OpenPepXLAlgorithm

class pyopenms.OpenPepXLAlgorithm

Bases: object

Cython implementation of _OpenPepXLAlgorithm

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1OpenPepXLAlgorithm.html

– Inherits from [‘DefaultParamHandler’]

__init__()

  • Cython signature: void OpenPepXLAlgorithm()

  • Cython signature: void OpenPepXLAlgorithm(OpenPepXLAlgorithm &)

Methods

__init__

  • Cython signature: void OpenPepXLAlgorithm()

getDefaults

Cython signature: Param getDefaults() Returns the default parameters

getName

Cython signature: String getName() Returns the name

getParameters

Cython signature: Param getParameters() Returns the parameters

getSubsections

Cython signature: libcpp_vector[String] getSubsections()

run

Cython signature: OpenPepXLAlgorithm_ExitCodes run(MSExperiment & unprocessed_spectra, ConsensusMap & cfeatures, libcpp_vector[FASTAEntry] & fasta_db, libcpp_vector[ProteinIdentification] & protein_ids, libcpp_vector[PeptideIdentification] & peptide_ids, OPXL_PreprocessedPairSpectra & preprocessed_pair_spectra, libcpp_vector[libcpp_pair[size_t,size_t]] & spectrum_pairs, libcpp_vector[libcpp_vector[CrossLinkSpectrumMatch]] & all_top_csms, MSExperiment & spectra)

setName

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

setParameters

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

alias of pyopenms.pyopenms_1.__OpenPepXLAlgorithm_ExitCodes

getDefaults()

Cython signature: Param getDefaults() Returns the default parameters

getName()

Cython signature: String getName() Returns the name

getParameters()

Cython signature: Param getParameters() Returns the parameters

getSubsections()

Cython signature: libcpp_vector[String] getSubsections()

run()

Cython signature: OpenPepXLAlgorithm_ExitCodes run(MSExperiment & unprocessed_spectra, ConsensusMap & cfeatures, libcpp_vector[FASTAEntry] & fasta_db, libcpp_vector[ProteinIdentification] & protein_ids, libcpp_vector[PeptideIdentification] & peptide_ids, OPXL_PreprocessedPairSpectra & preprocessed_pair_spectra, libcpp_vector[libcpp_pair[size_t,size_t]] & spectrum_pairs, libcpp_vector[libcpp_vector[CrossLinkSpectrumMatch]] & all_top_csms, MSExperiment & spectra)

Parameters

  • unprocessed_spectra – The input PeakMap of experimental spectra

  • cfeatures – The input cfeatures

  • fasta_db – The protein database containing targets and decoys

  • protein_ids – A result vector containing search settings. Should contain one PeptideIdentification

  • peptide_ids – A result vector containing cross-link spectrum matches as PeptideIdentifications and PeptideHits. Should be empty

  • preprocessed_pair_spectra – A result structure containing linear and cross-linked ion spectra. Will be overwritten. This is only necessary for writing out xQuest type spectrum files

  • spectrum_pairs – A result vector containing paired spectra indices. Should be empty. This is only necessary for writing out xQuest type spectrum files

  • all_top_csms – A result vector containing cross-link spectrum matches as CrossLinkSpectrumMatches. Should be empty. This is only necessary for writing out xQuest type spectrum files

  • spectra – A result vector containing the input spectra after preprocessing and filtering. Should be empty. This is only necessary for writing out xQuest type spectrum files

setName()

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

setParameters()

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