OpenMS  3.0.0
RNPxlFragmentAnnotationHelper.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Timo Sachsenberg $
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34 
35 #pragma once
36 
41 
42 #include <set>
43 #include <map>
44 #include <vector>
45 #include <algorithm>
46 
47 namespace OpenMS
48 {
49 namespace Internal
50 {
51 
57 class OPENMS_DLLAPI RNPxlFragmentAnnotationHelper
58 {
59  public:
60 
62  struct OPENMS_DLLAPI FragmentAnnotationDetail_
63  {
64  FragmentAnnotationDetail_(String s, int z, double m, double i):
65  shift(s),
66  charge(z),
67  mz(m),
68  intensity(i)
69  {}
71  int charge;
72  double mz;
73  double intensity;
74 
75  bool operator<(const FragmentAnnotationDetail_& other) const
76  {
77  return std::tie(charge, shift, mz, intensity) <
78  std::tie(other.charge, other.shift, other.mz, other.intensity);
79  }
80 
81  bool operator==(const FragmentAnnotationDetail_& other) const
82  {
83  double mz_diff = fabs(mz - other.mz);
84  double intensity_diff = fabs(intensity - other.intensity);
85  return (charge == other.charge && shift == other.shift && mz_diff < 1e-6 && intensity_diff < 1e-6); // mz and intensity difference comparison actually not needed but kept for completeness
86  }
87  };
88 
89  static String getAnnotatedImmoniumIon(char c, const String& fragment_shift_name);
90 
92  static std::vector<PeptideHit::PeakAnnotation> fragmentAnnotationDetailsToPHFA(
93  const String& ion_type,
94  std::map<Size, std::vector<FragmentAnnotationDetail_> > ion_annotation_details);
95 
96  static std::vector<PeptideHit::PeakAnnotation> shiftedToPHFA(
97  const std::map<String,
98  std::set<std::pair<String, double> > >& shifted_ions);
99 
100 
101  static String shiftedIonsToString(const std::vector<PeptideHit::PeakAnnotation>& as);
102 
103  static void addShiftedPeakFragmentAnnotation_(const std::map<Size, std::vector<FragmentAnnotationDetail_>>& shifted_b_ions,
104  const std::map<Size, std::vector<FragmentAnnotationDetail_>>& shifted_y_ions,
105  const std::map<Size, std::vector<FragmentAnnotationDetail_>>& shifted_a_ions,
106  const std::vector<PeptideHit::PeakAnnotation>& shifted_immonium_ions,
107  const std::vector<PeptideHit::PeakAnnotation>& annotated_marker_ions,
108  const std::vector<PeptideHit::PeakAnnotation>& annotated_precursor_ions,
109  std::vector<PeptideHit::PeakAnnotation>& fas);
110 };
111 } // namespace Internal
112 } // namespace OpenMS
113 
114 
OpenMS::Internal::RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_::mz
double mz
Definition: RNPxlFragmentAnnotationHelper.h:72
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::Constants::c
const double c
Definition: Constants.h:209
Constants.h
OpenMS::Internal::RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_::operator==
bool operator==(const FragmentAnnotationDetail_ &other) const
Definition: RNPxlFragmentAnnotationHelper.h:81
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
PeptideHit.h
OpenMS::Internal::RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_::FragmentAnnotationDetail_
FragmentAnnotationDetail_(String s, int z, double m, double i)
Definition: RNPxlFragmentAnnotationHelper.h:64
OpenMS::Internal::RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_::operator<
bool operator<(const FragmentAnnotationDetail_ &other) const
Definition: RNPxlFragmentAnnotationHelper.h:75
String.h
OpenMS::Internal::RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_::intensity
double intensity
Definition: RNPxlFragmentAnnotationHelper.h:73
OpenMS::Internal::RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_::shift
String shift
Definition: RNPxlFragmentAnnotationHelper.h:70
OpenMS::Internal::RNPxlFragmentAnnotationHelper
Convenience functions to construct appealing fragment annotation strings and store them as PeptideHit...
Definition: RNPxlFragmentAnnotationHelper.h:57
StandardTypes.h
OpenMS::Internal::RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_::charge
int charge
Definition: RNPxlFragmentAnnotationHelper.h:71
OpenMS::Internal::RNPxlFragmentAnnotationHelper::FragmentAnnotationDetail_
Single fragment annotation.
Definition: RNPxlFragmentAnnotationHelper.h:62