OpenMS  2.5.0
Classes | Static Public Member Functions | List of all members
SiriusMzTabWriter Class Reference

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

Classes

struct  SiriusAdapterHit
 Internal structure used in SiriusAdapter that is used for the conversion of the sirius output to an mzTab.SiriusAdapterHit: formula (String) - Sumformula adduct (String) - Assigned adduct rank (int) - Rank of the possible sumformula for a compound (spectrum) calculated by Sirius score (double) - Overall score of the possible sumformula for a compound (spectrum) calculated by Sirius treescore (double) - Fragmentation pattern score isoscore (double) - Isotope pattern score explainedpeaks (int) - Number of explained peaks explainedintensity (double) - Relative amount of explained intensity. More...
 
struct  SiriusAdapterIdentification
 
struct  SiriusAdapterRun
 

Static Public Member Functions

static int extract_scan_index (const String &path)
 Extract scan_index from filepath. More...
 
static void read (const std::vector< String > &sirius_output_paths, const String &original_input_mzml, const Size &top_n_hits, MzTab &result)
 Conversion of sirius output to mzTab. More...
 

Class Documentation

◆ OpenMS::SiriusMzTabWriter::SiriusAdapterHit

struct OpenMS::SiriusMzTabWriter::SiriusAdapterHit

Internal structure used in SiriusAdapter that is used for the conversion of the sirius output to an mzTab.

SiriusAdapterHit: formula (String) - Sumformula adduct (String) - Assigned adduct rank (int) - Rank of the possible sumformula for a compound (spectrum) calculated by Sirius score (double) - Overall score of the possible sumformula for a compound (spectrum) calculated by Sirius treescore (double) - Fragmentation pattern score isoscore (double) - Isotope pattern score explainedpeaks (int) - Number of explained peaks explainedintensity (double) - Relative amount of explained intensity.

SiriusAdapterIdentification: scan_index (int) - Index of the spectrum used scan_number (int) - NativeId of the spectrum used feature_id (String) - FeatureId (if spectrum was assigned to a feature) hits (vector<SiriusAdapterHit>)

SiriusAdapterRun: identifications (vector<SiriusAdapterIdentification>)

Store a specific

Parameters
numberof lines from sirius output
Returns
mzTab
Class Members
String adduct
double explainedintensity
int explainedpeaks
String formula
double isoscore
int rank
double score
double treescore

◆ OpenMS::SiriusMzTabWriter::SiriusAdapterIdentification

struct OpenMS::SiriusMzTabWriter::SiriusAdapterIdentification
Class Members
String feature_id
vector< SiriusAdapterHit > hits
double mz
String native_id
double rt
int scan_index
int scan_number

◆ OpenMS::SiriusMzTabWriter::SiriusAdapterRun

struct OpenMS::SiriusMzTabWriter::SiriusAdapterRun
Class Members
vector< SiriusAdapterIdentification > identifications

Member Function Documentation

◆ extract_scan_index()

static int extract_scan_index ( const String path)
static

Extract scan_index from filepath.

◆ read()

static void read ( const std::vector< String > &  sirius_output_paths,
const String original_input_mzml,
const Size top_n_hits,
MzTab result 
)
static

Conversion of sirius output to mzTab.

Output of Sirius is one directory per spectrum/compound

Parameters
sirius_output_pathsPath to output directories of Sirius
original_input_mzmlPath to mzml input of SiriusAdapter
top_n_hitsTop n entries for each compound written to the result file
Returns
: Result written to mzTab