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IsotopeWavelet.h
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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.
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29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg$
32 // $Authors: $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/IsotopeWaveletConstants.h>
38 #include <OpenMS/KERNEL/MSSpectrum.h>
39 #include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/CoarseIsotopePatternGenerator.h>
40
41 namespace OpenMS
42 {
50 class OPENMS_DLLAPI IsotopeWavelet
51 {
52 public:
53
55 static IsotopeWavelet * init(const double max_m, const UInt max_charge);
56
58 static IsotopeWavelet * getInstance()
59 {
60 return me_;
61 }
62
64 static void destroy();
65
66
76 static double getValueByMass(const double t, const double m, const UInt z, const Int mode = +1)
77 {
78 return getValueByLambda(getLambdaL(m * z - z * mode * Constants::IW_PROTON_MASS), t * z + 1);
79 }
80
89 static double getValueByLambda(const double lambda, const double tz1);
90
103 static double getValueByLambdaExtrapol(const double lambda, const double tz1);
104
105 static double getValueByLambdaExact(const double lambda, const double tz1);
106
107
109 static UInt getMaxCharge()
110 {
111 return max_charge_;
112 }
113
115 static void setMaxCharge(const UInt max_charge)
116 {
117 max_charge_ = max_charge;
118 }
119
124 static double getTableSteps()
125 {
126 return table_steps_;
127 }
128
133 static double getInvTableSteps()
134 {
135 return inv_table_steps_;
136 }
137
139 static void setTableSteps(const double table_steps)
140 {
141 inv_table_steps_ = 1. / table_steps;
142 table_steps_ = table_steps;
143 }
144
146 static double getLambdaL(const double m);
147
148
153 static const IsotopeDistribution::ContainerType & getAveragine(const double m, UInt * size = nullptr);
154
155
157 static Size getGammaTableMaxIndex()
158 {
159 return gamma_table_max_index_;
160 }
161
163 static Size getExpTableMaxIndex()
164 {
165 return exp_table_max_index_;
166 }
167
170 static float myPow(float a, float b);
171
172 static UInt getMzPeakCutOffAtMonoPos(const double mass, const UInt z);
173
174 static UInt getNumPeakCutOff(const double mass, const UInt z);
175
176 static UInt getNumPeakCutOff(const double mz);
177
178
179 protected:
180
182 static IsotopeWavelet * me_;
183
185 IsotopeWavelet();
186
190 IsotopeWavelet(const double max_m, const UInt max_charge);
191
192
194 virtual ~IsotopeWavelet();
195
196
205 static void preComputeExpensiveFunctions_(const double max_m);
206
207
210 static void computeIsotopeDistributionSize_(const double max_m);
211
212
217 static float myPow2_(float i);
218
223 static float myLog2_(float i);
224
226 union fi_
227 {
228 Int i;
229 float f;
230 };
231
233 static UInt max_charge_;
234
236 static double table_steps_;
237 static double inv_table_steps_;
238
240 static std::vector<double> gamma_table_;
241 static std::vector<double> gamma_table_new_;
242
244 static std::vector<double> exp_table_;
245
247 static std::vector<double> sine_table_;
248
250 static CoarseIsotopePatternGenerator solver_;
251 static IsotopeDistribution averagine_;
252
253 static Size gamma_table_max_index_;
254 static Size exp_table_max_index_;
255
256 };
257
258 } //namespace
259
OpenMS::IsotopeWavelet::gamma_table_
static std::vector< double > gamma_table_
Definition: IsotopeWavelet.h:240
OpenMS::IsotopeWavelet
Implements the isotope wavelet function.
Definition: IsotopeWavelet.h:50
OpenMS::IsotopeWavelet::inv_table_steps_
static double inv_table_steps_
Definition: IsotopeWavelet.h:237
OpenMS::IsotopeWavelet::getMaxCharge
static UInt getMaxCharge()
Returns the largest charge state we will consider.
Definition: IsotopeWavelet.h:109
OpenMS::IsotopeWavelet::sine_table_
static std::vector< double > sine_table_
Definition: IsotopeWavelet.h:247
OpenMS::IsotopeWavelet::gamma_table_max_index_
static Size gamma_table_max_index_
Definition: IsotopeWavelet.h:253
OpenMS::Constants::IW_PROTON_MASS
const double IW_PROTON_MASS
Definition: IsotopeWaveletConstants.h:68
OpenMS::IsotopeDistribution
Definition: IsotopeDistribution.h:64
OpenMS::IsotopeWavelet::fi_::i
Int i
Definition: IsotopeWavelet.h:228
OpenMS::IsotopeWavelet::getExpTableMaxIndex
static Size getExpTableMaxIndex()
Returns the largest possible index for the pre-sampled exp table.
Definition: IsotopeWavelet.h:163
OpenMS::IsotopeWavelet::me_
static IsotopeWavelet * me_
Definition: IsotopeWavelet.h:182
OpenMS::IsotopeWavelet::getInstance
static IsotopeWavelet * getInstance()
Definition: IsotopeWavelet.h:58
OpenMS::IsotopeWavelet::averagine_
static IsotopeDistribution averagine_
Definition: IsotopeWavelet.h:251
OpenMS::IsotopeWavelet::fi_::f
float f
Definition: IsotopeWavelet.h:229
OpenMS::IsotopeWavelet::exp_table_
static std::vector< double > exp_table_
Definition: IsotopeWavelet.h:244
IsotopeWaveletConstants.h
OpenMS::IsotopeWavelet::getInvTableSteps
static double getInvTableSteps()
Returns the inv_table_steps_ parameter.
Definition: IsotopeWavelet.h:133
OpenMS::IsotopeWavelet::getTableSteps
static double getTableSteps()
Returns the table_steps_ parameter.
Definition: IsotopeWavelet.h:124
OpenMS::IsotopeWavelet::gamma_table_new_
static std::vector< double > gamma_table_new_
Definition: IsotopeWavelet.h:241
CoarseIsotopePatternGenerator.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MSSpectrum.h
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::IsotopeWavelet::table_steps_
static double table_steps_
Definition: IsotopeWavelet.h:236
OpenMS::IsotopeWavelet::setTableSteps
static void setTableSteps(const double table_steps)
Sets the table_steps parameter.
Definition: IsotopeWavelet.h:139
OpenMS::CoarseIsotopePatternGenerator
Isotope pattern generator for coarse isotope distributions.
Definition: CoarseIsotopePatternGenerator.h:96
int
OpenMS::IsotopeWavelet::exp_table_max_index_
static Size exp_table_max_index_
Definition: IsotopeWavelet.h:254
OpenMS::IsotopeWavelet::setMaxCharge
static void setMaxCharge(const UInt max_charge)
Sets the max_charge parameter.
Definition: IsotopeWavelet.h:115
OpenMS::IsotopeWavelet::getGammaTableMaxIndex
static Size getGammaTableMaxIndex()
Returns the largest possible index for the pre-sampled gamma table.
Definition: IsotopeWavelet.h:157
OpenMS::IsotopeWavelet::solver_
static CoarseIsotopePatternGenerator solver_
Definition: IsotopeWavelet.h:250
OpenMS::IsotopeWavelet::fi_
Internal union for fast computation of the power function.
Definition: IsotopeWavelet.h:226
OpenMS::IsotopeWavelet::getValueByMass
static double getValueByMass(const double t, const double m, const UInt z, const Int mode=+1)
Returns the value of the isotope wavelet at position t. Usually, you do not need to call this functio...
Definition: IsotopeWavelet.h:76
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::IsotopeWavelet::max_charge_
static UInt max_charge_
Definition: IsotopeWavelet.h:233
OpenMS::IsotopeDistribution::ContainerType
std::vector< MassAbundance > ContainerType
Definition: IsotopeDistribution.h:72