OpenMS
MissedCleavages.h
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1 // Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Chris Bielow $
6 // $Authors: Swenja Wagner, Patricia Scheil $
7 // --------------------------------------------------------------------------
8 
9 
10 #pragma once
11 
15 #include <OpenMS/QC/QCBase.h>
16 #include <map>
17 #include <vector>
18 namespace OpenMS
19 {
20  class FeatureMap;
31  class OPENMS_DLLAPI MissedCleavages : public QCBase
32  {
33  private:
34  typedef std::map<UInt32, UInt32> MapU32;
37 
38  public:
40  MissedCleavages() = default;
41 
43  virtual ~MissedCleavages() = default;
44 
54  void compute(FeatureMap& fmap);
55  void compute(std::vector<ProteinIdentification>& prot_ids, std::vector<PeptideIdentification>& pep_ids);
56 
58  const String& getName() const override;
59 
61  const std::vector<std::map<UInt32, UInt32>>& getResults() const;
62 
67  QCBase::Status requirements() const override;
68 
69  private:
71  std::vector<std::map<UInt32, UInt32>> mc_result_;
72  };
73 } // namespace OpenMS
A container for features.
Definition: FeatureMap.h:80
Stores and handles combinations of enum values, e.g. a set of flags as bits flipped in an UInt64.
Definition: FlagSet.h:28
This class is a metric for the QualityControl TOPP Tool.
Definition: MissedCleavages.h:32
std::map< UInt32, UInt32 > MapU32
Definition: MissedCleavages.h:34
void compute(std::vector< ProteinIdentification > &prot_ids, std::vector< PeptideIdentification > &pep_ids)
std::vector< std::map< UInt32, UInt32 > > mc_result_
container that stores results
Definition: MissedCleavages.h:71
virtual ~MissedCleavages()=default
destructor
void compute(FeatureMap &fmap)
Counts the number of missed cleavages per PeptideIdentification.
const String & getName() const override
returns the name of the metric
QCBase::Status requirements() const override
Returns the input data requirements of the compute(...) function.
MissedCleavages()=default
constructor
const std::vector< std::map< UInt32, UInt32 > > & getResults() const
returns the result as maps of number of missed_cleavages to counts; one map for each call to compute(...
void get_missed_cleavages_from_peptide_identification_(const ProteaseDigestion &digestor, MapU32 &result, const UInt32 &max_mc, PeptideIdentification &pep_id)
collects number of missed cleavages from PeptideIdentification in a result map (missed cleavages: occ...
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:39
Class for the enzymatic digestion of proteins represented as AASequence or String.
Definition: ProteaseDigestion.h:32
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
OPENMS_UINT32_TYPE UInt32
Unsigned integer type (32bit)
Definition: Types.h:37
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:22