OpenMS
IdentificationSummary.h
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1 // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Axel Walter $
6 // $Authors: Axel Walter $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
14 #include <OpenMS/QC/QCBase.h>
15 #include <vector>
24 namespace OpenMS
25 {
26  class OPENMS_DLLAPI IdentificationSummary : public QCBase
27  {
28  public:
30  IdentificationSummary() = default;
31 
33  virtual ~IdentificationSummary() = default;
34 
35  // small struct for unique peptide / protein identifications (considering sequence only)
36  // count: number of unique identifications, fdr_threshold: significance threshold if score type is FDR, else -1
37  struct OPENMS_DLLAPI UniqueID {
38  UInt count = 0;
39  float fdr_threshold = -1.0;
40  };
41 
42  // stores identification summary values calculated by compute function
43  struct OPENMS_DLLAPI Result {
44  UInt peptide_spectrum_matches = 0;
47  float missed_cleavages_mean = 0;
48  double protein_hit_scores_mean = 0;
49  double peptide_length_mean = 0;
50 
51  bool operator==(const Result& rhs) const;
52  };
53 
68  Result compute(std::vector<ProteinIdentification>& prot_ids, PeptideIdentificationList& pep_ids);
69 
70  const String& getName() const override;
71 
72  QCBase::Status requirements() const override;
73 
74  private:
75  const String name_ = "Summary of detected Proteins and Peptides from idXML file";
76  };
77 } // namespace OpenMS
Stores and handles combinations of enum values, e.g. a set of flags as bits flipped in an UInt64.
Definition: FlagSet.h:28
Definition: IdentificationSummary.h:27
IdentificationSummary()=default
Constructor.
const String & getName() const override
Returns the name of the metric.
virtual ~IdentificationSummary()=default
Destructor.
QCBase::Status requirements() const override
Returns the input data requirements of the compute(...) function.
Result compute(std::vector< ProteinIdentification > &prot_ids, PeptideIdentificationList &pep_ids)
computes a summary of an idXML file
Definition: IdentificationSummary.h:37
Container for peptide identifications from multiple spectra.
Definition: PeptideIdentificationList.h:66
This class serves as an abstract base class for all QC classes.
Definition: QCBase.h:29
A more convenient string class.
Definition: String.h:34
unsigned int UInt
Unsigned integer type.
Definition: Types.h:64
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
Definition: IdentificationSummary.h:43
UniqueID unique_peptides
Definition: IdentificationSummary.h:45
bool operator==(const Result &rhs) const
UniqueID unique_proteins
Definition: IdentificationSummary.h:46