OpenMS
SiriusMSConverter.h
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31 // $Maintainer: Oliver Alka $
32 // $Authors: Oliver Alka $
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34 
35 #pragma once
36 
40 #include <fstream>
41 
42 namespace OpenMS
43 {
44 
45  class OPENMS_DLLAPI SiriusMSFile
46  {
47 public:
48 
51  {
52  public:
59  };
60 
64  {
65  public:
67  double pmass;
68  double pint_mono;
69  double rt;
70  double fmz;
73  int charge;
79  std::vector<String> native_ids;
81  std::vector<String> m_ids;
83  std::vector<String> scan_indices;
84  std::vector<String> specrefs;
85  };
86 
109  static void store(const MSExperiment& spectra,
110  const OpenMS::String& msfile,
111  const FeatureMapping::FeatureToMs2Indices& feature_mapping,
112  const bool& feature_only,
113  const int& isotope_pattern_iterations,
114  const bool no_mt_info,
115  std::vector<SiriusMSFile::CompoundInfo>& v_cmpinfo);
116 
117 
118  protected:
143  static void writeMsFile_(std::ofstream& os,
144  const MSExperiment& spectra,
145  const std::vector<size_t>& ms2_spectra_index,
146  const SiriusMSFile::AccessionInfo& ainfo,
147  const StringList& adducts,
148  const std::vector<String>& v_description,
149  const std::vector<String>& v_sumformula,
150  const std::vector<std::pair<double,double>>& f_isotopes,
151  int& feature_charge,
152  uint64_t& feature_id,
153  const double& feature_rt,
154  const double& feature_mz,
155  bool& writecompound,
156  const bool& no_masstrace_info_isotope_pattern,
157  const int& isotope_pattern_iterations,
158  int& count_skipped_spectra,
159  int& count_assume_mono,
160  int& count_no_ms1,
161  std::vector<SiriusMSFile::CompoundInfo>& v_cmpinfo);
162 
163 
164 
173  static Int getHighestIntensityPeakInMZRange_(double test_mz,
174  const MSSpectrum& spectrum,
175  double tolerance,
176  bool ppm);
177 
187  static std::vector<Peak1D> extractPrecursorIsotopePattern_(const double& precursor_mz,
188  const MSSpectrum& precursor_spectrum,
189  int& iterations,
190  const int& charge);
191 
192 
193 
194  };
195 
196 } // namespace OpenMS
Stores preprocessed feature mapping information.
Definition: FeatureMapping.h:59
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:72
The representation of a 1D spectrum.
Definition: MSSpectrum.h:70
Definition: SiriusMSConverter.h:46
String sf_type
sourcefile type for mztab-m
Definition: SiriusMSConverter.h:54
static std::vector< Peak1D > extractPrecursorIsotopePattern_(const double &precursor_mz, const MSSpectrum &precursor_spectrum, int &iterations, const int &charge)
Extract precursor isotope pattern if no feature information is available based on C12C13 distance.
String native_id_accession
nativeID accession for mztab-m
Definition: SiriusMSConverter.h:57
std::vector< String > native_ids
native ids of the associated spectra
Definition: SiriusMSConverter.h:79
String m_ids_id
concatenated list of native ids and identifier for multiple possible identification via AMS ("|" sepa...
Definition: SiriusMSConverter.h:82
String source_file
sourcefile for mztab-m
Definition: SiriusMSConverter.h:77
String native_ids_id
concatenated list of the associated spectra
Definition: SiriusMSConverter.h:80
String specref_format
spectra ref format for mztab-m
Definition: SiriusMSConverter.h:76
String native_id_type
nativeID type for mztab-m
Definition: SiriusMSConverter.h:58
static void store(const MSExperiment &spectra, const OpenMS::String &msfile, const FeatureMapping::FeatureToMs2Indices &feature_mapping, const bool &feature_only, const int &isotope_pattern_iterations, const bool no_mt_info, std::vector< SiriusMSFile::CompoundInfo > &v_cmpinfo)
Internal structure used in SiriusAdapter that is used for the conversion of a MzMlFile to an internal...
String sf_accession
sourcefile accessions for mztab-m
Definition: SiriusMSConverter.h:56
String source_format
format of the sourcefile for mztab-m
Definition: SiriusMSConverter.h:78
double pint_mono
parent/precursor intensity of the compound
Definition: SiriusMSConverter.h:68
String cmp
query_id used compound in .ms file
Definition: SiriusMSConverter.h:66
std::vector< String > scan_indices
index of the associated spectra
Definition: SiriusMSConverter.h:83
String formula
sumformula of the compound
Definition: SiriusMSConverter.h:72
String sf_filename
sourcefile name for mztab-m
Definition: SiriusMSConverter.h:55
String sf_path
sourcefile path for mztab-m
Definition: SiriusMSConverter.h:53
String ionization
adduct information
Definition: SiriusMSConverter.h:74
String des
description/name of the compound
Definition: SiriusMSConverter.h:75
static Int getHighestIntensityPeakInMZRange_(double test_mz, const MSSpectrum &spectrum, double tolerance, bool ppm)
Find highest intensity peak near target mz to test if within a margin of error.
double pmass
parent/precursor mass of the compound
Definition: SiriusMSConverter.h:67
double rt
retention time of the compound
Definition: SiriusMSConverter.h:69
int charge
precursor/feature charge
Definition: SiriusMSConverter.h:73
std::vector< String > specrefs
spectra reference for mztab-m
Definition: SiriusMSConverter.h:84
double fmz
annotated mass of a feature (if available)
Definition: SiriusMSConverter.h:70
std::vector< String > m_ids
native ids and identifier for multiple possible identification via AMS ("|" separator)
Definition: SiriusMSConverter.h:81
static void writeMsFile_(std::ofstream &os, const MSExperiment &spectra, const std::vector< size_t > &ms2_spectra_index, const SiriusMSFile::AccessionInfo &ainfo, const StringList &adducts, const std::vector< String > &v_description, const std::vector< String > &v_sumformula, const std::vector< std::pair< double, double >> &f_isotopes, int &feature_charge, uint64_t &feature_id, const double &feature_rt, const double &feature_mz, bool &writecompound, const bool &no_masstrace_info_isotope_pattern, const int &isotope_pattern_iterations, int &count_skipped_spectra, int &count_assume_mono, int &count_no_ms1, std::vector< SiriusMSFile::CompoundInfo > &v_cmpinfo)
Internal structure to write the .ms file (called in store function)
String fid
annotated feature_id (if available)
Definition: SiriusMSConverter.h:71
< class to store information about accessions
Definition: SiriusMSConverter.h:51
Definition: SiriusMSConverter.h:64
A more convenient string class.
Definition: String.h:60
int Int
Signed integer type.
Definition: Types.h:102
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48