OpenMS  3.0.0
PeptideProteinResolution.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2022.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Julianus Pfeuffer $
32 // $Authors: Julianus Pfeuffer $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
37 #include <OpenMS/CONCEPT/Types.h>
41 #include <vector>
42 #include <set>
43 
44 namespace OpenMS
45 {
48  struct OPENMS_DLLAPI ConnectedComponent
49  {
50  std::set<Size> prot_grp_indices;
51  std::set<Size> pep_indices;
53  friend std::ostream& operator<<(std::ostream& os, const ConnectedComponent& conn_comp);
54  };
55 
79  class OPENMS_DLLAPI PeptideProteinResolution
80  {
81 
82  private:
88  typedef std::map<Size, std::set<Size> > IndexMap_;
89 
91  // TODO WIP for better tie resolution
92  // std::vector<std::pair<bool,bool>> indist_prot_grp_td_;
97 
101  std::map<String, Size> prot_acc_to_indist_prot_grp_;
102 
105 
106  public:
109  PeptideProteinResolution(bool statistics = false);
110 
111 
119  static void resolve(ProteinIdentification& protein,
120  std::vector<PeptideIdentification>& peptides,
121  bool resolve_ties,
122  bool targets_first);
123 
128  static void run(std::vector<ProteinIdentification>& inferred_protein_id,
129  std::vector<PeptideIdentification>& inferred_peptide_ids);
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 
OpenMS::ConnectedComponent::pep_indices
std::set< Size > pep_indices
Definition: PeptideProteinResolution.h:51
OpenMS::PeptideProteinResolution
Resolves shared peptides based on protein scores.
Definition: PeptideProteinResolution.h:79
OpenMS::PeptideProteinResolution::statistics_
bool statistics_
log debug information?
Definition: PeptideProteinResolution.h:104
Types.h
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::PeptideProteinResolution::prot_acc_to_indist_prot_grp_
std::map< String, Size > prot_acc_to_indist_prot_grp_
Definition: PeptideProteinResolution.h:101
OpenMS::PeptideProteinResolution::IndexMap_
std::map< Size, std::set< Size > > IndexMap_
Definition: PeptideProteinResolution.h:88
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:70
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::PeptideProteinResolution::pep_to_indist_prot_grp_
IndexMap_ pep_to_indist_prot_grp_
mapping indist. protein group indices <- peptide identification indices
Definition: PeptideProteinResolution.h:96
ProteinIdentification.h
OpenMS::ConnectedComponent::prot_grp_indices
std::set< Size > prot_grp_indices
Definition: PeptideProteinResolution.h:50
OpenMS::operator<<
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
OpenMS::ConnectedComponent
Definition: PeptideProteinResolution.h:48
PeptideIdentification.h
StandardTypes.h
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:94