#include <OpenMS/FORMAT/DATAACCESS/SiriusFragmentAnnotation.h>
◆ extract_columnname_to_columnindex()
static std::map< std::string, Size > extract_columnname_to_columnindex |
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const CsvFile & |
csvfile | ) |
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Extract columnname and index based in SIRIUS entries.
◆ extractAndResolveSiriusAnnotations()
static std::vector<SiriusTargetDecoySpectra> extractAndResolveSiriusAnnotations |
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const std::vector< String > & |
sirius_workspace_subdirs, |
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double |
score_threshold, |
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bool |
use_exact_mass, |
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bool |
decoy_generation |
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) |
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static |
extractAndResolveSiriusAnnotations Extract and resolves SIRIUS target and/or decoy annotation for mapping native_id to MSSpectrum.
- Returns
- map native_id to annotated MSSpectrum (target or decoy)
If there are multiple identifications for a feature with the same MS2 spectras (concatenated native ids) the identification with the higher SIRIUS score is chosen (currently based on the explained peak intensities).
- Parameters
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sirius_workspace_subdirs | Vector of paths to SIRIUS subdirectories. |
score_threshold | Only use spectra over a certain score threshold (0-1) |
use_exact_mass | Option to use exact mass instead of peak mz in MSSpectrum. |
decoy_generation | Extract decoy spectra from SIRIUS subdirectories. |
◆ extractAnnotationsFromSiriusFile()
static std::vector<MSSpectrum> extractAnnotationsFromSiriusFile |
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const String & |
path_to_sirius_workspace, |
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Size |
max_rank = 1 , |
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bool |
decoy = false , |
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bool |
use_exact_mass = false |
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) |
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static |
extractSiriusFragmentAnnotationMapping
Extract concatenated native ids and concatenated m_ids (unique identifier) from (./spectrum.ms) and annotations from spectra/decoy subfolder
If decoy
is true, uses fragment annotation (./spectra/1_sumformula.tsv) from SIRIUS output (per compound) else uses fragment annotation (./decoy/1_sumformula.tsv) from SIRIUS/PASSATUTTO output (per compound).
- Returns
- annotated decoy MSSpectrum with associated native id
MetaValues: peak_mz annotated_sumformula annotated_adduct
The data is stored in a MSSpectrum, which contains a Peak1D (mz or exact mass [depending on use_exact_mass
], int), a FloatDataArray for targets only (exact mass or mz [depending on use_exact_mass
]), a StringDataArray (explanation), and a StringDataArray (ionization).
MSSpectrum
Peak1D | | [FloatDataArray] | StringDataArray | StringDataArray |
mz | intensity | [exact_mass] | explanation | ionization |
56.050855 | 20794.85 | [56.049476] | C3H5N | [M + H]+ |
- Parameters
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path_to_sirius_workspace | Path to SIRIUS workspace. |
max_rank | Up to which rank to extract annotations maximally. Auto-stops at last candidate. |
decoy | Extract annotations for decoys? Or else targets. Run twice if you want both |
use_exact_mass | Option to use exact mass instead of peak mz in MSSpectrum. |
◆ extractCompoundRankingAndFilename_()
static std::map< Size, String > extractCompoundRankingAndFilename_ |
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const String & |
path_to_sirius_workspace | ) |
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staticprotected |
extractCompoundRankingAndFilename Extract compound ranking and filename (./formula_candidates.tsv).
- Returns
- a map with specified rank and filename (formula_adduct.tsv) (based on the annotation)
- Parameters
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path_to_sirius_workspace | Path to SIRIUS workspace. |
◆ extractCompoundRankingAndScore_()
static std::map< Size, double > extractCompoundRankingAndScore_ |
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const String & |
path_to_sirius_workspace | ) |
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staticprotected |
extractCompoundRankingAndFilename Extract compound ranking and score (./formula_candidates.tsv).
- Returns
- a map with specified rank and score (explainedIntensity) (based on the annotation)
- Parameters
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path_to_sirius_workspace | Path to SIRIUS workspace. |
◆ extractConcatMIDsFromSiriusMS_()
extractConcatMIDsFromSiriusMS Extract m_ids from SIRIUS output (./spectrum.ms) and concatenates them. M_id is the native id + an index, which is incremented based on the number of possible identifications (accurate mass search).
- Returns
- String m_id of current SIRIUS compound
- Parameters
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path_to_sirius_workspace | Path to SIRIUS workspace. |
◆ extractConcatNativeIDsFromSiriusMS_()
extractConcatNativeIDsFromSiriusMS Extract concatenated native id from SIRIUS output (./spectrum.ms) and concatenates them.
- Returns
- String native id of current SIRIUS compound
- Parameters
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path_to_sirius_workspace | Path to SIRIUS workspace. |
◆ extractFeatureIDFromSiriusMS_()
extractConcatMIDsFromSiriusMS Extract fid (i.e. original OpenMS feature ID) from SIRIUS output (./spectrum.ms).
- Returns
- String fid of current SIRIUS workspace
- Parameters
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path_to_sirius_workspace | Path to SIRIUS workspace. |