| OpenMS 2.5.0

Contaminants.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Chris Bielow $
32 // $Authors: Dominik Schmitz, Chris Bielow$
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/FeatureMap.h>
38 #include <OpenMS/FORMAT/FASTAFile.h>
39 #include <OpenMS/METADATA/PeptideIdentification.h>
40 #include <unordered_set>
41 #include <OpenMS/QC/QCBase.h>
42
43
44 namespace OpenMS
45 {
52 class OPENMS_DLLAPI Contaminants: public QCBase
53 {
54 public:
56 struct ContaminantsSummary
57 {
59 double assigned_contaminants_ratio;
60
62 double unassigned_contaminants_ratio;
63
65 double all_contaminants_ratio;
66
68 double assigned_contaminants_intensity_ratio;
69
71 std::pair<Int64, Int64> empty_features;
72 };
73
75 Contaminants() = default;
76
78 virtual ~Contaminants() = default;
79
95 void compute(FeatureMap& features, const std::vector<FASTAFile::FASTAEntry>& contaminants);
96
98 const String& getName() const override;
99
101 const std::vector<Contaminants::ContaminantsSummary>& getResults();
102
107 Status requires() const override;
108
109 private:
111 const String name_ = "Contaminants";
112
114 std::vector<Contaminants::ContaminantsSummary> results_;
115
117 std::unordered_set<String> digested_db_;
118
130 void compare_(const String& key, PeptideHit& pep_hit, Int64& total, Int64& cont, double& sum_total, double& sum_cont, double intensity);
131 };
132 } // namespace OpenMS
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::QCBase
This class serves as an abstract base class for all QC classes.
Definition: QCBase.h:52
OpenMS::QCBase::Status
Storing a status of available/needed inputs (i.e. a set of Requires) as UInt64.
Definition: QCBase.h:118
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
OpenMS::Contaminants::results_
std::vector< Contaminants::ContaminantsSummary > results_
container that stores results
Definition: Contaminants.h:114
OpenMS::Contaminants::ContaminantsSummary::assigned_contaminants_ratio
double assigned_contaminants_ratio
(#contaminants in assigned/ #peptides in assigned)
Definition: Contaminants.h:59
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:71
OpenMS::Contaminants
This class is a metric for the QualityControl TOPP tool.
Definition: Contaminants.h:52
OpenMS::Contaminants::ContaminantsSummary::all_contaminants_ratio
double all_contaminants_ratio
(#all contaminants/ #peptides in all)
Definition: Contaminants.h:65
FeatureMap.h
OpenMS::Contaminants::ContaminantsSummary
structure for storing results
Definition: Contaminants.h:56
FASTAFile.h
PeptideIdentification.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:54
OpenMS::Contaminants::digested_db_
std::unordered_set< String > digested_db_
unordered set that contains the contaminant sequences
Definition: Contaminants.h:117
OpenMS::Contaminants::ContaminantsSummary::unassigned_contaminants_ratio
double unassigned_contaminants_ratio
(#contaminants in unassigned/ #peptides in unassigned)
Definition: Contaminants.h:62
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:68
OpenMS::Int64
OPENMS_INT64_TYPE Int64
Signed integer type (64bit)
Definition: Types.h:70
QCBase.h