OpenMS  3.0.0
Contaminants.h
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31 // $Maintainer: Chris Bielow $
32 // $Authors: Dominik Schmitz, Chris Bielow$
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34 
35 #pragma once
36 
40 #include <OpenMS/QC/QCBase.h>
41 
42 #include <unordered_set>
43 
44 
45 namespace OpenMS
46 {
53  class OPENMS_DLLAPI Contaminants: public QCBase
54  {
55  public:
58  {
61 
64 
67 
70 
72  std::pair<Int64, Int64> empty_features;
73  };
74 
76  Contaminants() = default;
77 
79  virtual ~Contaminants() = default;
80 
96  void compute(FeatureMap& features, const std::vector<FASTAFile::FASTAEntry>& contaminants);
97 
99  const String& getName() const override;
100 
102  const std::vector<Contaminants::ContaminantsSummary>& getResults();
103 
108  Status requires() const override;
109 
110  private:
112  const String name_ = "Contaminants";
113 
115  std::vector<Contaminants::ContaminantsSummary> results_;
116 
118  std::unordered_set<String> digested_db_;
119 
131  void compare_(const String& key, PeptideHit& pep_hit, Int64& total, Int64& cont, double& sum_total, double& sum_cont, double intensity);
132  };
133 } // namespace OpenMS
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Int64
OPENMS_INT64_TYPE Int64
Signed integer type (64bit)
Definition: Types.h:70
OpenMS::Contaminants::ContaminantsSummary::unassigned_contaminants_ratio
double unassigned_contaminants_ratio
(#contaminants in unassigned/ #peptides in unassigned)
Definition: Contaminants.h:63
OpenMS::Contaminants::ContaminantsSummary
structure for storing results
Definition: Contaminants.h:57
OpenMS::Contaminants::ContaminantsSummary::empty_features
std::pair< Int64, Int64 > empty_features
(features without peptideidentification or with peptideidentifications but without hits; all features...
Definition: Contaminants.h:72
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::Contaminants::results_
std::vector< Contaminants::ContaminantsSummary > results_
container that stores results
Definition: Contaminants.h:115
FASTAFile.h
OpenMS::Contaminants::ContaminantsSummary::assigned_contaminants_ratio
double assigned_contaminants_ratio
(#contaminants in assigned/ #peptides in assigned)
Definition: Contaminants.h:60
OpenMS::QCBase
This class serves as an abstract base class for all QC classes.
Definition: QCBase.h:54
OpenMS::Contaminants::ContaminantsSummary::all_contaminants_ratio
double all_contaminants_ratio
(#all contaminants/ #peptides in all)
Definition: Contaminants.h:66
FeatureMap.h
OpenMS::Contaminants::ContaminantsSummary::assigned_contaminants_intensity_ratio
double assigned_contaminants_intensity_ratio
(intensity of contaminants in assigned/ intensity of peptides in assigned)
Definition: Contaminants.h:69
OpenMS::Contaminants
This class is a metric for the QualityControl TOPP tool.
Definition: Contaminants.h:53
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::FlagSet
Stores and handles combinations of enum values, e.g. a set of flags as bits flipped in an UInt64.
Definition: FlagSet.h:53
OpenMS::Contaminants::digested_db_
std::unordered_set< String > digested_db_
unordered set that contains the contaminant sequences
Definition: Contaminants.h:118
PeptideIdentification.h
QCBase.h
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:55