OpenMS
SiriusAdapterAlgorithm Class Reference

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

Inheritance diagram for SiriusAdapterAlgorithm:
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Collaboration diagram for SiriusAdapterAlgorithm:
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Classes

class  Fingerid
 
class  ParameterModifier
 
class  ParameterSection
 
class  Passatutto
 
class  Preprocessing
 
class  Project
 
class  Sirius
 
class  SiriusTemporaryFileSystemObjects
 Struct for temporary folder structure. More...
 

Public Member Functions

 SiriusAdapterAlgorithm ()
 default constructor More...
 
bool isFeatureOnly () const
 
UInt getFilterByNumMassTraces () const
 
double getPrecursorMzTolerance () const
 
double getPrecursorRtTolerance () const
 
bool precursorMzToleranceUnitIsPPM () const
 
bool isNoMasstraceInfoIsotopePattern () const
 
int getIsotopePatternIterations () const
 
int getNumberOfSiriusCandidates () const
 Accessors for Sirius Parameters. More...
 
void updateExistingParameter (const Param &param)
 Updates all parameters that already exist in this DefaultParamHandler with the values provided by the input param object. More...
 
bool hasFullNameParameter (const String &name) const
 Checks whether this DefaultParamHandler has a ParamEntry with the provided name. More...
 
void preprocessingSirius (const String &featureinfo, const MSExperiment &spectra, FeatureMapping::FeatureMappingInfo &fm_info, FeatureMapping::FeatureToMs2Indices &feature_mapping) const
 Preprocessing needed for SIRIUS. More...
 
void logFeatureSpectraNumber (const String &featureinfo, const FeatureMapping::FeatureToMs2Indices &feature_mapping, const MSExperiment &spectra) const
 logs number of features and spectra used More...
 
void logInSiriusAccount (String &executable, const String &email, const String &password) const
 Log in to Sirius with personal user account (required in Sirius >= 5). More...
 
const vector< StringcallSiriusQProcess (const String &tmp_ms_file, const String &tmp_out_dir, String &executable, const String &out_csifingerid, const bool decoy_generation) const
 Call SIRIUS with QProcess. More...
 
- 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...
 
DefaultParamHandleroperator= (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 ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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 String determineSiriusExecutable (String &executable)
 Checks if the provided String points to a valid SIRIUS executable, otherwise tries to select the executable from the environment. More...
 
static void sortSiriusWorkspacePathsByScanIndex (std::vector< String > &subdirs)
 Sort function using the extracted scan_index from the sirius workspace file path. More...
 
- Static Public Member Functions inherited from DefaultParamHandler
static void writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
 Writes all parameters to meta values. More...
 

Private Types

using SiriusSubtool = ParameterSection
 

Private Attributes

Preprocessing preprocessing
 
Project project
 
Sirius sirius
 
Fingerid fingerid
 
Passatutto passatutto
 

Additional Inherited Members

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

Member Typedef Documentation

◆ SiriusSubtool

Constructor & Destructor Documentation

◆ SiriusAdapterAlgorithm()

default constructor

Member Function Documentation

◆ callSiriusQProcess()

const vector<String> callSiriusQProcess ( const String tmp_ms_file,
const String tmp_out_dir,
String executable,
const String out_csifingerid,
const bool  decoy_generation 
) const

Call SIRIUS with QProcess.

Parameters
tmp_ms_filepath to temporary .ms file
tmp_out_dirpath to temporary output folder
executablepath to executable
out_csifingeridpath to CSI:FingerID output (can be empty).
Returns
Vector with paths to a compound

◆ determineSiriusExecutable()

static String determineSiriusExecutable ( String executable)
static

Checks if the provided String points to a valid SIRIUS executable, otherwise tries to select the executable from the environment.

Returns
Path to SIRIUS executable
Parameters
executablePath to the potential executable

◆ getFilterByNumMassTraces()

UInt getFilterByNumMassTraces ( ) const
inline

◆ getIsotopePatternIterations()

int getIsotopePatternIterations ( ) const
inline

◆ getNumberOfSiriusCandidates()

int getNumberOfSiriusCandidates ( ) const
inline

Accessors for Sirius Parameters.

◆ getPrecursorMzTolerance()

double getPrecursorMzTolerance ( ) const
inline

◆ getPrecursorRtTolerance()

double getPrecursorRtTolerance ( ) const
inline

◆ hasFullNameParameter()

bool hasFullNameParameter ( const String name) const

Checks whether this DefaultParamHandler has a ParamEntry with the provided name.

Parameters
nameThe name of the ParamEntry that should be checked for its existence in this DefaultParamHandler
Returns
Whether this DefaultParamHandler has an ParamEntry for the provided name.

◆ isFeatureOnly()

bool isFeatureOnly ( ) const
inline

◆ isNoMasstraceInfoIsotopePattern()

bool isNoMasstraceInfoIsotopePattern ( ) const
inline

◆ logFeatureSpectraNumber()

void logFeatureSpectraNumber ( const String featureinfo,
const FeatureMapping::FeatureToMs2Indices feature_mapping,
const MSExperiment spectra 
) const

logs number of features and spectra used

Prints the number of features and spectra used (OPENMS_LOG_INFO)

Parameters
featureinfoPath to featureXML
feature_mappingFeatureToMs2Indices with feature mapping
spectraInput of MSExperiment with spectra information

◆ logInSiriusAccount()

void logInSiriusAccount ( String executable,
const String email,
const String password 
) const

Log in to Sirius with personal user account (required in Sirius >= 5).

Parameters
emailUser account E-Mail.
passwordUser account password.

◆ precursorMzToleranceUnitIsPPM()

bool precursorMzToleranceUnitIsPPM ( ) const
inline

◆ preprocessingSirius()

void preprocessingSirius ( const String featureinfo,
const MSExperiment spectra,
FeatureMapping::FeatureMappingInfo fm_info,
FeatureMapping::FeatureToMs2Indices feature_mapping 
) const

Preprocessing needed for SIRIUS.

Returns
FeatureToMS2Indices

Filter number of masstraces and perform feature mapping.

Parameters
featureinfoPath to featureXML
spectraInput of MSExperiment with spectra information
fm_infoEmtpy - stores FeatureMaps and KDTreeMaps internally
feature_mappingEmpty FeatureToMs2Indices

◆ sortSiriusWorkspacePathsByScanIndex()

static void sortSiriusWorkspacePathsByScanIndex ( std::vector< String > &  subdirs)
static

Sort function using the extracted scan_index from the sirius workspace file path.

Returns
Vector of sorted sirius workspace paths based on the scan_index

◆ updateExistingParameter()

void updateExistingParameter ( const Param param)

Updates all parameters that already exist in this DefaultParamHandler with the values provided by the input param object.

Parameters
paramThe Param object supplying updated parameter values. Keys that exist in the param parameter, but not in this DefaultParamHander, are ignored.

Member Data Documentation

◆ fingerid

Fingerid fingerid
private

◆ passatutto

Passatutto passatutto
private

◆ preprocessing

Preprocessing preprocessing
private

◆ project

Project project
private

◆ sirius

Sirius sirius
private