OpenMS
TMTTenPlexQuantitationMethod.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: Timo Sachsenberg $
32 // $Authors: Stephan Aiche $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
37 #include <OpenMS/config.h>
38 
40 
41 namespace OpenMS
42 {
48  class OPENMS_DLLAPI TMTTenPlexQuantitationMethod :
50  {
51 public:
54 
56  ~TMTTenPlexQuantitationMethod() override = default;
57 
60 
63 
66 
67  const String& getMethodName() const override;
68 
69  const IsobaricChannelList& getChannelInformation() const override;
70 
71  Size getNumberOfChannels() const override;
72 
74 
75  Size getReferenceChannel() const override;
76 
78 
79  private:
82 
84  static const String name_;
85 
88 
90  static const std::vector<std::string> channel_names_;
91 
92  protected:
95 
97  void updateMembers_() override;
98 
99  };
100 } // namespace
101 
Abstract base class describing an isobaric quantitation method in terms of the used channels and an i...
Definition: IsobaricQuantitationMethod.h:58
std::vector< IsobaricChannelInformation > IsobaricChannelList
Definition: IsobaricQuantitationMethod.h:98
A more convenient string class.
Definition: String.h:60
TMT 10plex quantitation to be used with the IsobaricQuantitation.
Definition: TMTTenPlexQuantitationMethod.h:50
static const std::vector< std::string > channel_names_
List of available channel names as they are presented to the user.
Definition: TMTTenPlexQuantitationMethod.h:90
const IsobaricChannelList & getChannelInformation() const override
Returns information on the different channels used by the quantitation method.
Size reference_channel_
The reference channel for this experiment.
Definition: TMTTenPlexQuantitationMethod.h:87
const String & getMethodName() const override
Methods to implement from IsobaricQuantitationMethod.
Size getReferenceChannel() const override
Returns the index of the reference channel in the IsobaricChannelList (see IsobaricQuantitationMethod...
void setDefaultParams_()
implemented for DefaultParamHandler
TMTTenPlexQuantitationMethod & operator=(const TMTTenPlexQuantitationMethod &rhs)
Assignment operator.
Size getNumberOfChannels() const override
Gives the number of channels available for this quantitation method.
~TMTTenPlexQuantitationMethod() override=default
d'tor
TMTTenPlexQuantitationMethod(const TMTTenPlexQuantitationMethod &other)
Copy c'tor.
TMTTenPlexQuantitationMethod()
Default c'tor.
void updateMembers_() override
implemented for DefaultParamHandler
static const String name_
The name of the quantitation method.
Definition: TMTTenPlexQuantitationMethod.h:84
Matrix< double > getIsotopeCorrectionMatrix() const override
Returns an isotope correction matrix suitable for the given quantitation method.
IsobaricChannelList channels_
the actual information on the different tmt10plex channels.
Definition: TMTTenPlexQuantitationMethod.h:81
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48