66 std::vector<ProteinIdentification>& prot_ids,
67 std::vector<PeptideIdentification>& pep_ids)
const;
69 void updateMembers_()
override;
85 static void preprocessSpectra_(
PeakMap& exp,
double fragment_mass_tolerance,
bool fragment_mass_tolerance_unit_ppm);
89 static void postProcessHits_(
const PeakMap& exp,
90 std::vector<std::vector<SimpleSearchEngineAlgorithm::AnnotatedHit_> >& annotated_hits,
91 std::vector<ProteinIdentification>& protein_ids,
92 std::vector<PeptideIdentification>& peptide_ids,
96 Size max_variable_mods_per_peptide,
99 Int peptide_missed_cleavages,
100 double precursor_mass_tolerance,
101 double fragment_mass_tolerance,
102 const String& precursor_mass_tolerance_unit_ppm,
103 const String& fragment_mass_tolerance_unit_ppm,
104 const Int precursor_min_charge,
105 const Int precursor_max_charge,
107 const String& database_name);
double fragment_mass_tolerance_
Definition: SimpleSearchEngineAlgorithm.h:117
Definition: SimpleSearchEngineAlgorithm.h:46
String fragment_mass_tolerance_unit_
Definition: SimpleSearchEngineAlgorithm.h:119
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:134
Size report_top_hits_
Definition: SimpleSearchEngineAlgorithm.h:135
Size precursor_min_charge_
Definition: SimpleSearchEngineAlgorithm.h:112
String enzyme_
Definition: SimpleSearchEngineAlgorithm.h:127
Size peptide_min_size_
Definition: SimpleSearchEngineAlgorithm.h:129
IntList precursor_isotopes_
Definition: SimpleSearchEngineAlgorithm.h:115
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Size precursor_max_charge_
Definition: SimpleSearchEngineAlgorithm.h:113
double precursor_mass_tolerance_
Definition: SimpleSearchEngineAlgorithm.h:109
StringList modifications_fixed_
Definition: SimpleSearchEngineAlgorithm.h:121
String peptide_motif_
Definition: SimpleSearchEngineAlgorithm.h:133
Size peptide_missed_cleavages_
Definition: SimpleSearchEngineAlgorithm.h:131
StringView sequence
Definition: SimpleSearchEngineAlgorithm.h:74
double score
main score
Definition: SimpleSearchEngineAlgorithm.h:76
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
StringList modifications_variable_
Definition: SimpleSearchEngineAlgorithm.h:123
Size peptide_max_size_
Definition: SimpleSearchEngineAlgorithm.h:130
StringView provides a non-owning view on an existing string.
Definition: String.h:488
Size modifications_max_variable_mods_per_peptide_
Definition: SimpleSearchEngineAlgorithm.h:125
Definition: ModifiedPeptideGenerator.h:58
Slimmer structure as storing all scored candidates in PeptideHit objects takes too much space...
Definition: SimpleSearchEngineAlgorithm.h:72
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
A more convenient string class.
Definition: String.h:58
static bool hasBetterScore(const AnnotatedHit_ &a, const AnnotatedHit_ &b)
Definition: SimpleSearchEngineAlgorithm.h:78
std::vector< PeptideHit::PeakAnnotation > fragment_annotations
Definition: SimpleSearchEngineAlgorithm.h:77
String precursor_mass_tolerance_unit_
Definition: SimpleSearchEngineAlgorithm.h:110
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
ExitCodes
Exit codes.
Definition: SimpleSearchEngineAlgorithm.h:54
SignedSize peptide_mod_index
enumeration index of the non-RNA peptide modification
Definition: SimpleSearchEngineAlgorithm.h:75
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46