| OpenMS 2.5.0

PeptideProteinResolution.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: Julianus Pfeuffer $
32 // $Authors: Julianus Pfeuffer $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/CONCEPT/LogStream.h>
38 #include <OpenMS/CONCEPT/Types.h>
39 #include <OpenMS/KERNEL/StandardTypes.h>
40 #include <OpenMS/METADATA/ProteinIdentification.h>
41 #include <OpenMS/METADATA/PeptideIdentification.h>
42 #include <vector>
43 #include <set>
44
45 namespace OpenMS
46 {
47
50 struct OPENMS_DLLAPI ConnectedComponent
51 {
52 std::set<Size> prot_grp_indices;
53 std::set<Size> pep_indices;
54
55 // Default constructor
56 ConnectedComponent();
57
59 friend std::ostream& operator << (std::ostream& os, const ConnectedComponent& conn_comp);
60 };
61
86 class OPENMS_DLLAPI PeptideProteinResolution
87 {
88
89 private:
95 typedef std::map<Size, std::set<Size> > IndexMap_;
96
98 // TODO WIP for better tie resolution
99 // std::vector<std::pair<bool,bool>> indist_prot_grp_td_;
101 IndexMap_ indist_prot_grp_to_pep_;
103 IndexMap_ pep_to_indist_prot_grp_;
104
108 std::map<String, Size> prot_acc_to_indist_prot_grp_;
109
111 bool statistics_;
112
113 public:
116 PeptideProteinResolution(bool statistics = false);
117
118
126 static void resolve(ProteinIdentification& protein,
127 std::vector<PeptideIdentification>& peptides,
128 bool resolve_ties,
129 bool targets_first);
130
137 void buildGraph(ProteinIdentification& protein,
138 const std::vector<PeptideIdentification>& peptides,
139 bool skip_sort = false);
140
147 void resolveGraph(ProteinIdentification& protein,
148 std::vector<PeptideIdentification>& peptides);
149
154 ConnectedComponent findConnectedComponent(Size& root_prot_grp);
155
156
170 void resolveConnectedComponent(ConnectedComponent& conn_comp,
171 ProteinIdentification& protein,
172 std::vector<PeptideIdentification>& peptides);
173 };
174
175 } //namespace OpenMS
176
ProteinIdentification.h
OpenMS::PeptideProteinResolution::statistics_
bool statistics_
log debug information?
Definition: PeptideProteinResolution.h:111
OpenMS::PeptideProteinResolution::prot_acc_to_indist_prot_grp_
std::map< String, Size > prot_acc_to_indist_prot_grp_
Definition: PeptideProteinResolution.h:108
OpenMS::ConnectedComponent
Definition: PeptideProteinResolution.h:50
StandardTypes.h
Types.h
OpenMS::PeptideProteinResolution::pep_to_indist_prot_grp_
IndexMap_ pep_to_indist_prot_grp_
mapping indist. protein group indices <- peptide identification indices
Definition: PeptideProteinResolution.h:103
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:71
OpenMS::operator<<
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
PeptideIdentification.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::PeptideProteinResolution::indist_prot_grp_to_pep_
IndexMap_ indist_prot_grp_to_pep_
if the protein group at index i contains a target (first) and/or decoy (second)
Definition: PeptideProteinResolution.h:101
LogStream.h
OpenMS::PeptideProteinResolution
Resolves shared peptides based on protein scores.
Definition: PeptideProteinResolution.h:86
OpenMS::ConnectedComponent::pep_indices
std::set< Size > pep_indices
Definition: PeptideProteinResolution.h:53
OpenMS::PeptideProteinResolution::IndexMap_
std::map< Size, std::set< Size > > IndexMap_
Definition: PeptideProteinResolution.h:95
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::ConnectedComponent::prot_grp_indices
std::set< Size > prot_grp_indices
Definition: PeptideProteinResolution.h:52