OpenMS  2.8.0
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 2002-2021.
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 
39 namespace OpenMS
40 {
41 
49  class OPENMS_DLLAPI ICPLLabeler :
50  public BaseLabeler
51  {
52 public:
53 
56 
58  ~ICPLLabeler() override;
59 
61  static BaseLabeler* create()
62  {
63  return new ICPLLabeler();
64  }
65 
67  static const String getProductName()
68  {
69  return "ICPL";
70  }
71 
72  // redeclaration of virtual methods
73  void preCheck(Param& param) const override;
74 
75  void setUpHook(SimTypes::FeatureMapSimVector& /* channels */) override;
76 
77  void postDigestHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
78 
79  void postRTHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
80 
81  void postDetectabilityHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
82 
83  void postIonizationHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
84 
85  void postRawMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
86 
87  void postRawTandemMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */, SimTypes::MSSimExperiment& /* simulated map */) override;
88 
89 protected:
90  void addModificationToPeptideHit_(Feature& feature, const String& modification) const;
91 
92  void addLabelToProteinHits_(SimTypes::FeatureMapSim& features, const String& label) const;
93 
94  Feature mergeFeatures_(Feature& labeled_channel_feature, const AASequence& unmodified_sequence, Map<String, Feature>& unlabeled_features_index) const;
95 
99 
100  void updateMembers_() override;
101 
102  String getUnmodifiedAASequence_(const Feature& feature, const String& label) const;
103 
104 private:
106  static const int LIGHT_FEATURE_MAPID_;
108  static const int MEDIUM_FEATURE_MAPID_;
110  static const int HEAVY_FEATURE_MAPID_;
111  };
112 } // namespace OpenMS
113 
Representation of a peptide/protein sequence.
Definition: AASequence.h:112
Abstract base class for all kinds of labeling techniques.
Definition: BaseLabeler.h:51
A container for features.
Definition: FeatureMap.h:106
An LC-MS feature.
Definition: Feature.h:72
Simulate ICPL experiments.
Definition: ICPLLabeler.h:51
String medium_channel_label_
Definition: ICPLLabeler.h:97
Feature mergeFeatures_(Feature &labeled_channel_feature, const AASequence &unmodified_sequence, Map< String, Feature > &unlabeled_features_index) const
void postRawTandemMSHook(SimTypes::FeatureMapSimVector &, SimTypes::MSSimExperiment &) override
Labeling after Tandem MS (e.g. iTRAQ)
ICPLLabeler()
default constructor
void addModificationToPeptideHit_(Feature &feature, const String &modification) const
void postIonizationHook(SimTypes::FeatureMapSimVector &) override
Labeling after ionization.
String getUnmodifiedAASequence_(const Feature &feature, const String &label) const
static const int MEDIUM_FEATURE_MAPID_
Map ID for the medium labeled channel.
Definition: ICPLLabeler.h:108
static BaseLabeler * create()
create new object (needed by Factory)
Definition: ICPLLabeler.h:61
void addLabelToProteinHits_(SimTypes::FeatureMapSim &features, const String &label) const
void postRTHook(SimTypes::FeatureMapSimVector &) override
Labeling after rt simulation.
void postDigestHook(SimTypes::FeatureMapSimVector &) override
Labeling between digestion and rt simulation.
void setUpHook(SimTypes::FeatureMapSimVector &) override
Hook to prepare the simulation process.
void postRawMSHook(SimTypes::FeatureMapSimVector &) override
Labeling after raw signal generation.
String heavy_channel_label_
Definition: ICPLLabeler.h:98
void postDetectabilityHook(SimTypes::FeatureMapSimVector &) override
Labeling after detectability simulation.
~ICPLLabeler() override
destructor
void updateMembers_() override
This method is used to update extra member variables at the end of the setParameters() method.
String light_channel_label_
Definition: ICPLLabeler.h:96
static const int LIGHT_FEATURE_MAPID_
Map ID for the light/unlabeled channel.
Definition: ICPLLabeler.h:106
static const String getProductName()
name of the model (needed by Factory)
Definition: ICPLLabeler.h:67
void preCheck(Param &param) const override
Checks the (simulation) params passed if they are consistent with the labeling technique.
static const int HEAVY_FEATURE_MAPID_
Map ID for the heavy labeled channel.
Definition: ICPLLabeler.h:110
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:73
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:52
Management and storage of parameters / INI files.
Definition: Param.h:70
A more convenient string class.
Definition: String.h:60
std::vector< FeatureMapSim > FeatureMapSimVector
Sim FeatureMap Vector.
Definition: SimTypes.h:99
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47