SiriusFragmentAnnotation Class Reference

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

Static Public Member Functions
static void	extractSiriusFragmentAnnotationMapping (const String &path_to_sirius_workspace, MSSpectrum &msspectrum_to_fill, bool use_exact_mass=false)
	extractSiriusFragmentAnnotationMapping Extract native id (./spectrum.ms) and fragment annotation (./spectra/1_sumformula.ms) from SIRIUS output (per compound). More...

Static Protected Member Functions
static OpenMS::String	extractNativeIDFromSiriusMS_ (const OpenMS::String &path_to_sirius_workspace)
	extractNativeIDFromSiriusMS Extract native id from SIRIUS output (./spectrum.ms). More...
static OpenMS::String	extractMIDFromSiriusMS_ (const String &path_to_sirius_workspace)
	extractMIDFromSiriusMS Extract mid from SIRIUS output (./spectrum.ms). Mid is the native id + an index, which is incremented based on the number of possible identifications (accurate mass search). More...
static void	extractAnnotationFromSiriusFile_ (const String &path_to_sirius_workspace, MSSpectrum &msspectrum_to_fill, bool use_exact_mass=false)
	extractAnnotationFromSiriusFile Extract fragment annotation from SIRIUS (./spectra/1_sumformula.ms). More...

Member Function Documentation

extractAnnotationFromSiriusFile_()

static void extractAnnotationFromSiriusFile_ ( const String &  path_to_sirius_workspace, MSSpectrum &  msspectrum_to_fill, bool  use_exact_mass = false  )

staticprotected

extractAnnotationFromSiriusFile Extract fragment annotation from SIRIUS (./spectra/1_sumformula.ms).

Returns

annotated (consensus) MSSpectrum (mz, int, exact mass, fragment explanation).

MetaValues: peak_mz: indicates which mass input was used in Peak1D (mz or exact_mass). annotated_sumformula annotated_adduct

Parameters

path_to_sirius_workspace	Path to SIRIUS workspace.
use_exact_mass	Option to use exact mass instead of peak mz in MSSpectrum.

extractMIDFromSiriusMS_()

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

staticprotected

extractMIDFromSiriusMS Extract mid from SIRIUS output (./spectrum.ms). Mid is the native id + an index, which is incremented based on the number of possible identifications (accurate mass search).

Returns

String mid of current SIRIUS compound

Parameters

path_to_sirius_workspace

Path to SIRIUS workspace.

extractNativeIDFromSiriusMS_()

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

staticprotected

extractNativeIDFromSiriusMS Extract native id from SIRIUS output (./spectrum.ms).

Returns

String native id of current SIRIUS compound

Parameters

path_to_sirius_workspace

Path to SIRIUS workspace.

extractSiriusFragmentAnnotationMapping()

static void extractSiriusFragmentAnnotationMapping ( const String &  path_to_sirius_workspace, MSSpectrum &  msspectrum_to_fill, bool  use_exact_mass = false  )

static

extractSiriusFragmentAnnotationMapping Extract native id (./spectrum.ms) and fragment annotation (./spectra/1_sumformula.ms) from SIRIUS output (per compound).

Returns

annotated (consensus) MSSpectrum with associated native id

MetaValues: peak_mz: indicates which mass input was used in Peak1D (mass or exact_mass). annotated_sumformula annotated_adduct

The data is stored in a MSSpectrum, which contains a Peak1D (mz, int), a FloatDataArry (exact mass), and a StringDataArry (explanation).

MSSpectrum

Peak1D		FloatDataArray	StringDataArray
mz	intensity	exact_mass	explanation
56.050855	20794.85	56.049476	C3H5N

Parameters

path_to_sirius_workspace	Path to SIRIUS workspace.
use_exact_mass	Option to use exact mass instead of peak mz in MSSpectrum.