OpenMS  2.5.0
BasicProteinInferenceAlgorithm.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 2002-2020.
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 #pragma once
35 
40 
41 namespace OpenMS
42 {
58  class OPENMS_DLLAPI BasicProteinInferenceAlgorithm :
59  public DefaultParamHandler,
60  public ProgressLogger
61  {
62  public:
63 
67  enum class AggregationMethod
68  {
69  PROD,
70  SUM,
71  MAXIMUM
72  };
73 
76 
80  void run(std::vector<PeptideIdentification> &pep_ids, std::vector<ProteinIdentification> &prot_ids) const;
81  void run(std::vector<PeptideIdentification> &pep_ids, ProteinIdentification &prot_id) const;
82 
83  private:
84 
94  void processRun_(
95  std::unordered_map<std::string, std::pair<ProteinHit*, Size>>& acc_to_protein_hitP_and_count,
96  std::unordered_map<std::string, std::map<Int, PeptideHit*>>& best_pep,
97  ProteinIdentification& prot_run,
98  std::vector<PeptideIdentification>& pep_ids,
99  Size min_peptides_per_protein) const;
100  };
101 } //namespace OpenMS
DefaultParamHandler.h
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:71
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::BasicProteinInferenceAlgorithm
Algorithm class that implements simple protein inference by aggregation of peptide scores....
Definition: BasicProteinInferenceAlgorithm.h:58
PeptideHit.h
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
ProgressLogger.h
ProteinIdentification.h
OpenMS::IntensityAveragingMethod::SUM
OpenMS::BasicProteinInferenceAlgorithm::AggregationMethod
AggregationMethod
The aggregation method.
Definition: BasicProteinInferenceAlgorithm.h:67