44 std::vector< PeptideIdentification > & pep_ids,
45 std::vector< ProteinIdentification > & prot_ids
54 const std::vector<ProteinIdentification>& poid,
55 const std::vector<PeptideIdentification>& peid)
const;
87 const std::vector< std::pair<Size, Size> >& spectrum_pairs,
88 const std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > >& all_top_csms,
89 const PeakMap& spectra,
const bool& test_mode =
false);
100 const std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > >& all_top_csms,
101 const PeakMap& spectra,
const bool& test_mode =
false);
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:23
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:45
The representation of a 1D spectrum.
Definition: MSSpectrum.h:44
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:27
A more convenient string class.
Definition: String.h:34
Used to load and store xQuest result files.
Definition: XQuestResultXMLFile.h:32
int n_hits_
Total number of hits within the result file.
Definition: XQuestResultXMLFile.h:123
double getMinScore() const
Returns minimum score among the hits in the file.
static void wrap_(const String &input, Size width, String &output)
A helper function, that takes one string containing one line and wraps it into several lines of a giv...
~XQuestResultXMLFile() override
double max_score_
Maximum score encountered in file.
Definition: XQuestResultXMLFile.h:125
void load(const String &filename, std::vector< PeptideIdentification > &pep_ids, std::vector< ProteinIdentification > &prot_ids)
Load the content of the xquest.xml file into the provided data structures.
static String getxQuestBase64EncodedSpectrum_(const PeakSpectrum &spec, const String &header, const bool &test_mode=false)
Transforms a PeakSpectrum into a base64 encoded string, which is the format used in spec....
static void writeXQuestXMLSpec(const String &out_file, const String &base_name, const OPXLDataStructs::PreprocessedPairSpectra &preprocessed_pair_spectra, const std::vector< std::pair< Size, Size > > &spectrum_pairs, const std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > > &all_top_csms, const PeakMap &spectra, const bool &test_mode=false)
Writes spec.xml output containing matching peaks between heavy and light spectra after comparing and ...
double min_score_
Minimum score encountered in file.
Definition: XQuestResultXMLFile.h:124
void store(const String &filename, const std::vector< ProteinIdentification > &poid, const std::vector< PeptideIdentification > &peid) const
Stores the identifications in a xQuest XML file.
static void writeXQuestXMLSpec(const String &out_file, const String &base_name, const std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > > &all_top_csms, const PeakMap &spectra, const bool &test_mode=false)
Writes spec.xml output containing spectra for visualization. This version of the function is meant to...
int getNumberOfHits() const
Returns the total number of hits in the file.
double getMaxScore() const
Returns maximum score among the hits in the file.
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:97
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
The PreprocessedPairSpectra struct represents the result of comparing a light and a heavy labeled spe...
Definition: OPXLDataStructs.h:278