OpenMS
ProteinInference.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 2002-2023.
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: Chris Bielow $
32 // $Authors: $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
37 #include <OpenMS/KERNEL/Peak2D.h>
38 
39 #include <vector>
40 
41 namespace OpenMS
42 {
43 
44  class PeptideHit;
45  class ConsensusMap;
46 
54  class OPENMS_DLLAPI ProteinInference
55  {
56 
57 public:
58 
60 
63 
66 
69 
83  void infer(ConsensusMap& consensus_map, const UInt reference_map);
84 
85 
86 protected:
87 
88  void infer_(ConsensusMap& consensus_map,
89  const size_t protein_idenfication_index,
90  const UInt reference_map);
91 
92  bool sortByUnique_(std::vector<PeptideHit>& peptide_hits_local, const bool is_higher_score_better);
93 
94  }; // !class
95 
96 } // !namespace
97 
A container for consensus elements.
Definition: ConsensusMap.h:92
float IntensityType
Intensity type.
Definition: Peak2D.h:62
[experimental class] given a peptide quantitation, infer corresponding protein quantities
Definition: ProteinInference.h:55
ProteinInference & operator=(const ProteinInference &rhs)
assignment operator
ProteinInference(const ProteinInference &cp)
copy constructor
void infer(ConsensusMap &consensus_map, const UInt reference_map)
given a peptide quantitation, infer corresponding protein quantities
ProteinInference()
Constructor.
Peak2D::IntensityType IntensityType
Definition: ProteinInference.h:59
void infer_(ConsensusMap &consensus_map, const size_t protein_idenfication_index, const UInt reference_map)
bool sortByUnique_(std::vector< PeptideHit > &peptide_hits_local, const bool is_higher_score_better)
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48