XQuestResultXMLFile

class pyopenms.XQuestResultXMLFile

Bases: object

Cython implementation of _XQuestResultXMLFile

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1XQuestResultXMLFile.html

– Inherits from [‘XMLFile’]

__init__()

• Cython signature: void XQuestResultXMLFile()

• Cython signature: void XQuestResultXMLFile(XQuestResultXMLFile &)

Methods

__init__	Cython signature: void XQuestResultXMLFile()
getMaxScore	Cython signature: double getMaxScore() Returns maximum score among the hits in the file
getMinScore	Cython signature: double getMinScore() Returns minimum score among the hits in the file
getNumberOfHits	Cython signature: int getNumberOfHits() Returns the total number of hits in the file
getVersion	Cython signature: String getVersion() Return the version of the schema
load	Cython signature: void load(const String & filename, libcpp_vector[PeptideIdentification] & pep_ids, libcpp_vector[ProteinIdentification] & prot_ids)
store	Cython signature: void store(const String & filename, libcpp_vector[ProteinIdentification] & poid, libcpp_vector[PeptideIdentification] & peid) Stores the identifications in a xQuest XML file
writeXQuestXMLSpec	Cython signature: void writeXQuestXMLSpec(const String & out_file, const String & base_name, 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, const bool & test_mode)

getMaxScore()

Cython signature: double getMaxScore() Returns maximum score among the hits in the file

getMinScore()

Cython signature: double getMinScore() Returns minimum score among the hits in the file

getNumberOfHits()

Cython signature: int getNumberOfHits() Returns the total number of hits in the file

getVersion()

Cython signature: String getVersion() Return the version of the schema

load()

Cython signature: void load(const String & filename, libcpp_vector[PeptideIdentification] & pep_ids, libcpp_vector[ProteinIdentification] & prot_ids)

Parameters

• filename – Filename of the file which is to be loaded

• pep_ids – Where the spectra with identifications of the input file will be loaded to

• prot_ids – Where the protein identification of the input file will be loaded to

store()

Cython signature: void store(const String & filename, libcpp_vector[ProteinIdentification] & poid, libcpp_vector[PeptideIdentification] & peid) Stores the identifications in a xQuest XML file

writeXQuestXMLSpec()

• Cython signature: void writeXQuestXMLSpec(const String & out_file, const String & base_name, 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, const bool & test_mode)

Parameters

• out_file – Path and filename for the output file

• base_name – The base_name should be the name of the input spectra file without the file ending. Used as part of an identifier string for the spectra

• preprocessed_pair_spectra – The preprocessed spectra after comparing and filtering

• spectrum_pairs – Indices of spectrum pairs in the input map

• all_top_csms – CrossLinkSpectrumMatches, from which the IDs were generated. Only spectra with matches are written out

• spectra – The spectra, that were searched as a PeakMap. The indices in spectrum_pairs correspond to spectra in this map - Cython signature: void writeXQuestXMLSpec(const String & out_file, const String & base_name, libcpp_vector[libcpp_vector[CrossLinkSpectrumMatch]] all_top_csms, MSExperiment spectra, const bool & test_mode)

Parameters

• out_file – Path and filename for the output file

• base_name – The base_name should be the name of the input spectra file without the file ending. Used as part of an identifier string for the spectra

• all_top_csms – CrossLinkSpectrumMatches, from which the IDs were generated. Only spectra with matches are written out

• spectra – The spectra, that were searched as a PeakMap