OpenMS  2.8.0
Classes | Static Public Member Functions | List of all members
CsiFingerIdMzTabWriter Class Reference

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

Classes

class  CsiAdapterHit
 Internal structure used in SiriusAdapter that is used for the conversion of the Csi:FingerID output to an mzTab. More...
 
class  CsiAdapterIdentification
 
class  CsiAdapterRun
 

Static Public Member Functions

static void read (const std::vector< String > &sirius_output_paths, const String &original_input_mzml, const Size &top_n_hits, MzTab &result)
 Conversion of CSI:FingerID output to mzTab. More...
 

Class Documentation

◆ OpenMS::CsiFingerIdMzTabWriter::CsiAdapterHit

class OpenMS::CsiFingerIdMzTabWriter::CsiAdapterHit

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

CsiAdapterHit: inchikey2D (String) inchi (String) rank (int) - Rank of the identification for a compound (spectrum) calculated by CSI:FingerID molecular_formula (String) - sumformula score (int) - Score of the identification for a compound (spectrum) calculated by CSI:FingerID name (String) smiles (String) pubchemids (vector<String>) - PubChemID as reference links (vector<String>) - Links to the database

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

CsiAdapterRun: identifications (vector<CSIAdapterIdentification>)

Collaboration diagram for CsiFingerIdMzTabWriter::CsiAdapterHit:
[legend]
Class Members
String adduct
String dbflags
unsigned int formula_rank
String inchi
String inchikey2D
vector< String > links
String molecular_formula
String name
vector< String > pubchemids
unsigned int rank
double score
String smiles
String xlogp

◆ OpenMS::CsiFingerIdMzTabWriter::CsiAdapterIdentification

class OpenMS::CsiFingerIdMzTabWriter::CsiAdapterIdentification
Collaboration diagram for CsiFingerIdMzTabWriter::CsiAdapterIdentification:
[legend]
Class Members
String feature_id
vector< CsiAdapterHit > hits
double mz
StringList native_ids
double rt
int scan_index
int scan_number

◆ OpenMS::CsiFingerIdMzTabWriter::CsiAdapterRun

class OpenMS::CsiFingerIdMzTabWriter::CsiAdapterRun
Collaboration diagram for CsiFingerIdMzTabWriter::CsiAdapterRun:
[legend]
Class Members
vector< CsiAdapterIdentification > identifications

Member Function Documentation

◆ 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 CSI:FingerID output to mzTab.

Output of CSI:FingerID is one directory per spectrum/compound

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