum<Peak1D> & debug);
171 
175  bool extractMzShiftsAndIntensities_(const MSSpectrum<Peak1D> &, const SILACFiltering::SpectrumInterpolation &, DoubleReal mz, DoubleReal picked_mz, const SILACFiltering &);
176 
180  bool extractMzShiftsAndIntensitiesPicked_(const MSSpectrum<Peak1D> &, DoubleReal mz, const SILACFiltering &);
181 
185  bool extractMzShiftsAndIntensitiesPickedToPattern_(const MSSpectrum<Peak1D> &, DoubleReal mz, const SILACFiltering &, SILACPattern & pattern);
186 
190  bool intensityFilter_();
191 
195  bool correlationFilter1_(const SILACFiltering::SpectrumInterpolation &, DoubleReal mz, const SILACFiltering &);
196 
200  bool correlationFilter2_(const SILACFiltering::SpectrumInterpolation &, DoubleReal mz, const SILACFiltering &);
201 
205  bool averageneFilter_(DoubleReal mz);
206 
207 public:
218  SILACFilter(std::vector<DoubleReal> mass_separations, Int charge, DoubleReal model_deviation, Int isotopes_per_peptide,
219  DoubleReal intensity_cutoff, DoubleReal intensity_correlation, bool allow_missing_peaks);
220 
224  std::vector<DoubleReal> getPeakPositions();
225 
229  const std::vector<DoubleReal> & getExpectedMzShifts();
230 
234  std::vector<SILACPattern> & getElements();
235 
239  Int getCharge();
240 
244  std::vector<DoubleReal> & getMassSeparations();
245  };
246 }
247 
248 #endif /* SILACFILTER_H_ */
Size isotopes_per_peptide_
number of peaks per peptide to search for
Definition: SILACFilter.h:83
DoubleReal model_deviation_
maximal value of which a predicted SILAC feature may deviate from the averagine model ...
Definition: SILACFilter.h:78
static IsotopeDistributionCache * isotope_distribution_
Definition: SILACFilter.h:103
std::vector< std::vector< DoubleReal > > exact_shifts_
exact m/z shift of isotopic peaks in a SILAC pattern relative to the mono-isotopic peak of the light ...
Definition: SILACFilter.h:143
DoubleReal intensity_cutoff_
minimal intensity of SILAC features
Definition: SILACFilter.h:88
DoubleReal isotope_distance_
distance between isotopic peaks of a peptide in [Th]
Definition: SILACFilter.h:128
Helper structure for a theoretical isotope pattern used in FeatureFinderAlgorithmPicked.
Definition: FeatureFinderAlgorithmPickedHelperStructs.h:277
Filter to use for SILACFiltering.
Definition: SILACFilter.h:58
bool allow_missing_peaks_
flag for missing peaks
Definition: SILACFilter.h:98
std::vector< DoubleReal > mass_separations_
mass shift(s) in [Da] to search for
Definition: SILACFilter.h:68
std::vector< SILACPattern > elements_
holds the recognized features
Definition: SILACFilter.h:133
Size number_of_peptides_
number of peptides [i.e. number of labelled peptides +1, e.g. for SILAC triplet =3] ...
Definition: SILACFilter.h:108
DoubleReal current_mz_
m/z at which the filter is currently applied to
Definition: SILACFilter.h:138
std::vector< DoubleReal > peak_positions_
peak positions of SILAC pattern
Definition: SILACFilter.h:113
std::vector< std::vector< DoubleReal > > exact_mz_positions_
m/z positions mz + exact_shifts in a SILAC pattern, where mz is the m/z of the mono-isotopic peak of ...
Definition: SILACFilter.h:148
Wrapper class for spectrum interpolation.
Definition: SILACFiltering.h:76
std::vector< DoubleReal > expected_mz_shifts_
m/z shifts relative to mono-isotopic peak of unlabelled peptide
Definition: SILACFilter.h:123
std::vector< std::vector< DoubleReal > > exact_intensities_
intensities at mz + exact_shifts in a SILAC pattern, where mz is the m/z of the mono-isotopic peak of...
Definition: SILACFilter.h:153
DoubleReal intensity_correlation_
minimal intensity correlation between regions of different peaks
Definition: SILACFilter.h:93
Int charge_
charge of the ions to search for
Definition: SILACFilter.h:73
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
IsotopeDistributionCache::TheoreticalIsotopePattern TheoreticalIsotopePattern
Definition: SILACFilter.h:63
A single SILAC pattern containing multiple found points.
Definition: SILACPattern.h:47
std::vector< DoubleReal > mz_peptide_separations_
m/z separtion between individual peptides [e.g. {0 Th, 4 Th, 5 Th}]
Definition: SILACFilter.h:118
Prealculate isotope distributions for interesting mass ranges.
Definition: IsotopeDistributionCache.h:46
int Int
Signed integer type.
Definition: Types.h:100
std::vector< std::vector< DoubleReal > > expected_shifts_
expected m/z shift of isotopic peaks in a SILAC pattern relative to the mono-isotopic peak of the lig...
Definition: SILACFilter.h:158
Filtering for SILAC data.
Definition: SILACFiltering.h:62

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