| OpenMS 2.5.0

SILACLabeler.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: Timo Sachsenberg $
32 // $Authors: Stephan Aiche$
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/SIMULATION/LABELING/BaseLabeler.h>
38
39 namespace OpenMS
40 {
41
42
50 class OPENMS_DLLAPI SILACLabeler :
51 public BaseLabeler
52 {
53 public:
54
56 SILACLabeler();
57
59 ~SILACLabeler() override;
60
62 static BaseLabeler* create()
63 {
64 return new SILACLabeler();
65 }
66
68 static const String getProductName()
69 {
70 return "SILAC";
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 Feature mergeFeatures_(Feature& labeled_channel_feature, const String& unmodified_sequence, Map<String, Feature>& unlabeled_features_index, Int index_channel_id, Int labeled_channel_id) const;
94
95 Feature mergeAllChannelFeatures_(Feature& heavy_channel_feature, const String& unmodified_feature_sequence, Map<String, Feature>& light_channel_feature_index, Map<String, Feature>& medium_channel_feature_index) const;
96
97 String medium_channel_lysine_label_;
98 String medium_channel_arginine_label_;
99
100 String heavy_channel_lysine_label_;
101 String heavy_channel_arginine_label_;
102
103 bool canModificationBeApplied_(const String& modification_id, const String& aa) const;
104
105 void applyLabelToProteinHit_(SimTypes::FeatureMapSim& protein_hit, const String& arginine_label, const String& lysine_label) const;
106
107 void updateMembers_() override;
108
109 String getUnmodifiedSequence_(const Feature& feature, const String& arginine_label, const String& lysine_label) const;
110
111 private:
113 static const int LIGHT_FEATURE_MAPID_;
115 static const int MEDIUM_FEATURE_MAPID_;
117 static const int HEAVY_FEATURE_MAPID_;
118 };
119
120 } // namespace OpenMS
121
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::SILACLabeler::medium_channel_arginine_label_
String medium_channel_arginine_label_
Definition: SILACLabeler.h:98
OpenMS::SILACLabeler::MEDIUM_FEATURE_MAPID_
static const int MEDIUM_FEATURE_MAPID_
Map ID for the medium labeled channel.
Definition: SILACLabeler.h:115
OpenMS::SILACLabeler::create
static BaseLabeler * create()
create new object (needed by Factory)
Definition: SILACLabeler.h:62
OpenMS::SimTypes::FeatureMapSimVector
std::vector< FeatureMapSim > FeatureMapSimVector
Sim FeatureMap Vector.
Definition: SimTypes.h:99
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
OpenMS::SILACLabeler::LIGHT_FEATURE_MAPID_
static const int LIGHT_FEATURE_MAPID_
Map ID for the light/unlabeled channel.
Definition: SILACLabeler.h:113
OpenMS::SILACLabeler::medium_channel_lysine_label_
String medium_channel_lysine_label_
Definition: SILACLabeler.h:97
OpenMS::SILACLabeler::getProductName
static const String getProductName()
name of the model (needed by Factory)
Definition: SILACLabeler.h:68
OpenMS::BaseLabeler
Abstract base class for all kinds of labeling techniques.
Definition: BaseLabeler.h:49
OpenMS::SILACLabeler::HEAVY_FEATURE_MAPID_
static const int HEAVY_FEATURE_MAPID_
Map ID for the heavy labeled channel.
Definition: SILACLabeler.h:117
OpenMS::Map
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
OpenMS::SILACLabeler
Simulate SILAC experiments.
Definition: SILACLabeler.h:50
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::SILACLabeler::heavy_channel_lysine_label_
String heavy_channel_lysine_label_
Definition: SILACLabeler.h:100
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:73
int
OpenMS::SILACLabeler::heavy_channel_arginine_label_
String heavy_channel_arginine_label_
Definition: SILACLabeler.h:101
BaseLabeler.h