| OpenMS 2.5.0

Ms2SpectrumStats.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: Chris Bielow $
32 // $Authors: Juliane Schmachtenberg, Chris Bielow $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/QC/QCBase.h>
38
39 #include <OpenMS/KERNEL/Peak1D.h>
40 #include <OpenMS/KERNEL/MSSpectrum.h>
41
42
43 namespace OpenMS
44 {
45 class FeatureMap;
46 class MSExperiment;
47 class PeptideIdentification;
48 class TransformationDescription;
49
67 class OPENMS_DLLAPI Ms2SpectrumStats : public QCBase
68 {
69 public:
70 struct ScanEvent
71 {
72 ScanEvent(UInt32 sem, bool ms2)
73 : scan_event_number(sem), ms2_presence(ms2)
74 {}
75 UInt32 scan_event_number;
76 bool ms2_presence;
77 };
78
80 Ms2SpectrumStats() = default;
81
83 virtual ~Ms2SpectrumStats() = default;
84
95 std::vector<PeptideIdentification> compute(const MSExperiment& exp, FeatureMap& features, const QCBase::SpectraMap& map_to_spectrum);
96
98 const String& getName() const override;
100 Status requires() const override;
101
102 private:
104 const String name_ = "Ms2SpectrumStats";
105
107 std::vector<ScanEvent> ms2_included_{};
108
110 void setScanEventNumber_(const MSExperiment& exp);
111
113 void setPresenceAndScanEventNumber_(PeptideIdentification& peptide_ID, const MSExperiment& exp, const QCBase::SpectraMap& map_to_spectrum);
114
116 std::vector<PeptideIdentification> getUnassignedPeptideIdentifications_(const MSExperiment& exp);
117
119 static MSSpectrum::PeakType::IntensityType getBPI_(const MSSpectrum& spec);
120 };
121 }
OpenMS::UInt32
OPENMS_UINT32_TYPE UInt32
Unsigned integer type (32bit)
Definition: Types.h:63
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::QCBase
This class serves as an abstract base class for all QC classes.
Definition: QCBase.h:52
OpenMS::Ms2SpectrumStats::ScanEvent::scan_event_number
UInt32 scan_event_number
Definition: Ms2SpectrumStats.h:75
OpenMS::Ms2SpectrumStats
QC metric to determine the number of MS2 scans per MS1 scan over RT.
Definition: Ms2SpectrumStats.h:67
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::QCBase::Status
Storing a status of available/needed inputs (i.e. a set of Requires) as UInt64.
Definition: QCBase.h:118
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
Peak1D.h
OpenMS::QCBase::SpectraMap
Map to find a spectrum via its NativeID.
Definition: QCBase.h:75
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::Ms2SpectrumStats::ScanEvent::ScanEvent
ScanEvent(UInt32 sem, bool ms2)
Definition: Ms2SpectrumStats.h:72
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MSSpectrum.h
float
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
OpenMS::Ms2SpectrumStats::ScanEvent::ms2_presence
bool ms2_presence
Definition: Ms2SpectrumStats.h:76
OpenMS::Ms2SpectrumStats::ScanEvent
Definition: Ms2SpectrumStats.h:70
QCBase.h