41 std::vector<ProteinIdentification>& prot_ids,
42 std::vector<PeptideIdentification>& pep_ids)
const;
53 double prefix_fraction = 0;
54 double suffix_fraction = 0;
55 double mean_error = 0.0;
73 std::vector<std::vector<SimpleSearchEngineAlgorithm::AnnotatedHit_> >& annotated_hits,
74 std::vector<ProteinIdentification>& protein_ids,
75 std::vector<PeptideIdentification>& peptide_ids,
79 Size max_variable_mods_per_peptide,
82 Int peptide_missed_cleavages,
83 double precursor_mass_tolerance,
84 double fragment_mass_tolerance,
85 const String& precursor_mass_tolerance_unit_ppm,
86 const String& fragment_mass_tolerance_unit_ppm,
87 const Int precursor_min_charge,
88 const Int precursor_max_charge,
90 const String& database_name)
const;
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:66
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:45
Definition: ModifiedPeptideGenerator.h:31
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:27
Definition: SimpleSearchEngineAlgorithm.h:24
static void preprocessSpectra_(PeakMap &exp, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm)
filter, deisotope, decharge spectra
ExitCodes search(const String &in_mzML, const String &in_db, std::vector< ProteinIdentification > &prot_ids, std::vector< PeptideIdentification > &pep_ids) const
search spectra against database
Size peptide_max_size_
Definition: SimpleSearchEngineAlgorithm.h:117
Size precursor_max_charge_
Definition: SimpleSearchEngineAlgorithm.h:96
Size precursor_min_charge_
Definition: SimpleSearchEngineAlgorithm.h:95
void postProcessHits_(const PeakMap &exp, std::vector< std::vector< SimpleSearchEngineAlgorithm::AnnotatedHit_ > > &annotated_hits, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids, Size top_hits, const ModifiedPeptideGenerator::MapToResidueType &fixed_modifications, const ModifiedPeptideGenerator::MapToResidueType &variable_modifications, Size max_variable_mods_per_peptide, const StringList &modifications_fixed, const StringList &modifications_variable, Int peptide_missed_cleavages, double precursor_mass_tolerance, double fragment_mass_tolerance, const String &precursor_mass_tolerance_unit_ppm, const String &fragment_mass_tolerance_unit_ppm, const Int precursor_min_charge, const Int precursor_max_charge, const String &enzyme, const String &database_name) const
filter and annotate search results most of the parameters are used to properly add meta data to the i...
Size report_top_hits_
Definition: SimpleSearchEngineAlgorithm.h:122
Size modifications_max_variable_mods_per_peptide_
Definition: SimpleSearchEngineAlgorithm.h:108
String precursor_mass_tolerance_unit_
Definition: SimpleSearchEngineAlgorithm.h:93
StringList modifications_fixed_
Definition: SimpleSearchEngineAlgorithm.h:104
String enzyme_
Definition: SimpleSearchEngineAlgorithm.h:110
Size peptide_min_size_
Definition: SimpleSearchEngineAlgorithm.h:116
String fragment_mass_tolerance_unit_
Definition: SimpleSearchEngineAlgorithm.h:102
IntList precursor_isotopes_
Definition: SimpleSearchEngineAlgorithm.h:98
bool decoys_
Definition: SimpleSearchEngineAlgorithm.h:112
StringList annotate_psm_
Definition: SimpleSearchEngineAlgorithm.h:114
double precursor_mass_tolerance_
Definition: SimpleSearchEngineAlgorithm.h:92
SimpleSearchEngineAlgorithm()
void updateMembers_() override
This method is used to update extra member variables at the end of the setParameters() method.
ExitCodes
Exit codes.
Definition: SimpleSearchEngineAlgorithm.h:30
StringList modifications_variable_
Definition: SimpleSearchEngineAlgorithm.h:106
double fragment_mass_tolerance_
Definition: SimpleSearchEngineAlgorithm.h:100
String peptide_motif_
Definition: SimpleSearchEngineAlgorithm.h:120
Size peptide_missed_cleavages_
Definition: SimpleSearchEngineAlgorithm.h:118
StringView provides a non-owning view on an existing string.
Definition: StringView.h:30
A more convenient string class.
Definition: String.h:34
int Int
Signed integer type.
Definition: Types.h:72
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:104
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:97
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:29
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:44
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
Slimmer structure as storing all scored candidates in PeptideHit objects takes too much space.
Definition: SimpleSearchEngineAlgorithm.h:48
static bool hasBetterScore(const AnnotatedHit_ &a, const AnnotatedHit_ &b)
Definition: SimpleSearchEngineAlgorithm.h:57
double score
main score
Definition: SimpleSearchEngineAlgorithm.h:51
StringView sequence
Definition: SimpleSearchEngineAlgorithm.h:49
std::vector< PeptideHit::PeakAnnotation > fragment_annotations
Definition: SimpleSearchEngineAlgorithm.h:52
SignedSize peptide_mod_index
enumeration index of the non-RNA peptide modification
Definition: SimpleSearchEngineAlgorithm.h:50