OpenMS  2.8.0
BasicProteinInferenceAlgorithm.h
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34 #pragma once
35 
41 
42 namespace OpenMS
43 {
44 
60  class OPENMS_DLLAPI BasicProteinInferenceAlgorithm :
61  public DefaultParamHandler,
62  public ProgressLogger
63  {
64  public:
65 
66  typedef std::unordered_map<std::string, std::map<Int, PeptideHit*>> SequenceToChargeToPSM;
67 
71  enum class AggregationMethod
72  {
73  PROD,
74  SUM,
75  BEST
76  };
77 
80 
86  void run(std::vector<PeptideIdentification>& pep_ids, std::vector<ProteinIdentification>& prot_ids) const;
87 
93  void run(std::vector<PeptideIdentification>& pep_ids, ProteinIdentification& prot_id) const;
94 
102  void run(ConsensusMap& cmap, ProteinIdentification& prot_id, bool include_unassigned) const;
103 
104  private:
105 
116  std::unordered_map<std::string, std::pair<ProteinHit*, Size>>& acc_to_protein_hitP_and_count,
117  SequenceToChargeToPSM& best_pep,
118  ProteinIdentification& prot_run,
119  std::vector<PeptideIdentification>& pep_ids) const;
120 
130  SequenceToChargeToPSM& best_pep,
131  std::vector<PeptideIdentification>& pep_ids,
132  const String& overall_score_type,
133  bool higher_better,
134  const std::string& run_id) const;
135 
145  std::unordered_map<std::string, std::pair<ProteinHit*, Size>>& acc_to_protein_hitP_and_count,
146  const SequenceToChargeToPSM& best_pep,
147  bool pep_scores,
148  bool higher_better) const;
149 
151  AggregationMethod aggFromString_(const std::string& method_string) const;
152 
156  const String& score_type,
157  const AggregationMethod& aggregation_method
158  ) const;
159 
161  double getInitScoreForAggMethod_(const AggregationMethod& aggregation_method, bool higher_better) const;
162 
164  typedef double (*fptr)(double, double);
165  fptr aggFunFromEnum_(const BasicProteinInferenceAlgorithm::AggregationMethod& agg_method, bool higher_better) const;
166  };
167 } //namespace OpenMS
Algorithm class that implements simple protein inference by aggregation of peptide scores....
Definition: BasicProteinInferenceAlgorithm.h:63
void run(std::vector< PeptideIdentification > &pep_ids, ProteinIdentification &prot_id) const
BasicProteinInferenceAlgorithm()
Default constructor.
void updateProteinScores_(std::unordered_map< std::string, std::pair< ProteinHit *, Size >> &acc_to_protein_hitP_and_count, const SequenceToChargeToPSM &best_pep, bool pep_scores, bool higher_better) const
aggregates and updates protein scores based on aggregation settings and aggregated peptide level resu...
std::unordered_map< std::string, std::map< Int, PeptideHit * > > SequenceToChargeToPSM
Definition: BasicProteinInferenceAlgorithm.h:66
void processRun_(std::unordered_map< std::string, std::pair< ProteinHit *, Size >> &acc_to_protein_hitP_and_count, SequenceToChargeToPSM &best_pep, ProteinIdentification &prot_run, std::vector< PeptideIdentification > &pep_ids) const
Performs simple aggregation-based inference on one protein run.
void checkCompat_(const String &score_type, const AggregationMethod &aggregation_method) const
void run(ConsensusMap &cmap, ProteinIdentification &prot_id, bool include_unassigned) const
double getInitScoreForAggMethod_(const AggregationMethod &aggregation_method, bool higher_better) const
get the initial score value based on the chosen aggregation_method, higher_better is needed for "best...
void aggregatePeptideScores_(SequenceToChargeToPSM &best_pep, std::vector< PeptideIdentification > &pep_ids, const String &overall_score_type, bool higher_better, const std::string &run_id) const
fills and updates the map of best peptide scores best_pep (by sequence or modified sequence,...
void run(std::vector< PeptideIdentification > &pep_ids, std::vector< ProteinIdentification > &prot_ids) const
AggregationMethod
The aggregation method.
Definition: BasicProteinInferenceAlgorithm.h:72
AggregationMethod aggFromString_(const std::string &method_string) const
get the AggregationMethod enum from a method_string
fptr aggFunFromEnum_(const BasicProteinInferenceAlgorithm::AggregationMethod &agg_method, bool higher_better) const
A container for consensus elements.
Definition: ConsensusMap.h:90
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:93
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:53
Representation of a protein identification run.
Definition: ProteinIdentification.h:72
A more convenient string class.
Definition: String.h:60
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47