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OpenMS
2.6.0
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Go to the documentation of this file.
64 ExitCodes search(
const String& in_mzML,
66 std::vector<ProteinIdentification>& prot_ids,
67 std::vector<PeptideIdentification>& pep_ids)
const;
69 void updateMembers_()
override;
89 static void preprocessSpectra_(
PeakMap& exp,
double fragment_mass_tolerance,
bool fragment_mass_tolerance_unit_ppm);
93 void postProcessHits_(
const PeakMap& exp,
94 std::vector<std::vector<SimpleSearchEngineAlgorithm::AnnotatedHit_> >& annotated_hits,
95 std::vector<ProteinIdentification>& protein_ids,
96 std::vector<PeptideIdentification>& peptide_ids,
100 Size max_variable_mods_per_peptide,
103 Int peptide_missed_cleavages,
104 double precursor_mass_tolerance,
105 double fragment_mass_tolerance,
106 const String& precursor_mass_tolerance_unit_ppm,
107 const String& fragment_mass_tolerance_unit_ppm,
108 const Int precursor_min_charge,
109 const Int precursor_max_charge,
111 const String& database_name)
const;
std::vector< PeptideHit::PeakAnnotation > fragment_annotations
Definition: SimpleSearchEngineAlgorithm.h:77
Size peptide_max_size_
Definition: SimpleSearchEngineAlgorithm.h:138
String peptide_motif_
Definition: SimpleSearchEngineAlgorithm.h:141
Base class for TOPP applications.
Definition: TOPPBase.h:144
Size peptide_min_size_
Definition: SimpleSearchEngineAlgorithm.h:137
void store(const String &filename, const std::vector< ProteinIdentification > &protein_ids, const std::vector< PeptideIdentification > &peptide_ids, const String &document_id="")
Stores the data in an idXML file.
String fragment_mass_tolerance_unit_
Definition: SimpleSearchEngineAlgorithm.h:123
static String basename(const String &file)
Returns the basename of the file (without the path).
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
A more convenient string class.
Definition: String.h:59
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
double precursor_mass_tolerance_
Definition: SimpleSearchEngineAlgorithm.h:113
StringList annotate_psm_
Definition: SimpleSearchEngineAlgorithm.h:135
Size report_top_hits_
Definition: SimpleSearchEngineAlgorithm.h:143
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
StringList modifications_variable_
Definition: SimpleSearchEngineAlgorithm.h:127
bool decoys_
Definition: SimpleSearchEngineAlgorithm.h:133
IntList precursor_isotopes_
Definition: SimpleSearchEngineAlgorithm.h:119
StringList modifications_fixed_
Definition: SimpleSearchEngineAlgorithm.h:125
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
String enzyme_
Definition: SimpleSearchEngineAlgorithm.h:131
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
double score
main score
Definition: SimpleSearchEngineAlgorithm.h:76
StringView provides a non-owning view on an existing string.
Definition: String.h:489
Size modifications_max_variable_mods_per_peptide_
Definition: SimpleSearchEngineAlgorithm.h:129
Size peptide_missed_cleavages_
Definition: SimpleSearchEngineAlgorithm.h:139
Definition: SimpleSearchEngineAlgorithm.h:46
String precursor_mass_tolerance_unit_
Definition: SimpleSearchEngineAlgorithm.h:114
Slimmer structure as storing all scored candidates in PeptideHit objects takes too much space.
Definition: SimpleSearchEngineAlgorithm.h:72
void setParameters(const Param ¶m)
Sets the parameters.
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
SignedSize peptide_mod_index
enumeration index of the non-RNA peptide modification
Definition: SimpleSearchEngineAlgorithm.h:75
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:134
Size precursor_min_charge_
Definition: SimpleSearchEngineAlgorithm.h:116
Size precursor_max_charge_
Definition: SimpleSearchEngineAlgorithm.h:117
StringView sequence
Definition: SimpleSearchEngineAlgorithm.h:74
Definition: ModifiedPeptideGenerator.h:58
Management and storage of parameters / INI files.
Definition: Param.h:73
double fragment_mass_tolerance_
Definition: SimpleSearchEngineAlgorithm.h:121
static bool hasBetterScore(const AnnotatedHit_ &a, const AnnotatedHit_ &b)
Definition: SimpleSearchEngineAlgorithm.h:78
void insert(const String &prefix, const Param ¶m)
ExitCodes
Exit codes.
Definition: SimpleSearchEngineAlgorithm.h:54
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
Used to load and store idXML files.
Definition: IdXMLFile.h:63