17 #include <unordered_set>
44 void insertRuns(std::vector<ProteinIdentification>&& prots,
45 std::vector<PeptideIdentification>&& peps);
46 void insertRuns(
const std::vector<ProteinIdentification>& prots,
47 const std::vector<PeptideIdentification>& peps);
58 std::vector<PeptideIdentification>& peps);
74 const std::vector<ProteinIdentification>& protRuns,
75 const String& experiment_type)
const;
84 const std::vector<ProteinIdentification>& protRuns,
86 const String& experiment_type)
const;
91 std::vector<ProteinIdentification>&& old_protRuns
98 std::vector<PeptideIdentification>&& pepIDs,
99 const std::map<String, Size>& runID_to_runIdx,
100 const std::vector<StringList>& originFiles,
106 std::vector<PeptideIdentification>&& pepIDs,
107 std::vector<ProteinIdentification>&& old_protRuns
127 bool filled_ =
false;
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:66
Creates a new Protein ID run into which other runs can be inserted. Creates union of protein hits but...
Definition: IDMergerAlgorithm.h:38
ProteinIdentification prot_result_
the resulting new Protein IDs
Definition: IDMergerAlgorithm.h:111
void movePepIDsAndRefProteinsToResultFaster_(std::vector< PeptideIdentification > &&pepIDs, std::vector< ProteinIdentification > &&old_protRuns)
bool(*)(const ProteinHit &, const ProteinHit &) equal_type
Definition: IDMergerAlgorithm.h:123
void insertProteinIDs_(std::vector< ProteinIdentification > &&old_protRuns)
void returnResultsAndClear(ProteinIdentification &prots, std::vector< PeptideIdentification > &peps)
Return the merged results and reset/clear all internal data.
bool checkOldRunConsistency_(const std::vector< ProteinIdentification > &protRuns, const ProteinIdentification &ref, const String &experiment_type) const
void insertRuns(const std::vector< ProteinIdentification > &prots, const std::vector< PeptideIdentification > &peps)
std::size_t(*)(const ProteinHit &) hash_type
Definition: IDMergerAlgorithm.h:122
static size_t accessionHash_(const ProteinHit &p)
Definition: IDMergerAlgorithm.h:116
std::vector< PeptideIdentification > pep_result_
the resulting new Peptide IDs
Definition: IDMergerAlgorithm.h:114
void insertRuns(std::vector< ProteinIdentification > &&prots, std::vector< PeptideIdentification > &&peps)
static bool accessionEqual_(const ProteinHit &p1, const ProteinHit &p2)
Definition: IDMergerAlgorithm.h:119
std::map< String, Size > file_origin_to_idx_
to keep track of the mzML origins of spectra
Definition: IDMergerAlgorithm.h:130
static void copySearchParams_(const ProteinIdentification &from, ProteinIdentification &to)
Copies over search parameters.
std::unordered_set< ProteinHit, hash_type, equal_type > collected_protein_hits_
Definition: IDMergerAlgorithm.h:124
String getNewIdentifier_() const
Returns the new identifier. The initial identifier plus a timestamp.
void updateAndMovePepIDs_(std::vector< PeptideIdentification > &&pepIDs, const std::map< String, Size > &runID_to_runIdx, const std::vector< StringList > &originFiles, bool annotate_origin)
String id_
the new identifier string
Definition: IDMergerAlgorithm.h:133
bool checkOldRunConsistency_(const std::vector< ProteinIdentification > &protRuns, const String &experiment_type) const
IDMergerAlgorithm(const String &runIdentifier="merged")
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:27
Representation of a protein hit.
Definition: ProteinHit.h:34
const String & getAccession() const
returns the accession of the protein
Representation of a protein identification run.
Definition: ProteinIdentification.h:50
A more convenient string class.
Definition: String.h:34
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19