| 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

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

Returns
  : Result written to mzTab