OpenMS  3.0.0
IdentificationSummary.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: Axel Walter $
32 // $Authors: Axel Walter $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
37 #include <OpenMS/QC/QCBase.h>
40 #include <vector>
49 namespace OpenMS
50 {
51  class OPENMS_DLLAPI IdentificationSummary : public QCBase
52  {
53  public:
55  IdentificationSummary() = default;
56 
58  virtual ~IdentificationSummary() = default;
59 
60  // small struct for unique peptide / protein identifications (considering sequence only)
61  // count: number of unique identifications, fdr_threshold: significance threshold if score type is FDR, else -1
62  struct OPENMS_DLLAPI UniqueID
63  {
64  UInt count = 0;
65  float fdr_threshold = -1.0;
66  };
67 
68  // stores identification summary values calculated by compute function
69  struct OPENMS_DLLAPI Result
70  {
71  UInt peptide_spectrum_matches = 0;
74  float missed_cleavages_mean = 0;
75  double protein_hit_scores_mean = 0;
76  double peptide_length_mean = 0;
77 
78  bool operator==(const Result& rhs) const;
79  };
80 
95  Result compute(std::vector<ProteinIdentification>& prot_ids,
96  std::vector<PeptideIdentification>& pep_ids);
97 
98  const String& getName() const override;
99 
100  QCBase::Status requires() const override;
101 
102  private:
103  const String name_ = "Summary of detected Proteins and Peptides from idXML file";
104  };
105 }
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::IdentificationSummary::Result::unique_proteins
UniqueID unique_proteins
Definition: IdentificationSummary.h:73
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::QCBase
This class serves as an abstract base class for all QC classes.
Definition: QCBase.h:54
ProteinIdentification.h
OpenMS::IdentificationSummary
Definition: IdentificationSummary.h:51
OpenMS::IdentificationSummary::UniqueID
Definition: IdentificationSummary.h:62
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::IdentificationSummary::Result
Definition: IdentificationSummary.h:69
OpenMS::Internal::operator==
bool operator==(const IDBoostGraph::ProteinGroup &lhs, const IDBoostGraph::ProteinGroup &rhs)
OpenMS::FlagSet
Stores and handles combinations of enum values, e.g. a set of flags as bits flipped in an UInt64.
Definition: FlagSet.h:53
PeptideIdentification.h
OpenMS::IdentificationSummary::Result::unique_peptides
UniqueID unique_peptides
Definition: IdentificationSummary.h:72
QCBase.h