| OpenMS 2.5.0

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

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

## Classes

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

struct 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>)

Class Members
String | inchi |
String | inchikey2D |
vector< String > | links |
String | molecular_formula |
String | name |
vector< String > | pubchemids |
unsigned int | rank |
double | score |
String | smiles |

## ◆ OpenMS::CsiFingerIdMzTabWriter::CsiAdapterIdentification

struct OpenMS::CsiFingerIdMzTabWriter::CsiAdapterIdentification

Class Members
String | feature_id |
vector< CsiAdapterHit > | hits |
double | mz |
String | native_id |
double | rt |
int | scan_index |
int | scan_number |

## ◆ OpenMS::CsiFingerIdMzTabWriter::CsiAdapterRun

struct OpenMS::CsiFingerIdMzTabWriter::CsiAdapterRun

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_paths | Path to output directories of Sirius
  original_input_mzml | Path to original input mzml of SiriusAdapter
  top_n_hits | Top n entries for each compound written to the result file

Returns
  Result written to mzTab