| OpenMS 2.5.0

Classes | Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
SiriusAdapterAlgorithm Class Reference

`#include <OpenMS/ANALYSIS/ID/SiriusAdapterAlgorithm.h>`

Inheritance diagram for SiriusAdapterAlgorithm:

## Classes

struct | SiriusTemporaryFileSystemObjects
| Struct for temporary folder structure. More...

## Public Member Functions

| SiriusAdapterAlgorithm ()
| default constructor More...
String | getFeatureOnly ()
String | getNoMasstraceInfoIsotopePattern ()
int | getIsotopePatternIterations ()
int | getCandidates ()
int | getTopNHits ()
Public Member Functions inherited from DefaultParamHandler
| DefaultParamHandler (const String &name)
| Constructor with name that is displayed in error messages. More...
| DefaultParamHandler (const DefaultParamHandler &rhs)
| Copy constructor. More...
virtual | ~DefaultParamHandler ()
| Destructor. More...
virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs)
| Assignment operator. More...
virtual bool | operator== (const DefaultParamHandler &rhs) const
| Equality operator. More...
void | setParameters (const Param &param)
| Sets the parameters. More...
const Param & | getParameters () const
| Non-mutable access to the parameters. More...
const Param & | getDefaults () const
| Non-mutable access to the default parameters. More...
const String & | getName () const
| Non-mutable access to the name. More...
void | setName (const String &name)
| Mutable access to the name. More...
const std::vector< String > & | getSubsections () const
| Non-mutable access to the registered subsections. More...

## Static Public Member Functions

static void | preprocessingSirius (const String &featureinfo, const MSExperiment &spectra, std::vector< FeatureMap > &v_fp, KDTreeFeatureMaps &fp_map_kd, const SiriusAdapterAlgorithm &sirius_algo, FeatureMapping::FeatureToMs2Indices &feature_mapping)
| Preprocessing needed for SIRIUS. More...
static void | checkFeatureSpectraNumber (const String &featureinfo, const FeatureMapping::FeatureToMs2Indices &feature_mapping, const MSExperiment &spectra, const SiriusAdapterAlgorithm &sirius_algo)
| logs number of features and spectra used More...
static const std::vector< String > | callSiriusQProcess (const String &tmp_ms_file, const String &tmp_out_dir, String &executable, const String &out_csifingerid, const SiriusAdapterAlgorithm &sirius_algo)
| Call SIRIUS with QProcess. More...

## Protected Member Functions

void | updateMembers_ () override
| This method is used to update extra member variables at the end of the setParameters() method. More...
Protected Member Functions inherited from DefaultParamHandler
void | defaultsToParam_ ()
| Updates the parameters after the defaults have been set in the constructor. More...

## Protected Attributes

unsigned int | filter_by_num_masstraces_
double | precursor_mz_tolerance_
String | precursor_mz_tolerance_unit_
double | precursor_rt_tolerance_
int | isotope_pattern_iterations_
String | feature_only_
String | no_masstrace_info_isotope_pattern_
String | profile_
int | candidates_
String | database_
int | noise_
int | ppm_max_
String | isotope_
String | elements_
int | compound_timeout_
int | tree_timeout_
int | top_n_hits_
int | cores_
String | auto_charge_
String | ion_tree_
String | no_recalibration_
String | most_intense_ms2_
Protected Attributes inherited from DefaultParamHandler
Param | param_
| Container for current parameters. More...
Param | defaults_
| Container for default parameters. This member should be filled in the constructor of derived classes! More...
std::vector< String > | subsections_
| Container for registered subsections. This member should be filled in the constructor of derived classes! More...
String | error_name_
| Name that is displayed in error messages during the parameter checking. More...
bool | check_defaults_
| If this member is set to false no checking if parameters in done;. More...
bool | warn_empty_defaults_
| If this member is set to false no warning is emitted when defaults are empty;. More...

## Constructor & Destructor Documentation

## ◆ SiriusAdapterAlgorithm()

SiriusAdapterAlgorithm | ( |  | ) |

default constructor

## Member Function Documentation

## ◆ callSiriusQProcess()

static const std::vector<String> callSiriusQProcess | ( | const String & | tmp_ms_file,
|  | const String & | tmp_out_dir,
|  | String & | executable,
|  | const String & | out_csifingerid,
|  | const SiriusAdapterAlgorithm & | sirius_algo
| ) |  |

static

Call SIRIUS with QProcess.

Returns
  Vector with paths to a compound

Parameters

  tmp_ms_file | path to temporary .ms file
  tmp_out_dir | path to temporary output folder
  executable | path to executable
  out_csifingerid | path to CSI:FingerID output (can be empty).
  sirius_algo | Parameters needed for SIRIUS

## ◆ checkFeatureSpectraNumber()

static void checkFeatureSpectraNumber | ( | const String & | featureinfo,
|  | const FeatureMapping::FeatureToMs2Indices & | feature_mapping,
|  | const MSExperiment & | spectra,
|  | const SiriusAdapterAlgorithm & | sirius_algo
| ) |  |

static

logs number of features and spectra used

Prints the number of features and spectra used (OPENMS_LOG_INFO)

Parameters

  featureinfo | Path to featureXML
  feature_mapping | FeatureToMs2Indices with feature mapping
  spectra | Input of MSExperiment with spectra information
  sirius_algo | Parameters needed for preprocessing

## ◆ getCandidates()

int getCandidates | ( |  | ) |

## ◆ getFeatureOnly()

String getFeatureOnly | ( |  | ) |

## ◆ getIsotopePatternIterations()

int getIsotopePatternIterations | ( |  | ) |

## ◆ getNoMasstraceInfoIsotopePattern()

String getNoMasstraceInfoIsotopePattern | ( |  | ) |

## ◆ getTopNHits()

int getTopNHits | ( |  | ) |

## ◆ preprocessingSirius()

static void preprocessingSirius | ( | const String & | featureinfo,
|  | const MSExperiment & | spectra,
|  | std::vector< FeatureMap > & | v_fp,
|  | KDTreeFeatureMaps & | fp_map_kd,
|  | const SiriusAdapterAlgorithm & | sirius_algo,
|  | FeatureMapping::FeatureToMs2Indices & | feature_mapping
| ) |  |

static

Preprocessing needed for SIRIUS.

Returns
  FeatureToMS2Indices

Filter number of masstraces and perform feature mapping.

Parameters

  featureinfo | Path to featureXML
  spectra | Input of MSExperiment with spectra information
  fp_map_kd | KDTree used for query and match spectra with features
  sirius_algo | Parameters needed for preprocessing
  feature_mapping | Empty FeatureToMs2Indices

## ◆ updateMembers_()

void updateMembers_ | ( |  | ) |

override protected virtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

## Member Data Documentation

## ◆ auto_charge_

String auto_charge_

protected

## ◆ candidates_

int candidates_

protected

## ◆ compound_timeout_

int compound_timeout_

protected

## ◆ cores_

int cores_

protected

## ◆ database_

String database_

protected

## ◆ elements_

String elements_

protected

## ◆ feature_only_

String feature_only_

protected

## ◆ filter_by_num_masstraces_

unsigned int filter_by_num_masstraces_

protected

## ◆ ion_tree_

String ion_tree_

protected

## ◆ isotope_

String isotope_

protected

## ◆ isotope_pattern_iterations_

int isotope_pattern_iterations_

protected

## ◆ most_intense_ms2_

String most_intense_ms2_

protected

## ◆ no_masstrace_info_isotope_pattern_

String no_masstrace_info_isotope_pattern_

protected

## ◆ no_recalibration_

String no_recalibration_

protected

## ◆ noise_

int noise_

protected

## ◆ ppm_max_

int ppm_max_

protected

## ◆ precursor_mz_tolerance_

double precursor_mz_tolerance_

protected

## ◆ precursor_mz_tolerance_unit_

String precursor_mz_tolerance_unit_

protected

## ◆ precursor_rt_tolerance_

double precursor_rt_tolerance_

protected

## ◆ profile_

String profile_

protected

## ◆ top_n_hits_

int top_n_hits_

protected

## ◆ tree_timeout_

int tree_timeout_

protected