OpenMS  3.0.0
ICPLLabeler.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: Timo Sachsenberg $
32 // $Authors: Stephan Aiche$
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
38 #include <map>
39 
40 namespace OpenMS
41 {
42 
50  class OPENMS_DLLAPI ICPLLabeler :
51  public BaseLabeler
52  {
53 public:
54 
56  ICPLLabeler();
57 
59  ~ICPLLabeler() override;
60 
62  static BaseLabeler* create()
63  {
64  return new ICPLLabeler();
65  }
66 
68  static const String getProductName()
69  {
70  return "ICPL";
71  }
72 
73  // redeclaration of virtual methods
74  void preCheck(Param& param) const override;
75 
76  void setUpHook(SimTypes::FeatureMapSimVector& /* channels */) override;
77 
78  void postDigestHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
79 
80  void postRTHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
81 
82  void postDetectabilityHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
83 
84  void postIonizationHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
85 
86  void postRawMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
87 
88  void postRawTandemMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */, SimTypes::MSSimExperiment& /* simulated map */) override;
89 
90 protected:
91  void addModificationToPeptideHit_(Feature& feature, const String& modification) const;
92 
93  void addLabelToProteinHits_(SimTypes::FeatureMapSim& features, const String& label) const;
94 
95  Feature mergeFeatures_(Feature& labeled_channel_feature, const AASequence& unmodified_sequence, std::map<String, Feature>& unlabeled_features_index) const;
96 
100 
101  void updateMembers_() override;
102 
103  String getUnmodifiedAASequence_(const Feature& feature, const String& label) const;
104 
105 private:
107  static const int LIGHT_FEATURE_MAPID_;
109  static const int MEDIUM_FEATURE_MAPID_;
111  static const int HEAVY_FEATURE_MAPID_;
112  };
113 } // namespace OpenMS
114 
OpenMS::ICPLLabeler::LIGHT_FEATURE_MAPID_
static const int LIGHT_FEATURE_MAPID_
Map ID for the light/unlabeled channel.
Definition: ICPLLabeler.h:107
OpenMS::ICPLLabeler::create
static BaseLabeler * create()
create new object (needed by Factory)
Definition: ICPLLabeler.h:62
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
BaseLabeler.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ICPLLabeler::MEDIUM_FEATURE_MAPID_
static const int MEDIUM_FEATURE_MAPID_
Map ID for the medium labeled channel.
Definition: ICPLLabeler.h:109
OpenMS::ICPLLabeler
Simulate ICPL experiments.
Definition: ICPLLabeler.h:50
OpenMS::SimTypes::FeatureMapSimVector
std::vector< FeatureMapSim > FeatureMapSimVector
Sim FeatureMap Vector.
Definition: SimTypes.h:99
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::ICPLLabeler::heavy_channel_label_
String heavy_channel_label_
Definition: ICPLLabeler.h:99
OpenMS::BaseLabeler
Abstract base class for all kinds of labeling techniques.
Definition: BaseLabeler.h:49
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
OpenMS::ICPLLabeler::getProductName
static const String getProductName()
name of the model (needed by Factory)
Definition: ICPLLabeler.h:68
OpenMS::ICPLLabeler::medium_channel_label_
String medium_channel_label_
Definition: ICPLLabeler.h:98
OpenMS::ICPLLabeler::HEAVY_FEATURE_MAPID_
static const int HEAVY_FEATURE_MAPID_
Map ID for the heavy labeled channel.
Definition: ICPLLabeler.h:111
OpenMS::ICPLLabeler::light_channel_label_
String light_channel_label_
Definition: ICPLLabeler.h:97