Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
ITRAQLabeler.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 2002-2013.
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: Chris Bielow $
33 // --------------------------------------------------------------------------
34 
35 #ifndef OPENMS_SIMULATION_LABELING_ITRAQLABELER_H
36 #define OPENMS_SIMULATION_LABELING_ITRAQLABELER_H
37 
40 
41 namespace OpenMS
42 {
43 
52  class OPENMS_DLLAPI ITRAQLabeler :
53  public BaseLabeler
54  {
55 public:
56 
60 
62  ITRAQLabeler();
63 
65  virtual ~ITRAQLabeler();
66 
68  static BaseLabeler * create()
69  {
70  return new ITRAQLabeler();
71  }
72 
74  static const String getProductName()
75  {
76  return "itraq";
77  }
78 
79  // redeclaration of virtual methods
80  void preCheck(Param & param) const;
81 
82  void setUpHook(FeatureMapSimVector & /* channels */);
83 
84  void postDigestHook(FeatureMapSimVector & /* features_to_simulate */);
85 
86  void postRTHook(FeatureMapSimVector & /* features_to_simulate */);
87 
88  void postDetectabilityHook(FeatureMapSimVector & /* features_to_simulate */);
89 
90  void postIonizationHook(FeatureMapSimVector & /* features_to_simulate */);
91 
92  void postRawMSHook(FeatureMapSimVector & /* features_to_simulate */);
93 
94  void postRawTandemMSHook(FeatureMapSimVector & /* features_to_simulate */, MSSimExperiment & /* simulated map */);
95 
96 protected:
97 
102  void addModificationToPeptideHit_(Feature & feature, const String & modification, const Size & pos) const;
103 
111  void labelPeptide_(const Feature & feature, FeatureMapSim & result) const;
112 
113  Feature mergeFeatures_(Feature & labeled_channel_feature, const AASequence & unmodified_sequence, std::map<AASequence, Feature> & unlabeled_features_index) const;
114 
116  void updateMembers_();
117 
118  // get the closest RT profile factor of a feature for a given RT
119  DoubleReal getRTProfileIntensity_(const Feature & f, const DoubleReal MS2_RT_time) const;
120 
122  Matrix<SimIntensityType> getItraqIntensity_(const Feature & f, const DoubleReal MS2_RT_time) const;
123 
124 
125  // Members:
126 
129 
133 
136 
139 
140  };
141 } // namespace OpenMS
142 
143 #endif //#ifndef OPENMS_SIMULATION_LABELING_ITRAQLabeler_H
A more convenient string class.
Definition: String.h:56
ChannelMapType channel_map_
Definition: ITRAQLabeler.h:132
IsotopeMatrices isotope_corrections_
Matrices with isotope correction values (one for each plex-type)
Definition: ITRAQLabeler.h:135
A container for features.
Definition: FeatureMap.h:111
Representation of a peptide/protein sequence.
Definition: AASequence.h:84
stores information on an iTRAQ channel
Definition: ItraqConstants.h:62
ItraqConstants::ChannelInfo ChannelInfo
Definition: ITRAQLabeler.h:57
static const String getProductName()
name of the model (needed by Factory)
Definition: ITRAQLabeler.h:74
ItraqConstants::IsotopeMatrices IsotopeMatrices
Definition: ITRAQLabeler.h:59
ItraqConstants::ChannelMapType ChannelMapType
Definition: ITRAQLabeler.h:58
static BaseLabeler * create()
create new object (needed by Factory)
Definition: ITRAQLabeler.h:68
An LC-MS feature.
Definition: Feature.h:66
Int itraq_type_
set to either ItraqConstants::FOURPLEX or ItraqConstants::EIGHTPLEX
Definition: ITRAQLabeler.h:128
Management and storage of parameters / INI files.
Definition: Param.h:69
Simulate iTRAQ experiments.
Definition: ITRAQLabeler.h:52
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
std::vector< FeatureMapSim > FeatureMapSimVector
Sim FeatureMap Vector.
Definition: SimTypes.h:80
std::vector< Matrix< double > > IsotopeMatrices
(user defined?) isotope correction matrix in (-2, -1, +1, +2) row style
Definition: ItraqConstants.h:75
int Int
Signed integer type.
Definition: Types.h:100
Map class based on the STL map (containing serveral convenience functions)
Definition: Map.h:50
Abstract base class for all kinds of labeling techniques.
Definition: BaseLabeler.h:54
DoubleReal y_labeling_efficiency_
efficiency of &quot;Y&quot; labeling
Definition: ITRAQLabeler.h:138
A two-dimensional matrix. Similar to std::vector, but uses a binary operator(,) for element access...
Definition: Matrix.h:79

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:15 using doxygen 1.8.5