PrecursorIonSelection

class pyopenms.PrecursorIonSelection

Bases: object

Cython implementation of _PrecursorIonSelection

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1PrecursorIonSelection.html

– Inherits from [‘DefaultParamHandler’]

__init__()

  • Cython signature: void PrecursorIonSelection()

  • Cython signature: void PrecursorIonSelection(PrecursorIonSelection &)

Methods

__init__

  • Cython signature: void PrecursorIonSelection()

getDefaults

Cython signature: Param getDefaults() Returns the default parameters

getLPSolver

Cython signature: SOLVER getLPSolver()

getMaxScore

Cython signature: double getMaxScore()

getName

Cython signature: String getName() Returns the name

getNextPrecursors

  • Cython signature: void getNextPrecursors(FeatureMap & features, FeatureMap & next_features, unsigned int number)

getParameters

Cython signature: Param getParameters() Returns the parameters

getSubsections

Cython signature: libcpp_vector[String] getSubsections()

rescore

Cython signature: void rescore(FeatureMap & features, libcpp_vector[PeptideIdentification] & new_pep_ids, libcpp_vector[ProteinIdentification] & prot_ids, PrecursorIonSelectionPreprocessing & preprocessed_db, bool check_meta_values)

reset

Cython signature: void reset()

setLPSolver

Cython signature: void setLPSolver(SOLVER solver)

setMaxScore

Cython signature: void setMaxScore(double & max_score)

setName

Cython signature: void setName(const String &) Sets the name

setParameters

Cython signature: void setParameters(Param & param) Sets the parameters

simulateRun

Cython signature: void simulateRun(FeatureMap & features, libcpp_vector[PeptideIdentification] & pep_ids, libcpp_vector[ProteinIdentification] & prot_ids, PrecursorIonSelectionPreprocessing & preprocessed_db, String path, MSExperiment & experiment, String precursor_path)

sortByTotalScore

Cython signature: void sortByTotalScore(FeatureMap & features) Sort features by total score
PrecursorIonSelection_Type

alias of pyopenms.pyopenms_3.__PrecursorIonSelection_Type

getDefaults()

Cython signature: Param getDefaults() Returns the default parameters

getLPSolver()

Cython signature: SOLVER getLPSolver()

getMaxScore()

Cython signature: double getMaxScore()

getName()

Cython signature: String getName() Returns the name

getNextPrecursors()

  • Cython signature: void getNextPrecursors(FeatureMap & features, FeatureMap & next_features, unsigned int number)

Parameters

  • features – FeatureMap with all possible precursors

  • next_features – FeatureMap with next precursors

  • number – Number of features to be reported - Cython signature: void getNextPrecursors(libcpp_vector[int] & solution_indices, libcpp_vector[IndexTriple] & variable_indices, libcpp_set[int] & measured_variables, FeatureMap & features, FeatureMap & new_features, unsigned int step_size, PSLPFormulation & ilp)

getParameters()

Cython signature: Param getParameters() Returns the parameters

getSubsections()

Cython signature: libcpp_vector[String] getSubsections()

rescore()

Cython signature: void rescore(FeatureMap & features, libcpp_vector[PeptideIdentification] & new_pep_ids, libcpp_vector[ProteinIdentification] & prot_ids, PrecursorIonSelectionPreprocessing & preprocessed_db, bool check_meta_values)

Parameters

  • features – FeatureMap with all possible precursors

  • new_pep_ids – Peptide identifications

  • prot_ids – Protein identifications

  • preprocessed_db – Information from preprocessed database

  • check_meta_values – True if the FeatureMap should be checked for the presence of required meta values

reset()

Cython signature: void reset()

setLPSolver()

Cython signature: void setLPSolver(SOLVER solver)

setMaxScore()

Cython signature: void setMaxScore(double & max_score)

setName()

Cython signature: void setName(const String &) Sets the name

setParameters()

Cython signature: void setParameters(Param & param) Sets the parameters

simulateRun()

Cython signature: void simulateRun(FeatureMap & features, libcpp_vector[PeptideIdentification] & pep_ids, libcpp_vector[ProteinIdentification] & prot_ids, PrecursorIonSelectionPreprocessing & preprocessed_db, String path, MSExperiment & experiment, String precursor_path)

Parameters

  • features – FeatureMap with all possible precursors

  • new_pep_ids – Peptide identifications

  • prot_ids – Protein identifications

  • preprocessed_db – Information from preprocessed database

  • step_size – Number of MS/MS spectra considered per iteration

  • path – Path to output file

sortByTotalScore()

Cython signature: void sortByTotalScore(FeatureMap & features) Sort features by total score