OpenMS  2.8.0
Classes | Static Public Member Functions | Static Protected Member Functions | List of all members
SiriusMSFile Class Reference

#include <OpenMS/ANALYSIS/ID/SiriusMSConverter.h>

Classes

class  AccessionInfo
 < class to store information about accessions More...
 
class  CompoundInfo
 

Static Public Member Functions

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 format. More...
 

Static Protected Member Functions

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) More...
 
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. More...
 
static std::vector< Peak1DextractPrecursorIsotopePattern_ (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. More...
 

Class Documentation

◆ OpenMS::SiriusMSFile::AccessionInfo

class OpenMS::SiriusMSFile::AccessionInfo

< class to store information about accessions

class to store the compound information needed for the mapping of compound and fragment annotated spectrum

Collaboration diagram for SiriusMSFile::AccessionInfo:
[legend]
Class Members
String native_id_accession nativeID accession for mztab-m
String native_id_type nativeID type for mztab-m
String sf_accession sourcefile accessions for mztab-m
String sf_filename sourcefile name for mztab-m
String sf_path sourcefile path for mztab-m
String sf_type sourcefile type for mztab-m

◆ OpenMS::SiriusMSFile::CompoundInfo

class OpenMS::SiriusMSFile::CompoundInfo
Collaboration diagram for SiriusMSFile::CompoundInfo:
[legend]
Class Members
int charge precursor/feature charge
String cmp query_id used compound in .ms file
String des description/name of the compound
String fid annotated feature_id (if available)
double fmz annotated mass of a feature (if available)
String formula sumformula of the compound
String ionization adduct information
vector< String > m_ids native ids and identifier for multiple possible identification via AMS ("|" separator)
String m_ids_id concatenated list of native ids and identifier for multiple possible identification via AMS ("|" separator) used for mapping of compounds and the annotated spectrum.
vector< String > native_ids native ids of the associated spectra
String native_ids_id concatenated list of the associated spectra
double pint_mono parent/precursor intensity of the compound
double pmass parent/precursor mass of the compound
double rt retention time of the compound
vector< String > scan_indices index of the associated spectra
String source_file sourcefile for mztab-m
String source_format format of the sourcefile for mztab-m
String specref_format spectra ref format for mztab-m
vector< String > specrefs spectra reference for mztab-m

Member Function Documentation

◆ extractPrecursorIsotopePattern_()

static std::vector<Peak1D> extractPrecursorIsotopePattern_ ( const double &  precursor_mz,
const MSSpectrum precursor_spectrum,
int &  iterations,
const int &  charge 
)
staticprotected

Extract precursor isotope pattern if no feature information is available based on C12C13 distance.

Parameters
precursor_mzPrecursor mass-to-charge
precursor_spectrumPrecursor spectrum
iterationsNumber of isotopes, which are tried to be extracted
chargeCharge of the precursor

◆ getHighestIntensityPeakInMZRange_()

static Int getHighestIntensityPeakInMZRange_ ( double  test_mz,
const MSSpectrum spectrum,
double  tolerance,
bool  ppm 
)
staticprotected

Find highest intensity peak near target mz to test if within a margin of error.

Parameters
test_mzMass-to-charge to test
spectrumSpectrum to test
toleranceTolerance window (e.g. 10)
ppmUnit of tolerance window either ppm or Da

◆ store()

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 
)
static

Internal structure used in SiriusAdapter that is used for the conversion of a MzMlFile to an internal format.

Store .ms file. Comments (see CompoundInfo) are written to SIRIUS .ms file and additionally stores in CompoundInfo struct. If adduct information for a spectrum is missing, no adduct information is added. In this case, SIRIUS assumes default adducts for the respective spectrum.

Returns
writes .ms file
stores CompoundInfo
Parameters
spectraPeakmap from input mzml.
msfileWrites .ms file from sirius.
feature_mappingAdducts and features (index).
feature_onlyOnly use features.
isotope_pattern_iterationsAt which depth to stop isotope_pattern extraction (if possible).
v_cmpinfoVector of CompoundInfo.

◆ writeMsFile_()

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 
)
staticprotected

Internal structure to write the .ms file (called in store function)

Parameters
osstream
spectraspectra
ms2_spectra_indexvector of index ms2 spectra (in feature)
ainfoaccession information
adductsvector of adducts
v_descriptionvector of descriptions
v_sumformulavector of sumformulas
f_isotopesisotope pattern of the feature
feature_chargefeature charge
feature_idfeature id
feature_rtfeatures retention time
feature_mzfeature mass to charge
writecompoundbool if new compound should be written in .ms file
no_masstrace_info_isotope_patternbool if isotope pattern should be extracted (if not in feature)
isotope_pattern_iterationsnumber of iterations (trying to find a C13 pattern)
count_skipped_spectracount number of skipped spectra
count_assume_monocount number of features where mono charge was assumed
count_no_ms1count number of compounds without a valid ms1 spectrum
v_cmpinfovector of CompoundInfo