| OpenMS 2.5.0

BaseModel.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
38 #include <OpenMS/KERNEL/DPeak.h>
39
40 namespace OpenMS
41 {
42
49 template <UInt D>
50 class BaseModel :
51 public DefaultParamHandler
52 {
53
54 public:
55
56 typedef double IntensityType;
57 typedef double CoordinateType;
58 typedef DPosition<D> PositionType;
59 typedef typename DPeak<D>::Type PeakType;
60 typedef std::vector<PeakType> SamplesType;
61
62
64 BaseModel() :
65 DefaultParamHandler("BaseModel")
66 {
67 defaults_.setValue("cutoff", 0.0, "Low intensity cutoff of the model. Peaks below this intensity are not considered part of the model.");
68 }
69
71 BaseModel(const BaseModel & source) :
72 DefaultParamHandler(source),
73 cut_off_(source.cut_off_)
74 {
75 }
76
78 ~BaseModel() override
79 {
80 }
81
83 virtual BaseModel & operator=(const BaseModel & source)
84 {
85 if (&source == this) return *this;
86
87 DefaultParamHandler::operator=(source);
88 cut_off_ = source.cut_off_;
89
90 return *this;
91 }
92
94 static void registerChildren();
95
97 virtual IntensityType getIntensity(const PositionType & pos) const = 0;
98
100 virtual bool isContained(const PositionType & pos) const
101 {
102 return getIntensity(pos) >= cut_off_;
103 }
104
109 template <typename PeakType>
110 void fillIntensity(PeakType & peak) const
111 {
112 peak.setIntensity(getIntensity(peak.getPosition()));
113 }
114
118 template <class PeakIterator>
119 void fillIntensities(PeakIterator begin, PeakIterator end) const
120 {
121 for (PeakIterator it = begin; it != end; ++it)
122 {
123 fillIntensity(*it);
124 }
125 }
126
128 virtual IntensityType getCutOff() const
129 {
130 return cut_off_;
131 }
132
134 virtual void setCutOff(IntensityType cut_off)
135 {
136 cut_off_ = cut_off;
137 param_.setValue("cutoff", cut_off_);
138 }
139
141 virtual void getSamples(SamplesType & cont) const = 0;
142
144 virtual void getSamples(std::ostream & os)
145 {
146 SamplesType samples;
147 getSamples(samples);
148 for (typename SamplesType::const_iterator it = samples.begin(); it != samples.end(); ++it)
149 {
150 os << *it << std::endl;
151 }
152 }
153
154 protected:
155 IntensityType cut_off_;
156
157 void updateMembers_() override
158 {
159 cut_off_ = (double)param_.getValue("cutoff");
160 }
161
162 };
163 }
164
OpenMS::BaseModel::isContained
virtual bool isContained(const PositionType &pos) const
check if position pos is part of the model regarding the models cut-off.
Definition: BaseModel.h:100
OpenMS::BaseModel::IntensityType
double IntensityType
Definition: BaseModel.h:56
OpenMS::DefaultParamHandler::defaults_
Param defaults_
Container for default parameters. This member should be filled in the constructor of derived classes!...
Definition: DefaultParamHandler.h:156
OpenMS::BaseModel::PeakType
DPeak< D >::Type PeakType
Definition: BaseModel.h:59
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::BaseModel::PositionType
DPosition< D > PositionType
Definition: BaseModel.h:58
OpenMS::BaseModel::updateMembers_
void updateMembers_() override
This method is used to update extra member variables at the end of the setParameters() method...
Definition: BaseModel.h:157
OpenMS::BaseModel::getSamples
virtual void getSamples(std::ostream &os)
fill stream with reasonable set of samples from the model (i.e. for printing)
Definition: BaseModel.h:144
OpenMS::Param::getValue
const DataValue & getValue(const String &key) const
Returns a value of a parameter.
OpenMS::BaseModel::fillIntensity
void fillIntensity(PeakType &peak) const
Convenience function to set the intensity of a peak to the predicted intensity at its current positio...
Definition: BaseModel.h:110
OpenMS::BaseModel::BaseModel
BaseModel(const BaseModel &source)
copy constructor
Definition: BaseModel.h:71
OpenMS::BaseModel::getIntensity
virtual IntensityType getIntensity(const PositionType &pos) const =0
access model predicted intensity at position pos
OpenMS::BaseModel
Abstract base class for all D-dimensional models.
Definition: BaseModel.h:50
OpenMS::BaseModel::~BaseModel
~BaseModel() override
Destructor.
Definition: BaseModel.h:78
OpenMS::DPeak
Metafunction to choose among Peak1D respectively Peak2D through a template argument.
Definition: DPeak.h:60
OpenMS::OptimizationFunctions::PeakIterator
RawDataVector::iterator PeakIterator
Profile data iterator type.
Definition: OptimizePick.h:52
OpenMS::BaseModel::fillIntensities
void fillIntensities(PeakIterator begin, PeakIterator end) const
Convenience function that applies fillIntensity() to an iterator range.
Definition: BaseModel.h:119
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
DPeak.h
OpenMS::BaseModel::SamplesType
std::vector< PeakType > SamplesType
Definition: BaseModel.h:60
OpenMS::Param::setValue
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
OpenMS::BaseModel::getSamples
virtual void getSamples(SamplesType &cont) const =0
get reasonable set of samples from the model (i.e. for printing)
OpenMS::BaseModel::getCutOff
virtual IntensityType getCutOff() const
get cutoff value
Definition: BaseModel.h:128
DefaultParamHandler.h
OpenMS::BaseModel::operator=
virtual BaseModel & operator=(const BaseModel &source)
assignment operator
Definition: BaseModel.h:83
OpenMS::DefaultParamHandler::operator=
virtual DefaultParamHandler & operator=(const DefaultParamHandler &rhs)
Assignment operator.
OpenMS::DPosition< D >
double
OpenMS::BaseModel::BaseModel
BaseModel()
Default constructor.
Definition: BaseModel.h:64
OpenMS::BaseModel::cut_off_
IntensityType cut_off_
Definition: BaseModel.h:155
OpenMS::BaseModel::registerChildren
static void registerChildren()
register all derived classes here (implemented in file BaseModel_impl.h)
OpenMS::BaseModel::CoordinateType
double CoordinateType
Definition: BaseModel.h:57
OpenMS::DefaultParamHandler::param_
Param param_
Container for current parameters.
Definition: DefaultParamHandler.h:149
OpenMS::BaseModel::setCutOff
virtual void setCutOff(IntensityType cut_off)
set cutoff value
Definition: BaseModel.h:134