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OpenMS
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#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< 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. More... | |
| 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
| 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 |
| class OpenMS::SiriusMSFile::CompoundInfo |
| 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 |
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staticprotected |
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staticprotected |
Find highest intensity peak near target mz to test if within a margin of error.
| test_mz | Mass-to-charge to test |
| spectrum | Spectrum to test |
| tolerance | Tolerance window (e.g. 10) |
| ppm | Unit of tolerance window either ppm or Da |
|
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.
| spectra | Peakmap from input mzml. |
| msfile | Writes .ms file from sirius. |
| feature_mapping | Adducts and features (index). |
| feature_only | Only use features. |
| isotope_pattern_iterations | At which depth to stop isotope_pattern extraction (if possible). |
| v_cmpinfo | Vector of CompoundInfo. |
|
staticprotected |
Internal structure to write the .ms file (called in store function)
| os | stream |
| spectra | spectra |
| ms2_spectra_index | vector of index ms2 spectra (in feature) |
| ainfo | accession information |
| adducts | vector of adducts |
| v_description | vector of descriptions |
| v_sumformula | vector of sumformulas |
| f_isotopes | isotope pattern of the feature |
| feature_charge | feature charge |
| feature_id | feature id |
| feature_rt | features retention time |
| feature_mz | feature mass to charge |
| writecompound | bool if new compound should be written in .ms file |
| no_masstrace_info_isotope_pattern | bool if isotope pattern should be extracted (if not in feature) |
| isotope_pattern_iterations | number of iterations (trying to find a C13 pattern) |
| count_skipped_spectra | count number of skipped spectra |
| count_assume_mono | count number of features where mono charge was assumed |
| count_no_ms1 | count number of compounds without a valid ms1 spectrum |
| v_cmpinfo | vector of CompoundInfo |
1.9.1 
