OpenMS  2.4.0
RNPxlDeisotoper.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Timo Sachsenberg $
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34 
35 #pragma once
36 
38 #include <OpenMS/CONCEPT/Types.h>
40 
41 namespace OpenMS
42 {
43 
44 class MSSpectrum;
45 
46 class OPENMS_DLLAPI Deisotoper
47 {
48  public:
49 
50  /* @brief Detect isotopic clusters in a fragment spectrum.
51 
52  * @param [spectra] Input spectra (sorted by m/z)
53  * @param [min_charge] The minimum charge considered
54  * @param [max_charge] The maximum charge considered
55  * @param [fragment_tolerance] The tolerance used to match isotopic peaks
56  * @oaram [fragment_unit_ppm] Whether ppm or m/z is used as tolerance
57  * @param [keep_only_deisotoped] Only monoisotopic peaks of fragments with isotopic pattern are retained
58  * @param [min_isopeaks] The minimum number of isotopic peaks (at least 2) required for an isotopic cluster
59  * @param [max_isopeaks] The maximum number of isotopic peaks (at least 2) considered for an isotopic cluster
60  * @param [make_single_charged] Convert deisotoped monoisotopic peak to single charge
61  * @param [annotate_charge] Annotate the charge to the peaks in the IntegerDataArray: "charge" (0 for unknown charge)
62  * Note: If make_single_charged is selected, the original charge (>=1) gets annotated.
63  */
64  static void deisotopeAndSingleCharge(MSSpectrum & spectra,
65  double fragment_tolerance,
66  bool fragment_unit_ppm,
67  int min_charge = 1,
68  int max_charge = 3,
69  bool keep_only_deisotoped = false,
70  unsigned int min_isopeaks = 3,
71  unsigned int max_isopeaks = 10,
72  bool make_single_charged = true,
73  bool annotate_charge = false);
74 };
75 
76 }
77 
Definition: RNPxlDeisotoper.h:46
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66