OpenMS  3.0.0
SimTypes.h
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31 // $Maintainer: Timo Sachsenberg$
32 // $Authors: Stephan Aiche, Chris Bielow$
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34 
35 #pragma once
36 
37 #include <vector>
38 #include <utility>
39 #include <map>
40 #include <utility>
41 #include <boost/shared_ptr.hpp>
42 
43 #include <boost/random/mersenne_twister.hpp>
44 
49 #include <OpenMS/KERNEL/Peak2D.h>
52 
53 namespace OpenMS
54 {
55 
56  namespace SimTypes
57  {
60 
63 
66 
69 
73  struct SimProtein
74  {
79 
84  entry(e),
85  meta(m)
86  {}
87  };
88 
90  typedef std::vector<SimProtein> SampleProteins;
91 
93  typedef std::vector<SampleProteins> SampleChannels;
94 
97 
99  typedef std::vector<FeatureMapSim> FeatureMapSimVector;
100 
103 
119  {
120 public:
121 
122  boost::random::mt19937_64& getBiologicalRng()
123  {
124  return biological_rng_;
125  }
126 
127  boost::random::mt19937_64& getTechnicalRng()
128  {
129  return technical_rng_;
130  }
131 
132  void setBiologicalRngSeed(unsigned long int seed)
133  {
134  biological_rng_.seed(seed);
135  }
136 
137  void setTechnicalRngSeed(unsigned long int seed)
138  {
139  technical_rng_.seed(seed);
140  }
141 
143  void initialize(bool biological_random, bool technical_random)
144  {
145  // use 0 as default seed to get reproducible experiments
146  if (biological_random)
147  {
148  biological_rng_ = boost::random::mt19937_64(std::time(nullptr));
149  }
150  else
151  {
152  biological_rng_ = boost::random::mt19937_64(0);
153  }
154 
155  if (technical_random)
156  {
157  technical_rng_ = boost::random::mt19937_64(std::time(nullptr));
158  }
159  else
160  {
161  technical_rng_ = boost::random::mt19937_64(0);
162  }
163  }
164 
165 private:
167  boost::random::mt19937_64 biological_rng_;
169  boost::random::mt19937_64 technical_rng_;
170 
171  };
172 
173  //Sim Shared Pointer type
174  typedef boost::shared_ptr<SimRandomNumberGenerator> MutableSimRandomNumberGeneratorPtr;
175 
176  }
177 
178 }
179 
OpenMS::BaseFeature::ChargeType
Int ChargeType
Type of charge values.
Definition: BaseFeature.h:66
double
OpenMS::SimTypes::SimIntensityType
Peak2D::IntensityType SimIntensityType
Abundance of proteins/peptides.
Definition: SimTypes.h:62
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::SimTypes::SimProtein::meta
MetaInfoInterface meta
MetaInfoInterface holding the abundance information.
Definition: SimTypes.h:78
OpenMS::SimTypes::SampleProteins
std::vector< SimProtein > SampleProteins
Container for FASTAEntry & abundance information.
Definition: SimTypes.h:90
OpenMS::SimTypes::MutableSimRandomNumberGeneratorPtr
boost::shared_ptr< SimRandomNumberGenerator > MutableSimRandomNumberGeneratorPtr
Definition: SimTypes.h:174
OpenMS::SimTypes::SimRandomNumberGenerator::initialize
void initialize(bool biological_random, bool technical_random)
Initialize the RNGs.
Definition: SimTypes.h:143
OpenMS::SimTypes::SimRandomNumberGenerator
Wrapper class for random number generators used by the simulation classes.
Definition: SimTypes.h:118
OpenMS::SimTypes::SimRandomNumberGenerator::setTechnicalRngSeed
void setTechnicalRngSeed(unsigned long int seed)
Definition: SimTypes.h:137
OpenMS::FASTAFile::FASTAEntry
FASTA entry type (identifier, description and sequence) The first String corresponds to the identifie...
Definition: FASTAFile.h:71
OpenMS::SimTypes::SampleChannels
std::vector< SampleProteins > SampleChannels
Container for multiple channels of SampleProteins.
Definition: SimTypes.h:93
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::SimTypes::SimRandomNumberGenerator::setBiologicalRngSeed
void setBiologicalRngSeed(unsigned long int seed)
Definition: SimTypes.h:132
Peak2D.h
OpenMS::SimTypes::SimRandomNumberGenerator::biological_rng_
boost::random::mt19937_64 biological_rng_
random number generator for biological variability
Definition: SimTypes.h:167
FASTAFile.h
OpenMS::SimTypes::SimCoordinateType
Peak2D::CoordinateType SimCoordinateType
Coordinate type in mz and rt dimension.
Definition: SimTypes.h:59
OpenMS::MetaInfoInterface
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
FeatureMap.h
OpenMS::SimTypes::SimRandomNumberGenerator::getTechnicalRng
boost::random::mt19937_64 & getTechnicalRng()
Definition: SimTypes.h:127
OpenMS::Peak1D
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:53
OpenMS::SimTypes::FeatureMapSimVector
std::vector< FeatureMapSim > FeatureMapSimVector
Sim FeatureMap Vector.
Definition: SimTypes.h:99
OpenMS::SimTypes::SimProtein
Plain data object holding sequence and abundance information on a single protein.
Definition: SimTypes.h:73
MSExperiment.h
OpenMS::SimTypes::SimChargeType
Feature::ChargeType SimChargeType
Charge of a peptide.
Definition: SimTypes.h:65
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
AASequence.h
OpenMS::SimTypes::SimProtein::SimProtein
SimProtein(FASTAFile::FASTAEntry &e, MetaInfoInterface &m)
c'tor
Definition: SimTypes.h:83
float
MetaInfoInterface.h
OpenMS::SimTypes::SimProtein::entry
FASTAFile::FASTAEntry entry
FASTAEntry holding the sequence information.
Definition: SimTypes.h:76
OpenMS::SimTypes::SimRandomNumberGenerator::getBiologicalRng
boost::random::mt19937_64 & getBiologicalRng()
Definition: SimTypes.h:122
OpenMS::SimTypes::SimPointType
Peak1D SimPointType
Raw data point.
Definition: SimTypes.h:68
StandardTypes.h
OpenMS::SimTypes::MSSimExperiment
PeakMap MSSimExperiment
Sim MSExperiment type.
Definition: SimTypes.h:102
OpenMS::SimTypes::SimRandomNumberGenerator::technical_rng_
boost::random::mt19937_64 technical_rng_
random number generator for technical variability
Definition: SimTypes.h:169
OpenMS::SimTypes::FeatureMapSim
FeatureMap FeatureMapSim
Sim FeatureMap.
Definition: SimTypes.h:96