#include <OpenMS/FORMAT/DATAACCESS/SiriusFragmentAnnotation.h>

Classes
class	SiriusTargetDecoySpectra
	SiriusTargetDecoySpectra holds the target and/or decoy information for one entry (subdirectory from SIRIUS) More...

Static Public Member Functions
static std::vector< SiriusTargetDecoySpectra >	extractAndResolveSiriusAnnotations (const std::vector< String > &sirius_workspace_subdirs, double score_threshold, bool use_exact_mass, bool decoy_generation)
	extractAndResolveSiriusAnnotations Extract and resolves SIRIUS target and/or decoy annotation for mapping native_id to MSSpectrum. More...

static std::vector< MSSpectrum >	extractAnnotationsFromSiriusFile (const String &path_to_sirius_workspace, Size max_rank=1, bool decoy=false, bool use_exact_mass=false)
	extractSiriusFragmentAnnotationMapping Extract concatenated native ids and concatenated m_ids (unique identifier) from (./spectrum.ms) and annotations from spectra/decoy subfolder More...

static std::map< std::string, Size >	extract_columnname_to_columnindex (const CsvFile &csvfile)
	Extract columnname and index based in SIRIUS entries. More...

Static Protected Member Functions
static OpenMS::String	extractConcatNativeIDsFromSiriusMS_ (const OpenMS::String &path_to_sirius_workspace)
	extractConcatNativeIDsFromSiriusMS Extract concatenated native id from SIRIUS output (./spectrum.ms) and concatenates them. More...

static OpenMS::String	extractConcatMIDsFromSiriusMS_ (const String &path_to_sirius_workspace)
	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). More...

static OpenMS::String	extractFeatureIDFromSiriusMS_ (const String &path_to_sirius_workspace)
	extractConcatMIDsFromSiriusMS Extract fid (i.e. original OpenMS feature ID) from SIRIUS output (./spectrum.ms). More...

static std::map< Size, String >	extractCompoundRankingAndFilename_ (const String &path_to_sirius_workspace)
	extractCompoundRankingAndFilename Extract compound ranking and filename (./formula_candidates.tsv). More...

static std::map< Size, double >	extractCompoundRankingAndScore_ (const String &path_to_sirius_workspace)
	extractCompoundRankingAndFilename Extract compound ranking and score (./formula_candidates.tsv). More...

Member Function Documentation

◆ extract_columnname_to_columnindex()

static std::map< std::string, Size > extract_columnname_to_columnindex ( const CsvFile & csvfile )

static

Extract columnname and index based in SIRIUS entries.

◆ extractAndResolveSiriusAnnotations()

static std::vector<SiriusTargetDecoySpectra> extractAndResolveSiriusAnnotations	(	const std::vector< String > &	sirius_workspace_subdirs,
		double	score_threshold,
		bool	use_exact_mass,
		bool	decoy_generation
	)

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

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	(	const String &	path_to_sirius_workspace,
		Size	max_rank = `1`,
		bool	decoy = `false`,
		bool	use_exact_mass = `false`
	)

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

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_ ( const String & path_to_sirius_workspace )

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

path_to_sirius_workspace Path to SIRIUS workspace.

◆ extractCompoundRankingAndScore_()

static std::map< Size, double > extractCompoundRankingAndScore_ ( const String & path_to_sirius_workspace )

staticprotected

extractCompoundRankingAndFilename Extract compound ranking and score (./formula_candidates.tsv).

Returns: a map with specified rank and score (explainedIntensity) (based on the annotation)

Parameters

path_to_sirius_workspace Path to SIRIUS workspace.

◆ extractConcatMIDsFromSiriusMS_()

static OpenMS::String extractConcatMIDsFromSiriusMS_ ( const String & path_to_sirius_workspace )

staticprotected

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

path_to_sirius_workspace Path to SIRIUS workspace.

◆ extractConcatNativeIDsFromSiriusMS_()

static OpenMS::String extractConcatNativeIDsFromSiriusMS_ ( const OpenMS::String & path_to_sirius_workspace )

staticprotected

extractConcatNativeIDsFromSiriusMS Extract concatenated native id from SIRIUS output (./spectrum.ms) and concatenates them.

Returns: String native id of current SIRIUS compound

Parameters

path_to_sirius_workspace Path to SIRIUS workspace.

◆ extractFeatureIDFromSiriusMS_()

static OpenMS::String extractFeatureIDFromSiriusMS_ ( const String & path_to_sirius_workspace )

staticprotected

extractConcatMIDsFromSiriusMS Extract fid (i.e. original OpenMS feature ID) from SIRIUS output (./spectrum.ms).

Returns: String fid of current SIRIUS workspace

Parameters

path_to_sirius_workspace Path to SIRIUS workspace.

Classes

Static Public Member Functions

Static Protected Member Functions

Member Function Documentation

◆ extract_columnname_to_columnindex()

◆ extractAndResolveSiriusAnnotations()

◆ extractAnnotationsFromSiriusFile()

◆ extractCompoundRankingAndFilename_()

◆ extractCompoundRankingAndScore_()

◆ extractConcatMIDsFromSiriusMS_()

◆ extractConcatNativeIDsFromSiriusMS_()

◆ extractFeatureIDFromSiriusMS_()