OpenMS
IsotopeWavelet.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 2002-2023.
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: $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
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 
59  {
60  return me_;
61  }
62 
64  static void destroy();
65 
66 
77  static double getValueByMass(const double t, const double m, const UInt z, const Int mode = +1)
78  {
79  return getValueByLambda(getLambdaL(m * z - z * mode * Constants::IW_PROTON_MASS), t * z + 1);
80  }
81 
91  static double getValueByLambda(const double lambda, const double tz1);
92 
106  static double getValueByLambdaExtrapol(const double lambda, const double tz1);
107 
108  static double getValueByLambdaExact(const double lambda, const double tz1);
109 
110 
113  {
114  return max_charge_;
115  }
116 
118  static void setMaxCharge(const UInt max_charge)
119  {
120  max_charge_ = max_charge;
121  }
122 
128  static double getTableSteps()
129  {
130  return table_steps_;
131  }
132 
138  static double getInvTableSteps()
139  {
140  return inv_table_steps_;
141  }
142 
144  static void setTableSteps(const double table_steps)
145  {
146  inv_table_steps_ = 1. / table_steps;
147  table_steps_ = table_steps;
148  }
149 
151  static double getLambdaL(const double m);
152 
153 
159  static const IsotopeDistribution::ContainerType & getAveragine(const double m, UInt * size = nullptr);
160 
161 
164  {
165  return gamma_table_max_index_;
166  }
167 
170  {
171  return exp_table_max_index_;
172  }
173 
176  static float myPow(float a, float b);
177 
178  static UInt getMzPeakCutOffAtMonoPos(const double mass, const UInt z);
179 
180  static UInt getNumPeakCutOff(const double mass, const UInt z);
181 
182  static UInt getNumPeakCutOff(const double mz);
183 
184 
185 protected:
186 
188  static IsotopeWavelet * me_;
189 
192 
196  IsotopeWavelet(const double max_m, const UInt max_charge);
197 
198 
200  virtual ~IsotopeWavelet();
201 
202 
212  static void preComputeExpensiveFunctions_(const double max_m);
213 
214 
217  static void computeIsotopeDistributionSize_(const double max_m);
218 
219 
224  static float myPow2_(float i);
225 
230  static float myLog2_(float i);
231 
233  union fi_
234  {
236  float f;
237  };
238 
241 
243  static double table_steps_;
244  static double inv_table_steps_;
245 
247  static std::vector<double> gamma_table_;
248  static std::vector<double> gamma_table_new_;
249 
251  static std::vector<double> exp_table_;
252 
254  static std::vector<double> sine_table_;
255 
259 
262 
263  };
264 
265 } //namespace
266 
Isotope pattern generator for coarse isotope distributions.
Definition: CoarseIsotopePatternGenerator.h:105
Definition: IsotopeDistribution.h:65
std::vector< MassAbundance > ContainerType
Definition: IsotopeDistribution.h:72
Implements the isotope wavelet function.
Definition: IsotopeWavelet.h:51
static double table_steps_
Definition: IsotopeWavelet.h:243
static void destroy()
static float myPow2_(float i)
Internally used function; uses register shifts for fast computation of the power function....
Int i
Definition: IsotopeWavelet.h:235
static UInt max_charge_
Definition: IsotopeWavelet.h:240
virtual ~IsotopeWavelet()
Destructor.
static IsotopeDistribution averagine_
Definition: IsotopeWavelet.h:258
static double getValueByLambdaExtrapol(const double lambda, const double tz1)
Returns the value of the isotope wavelet at position t. This function is usually significantly slower...
static UInt getNumPeakCutOff(const double mass, const UInt z)
static double getValueByLambdaExact(const double lambda, const double tz1)
static std::vector< double > gamma_table_
Definition: IsotopeWavelet.h:247
static double inv_table_steps_
Definition: IsotopeWavelet.h:244
static IsotopeWavelet * init(const double max_m, const UInt max_charge)
static double getTableSteps()
Returns the table_steps_ parameter.
Definition: IsotopeWavelet.h:128
static UInt getMaxCharge()
Returns the largest charge state we will consider.
Definition: IsotopeWavelet.h:112
static std::vector< double > exp_table_
Definition: IsotopeWavelet.h:251
static std::vector< double > gamma_table_new_
Definition: IsotopeWavelet.h:248
static Size gamma_table_max_index_
Definition: IsotopeWavelet.h:260
static Size getGammaTableMaxIndex()
Returns the largest possible index for the pre-sampled gamma table.
Definition: IsotopeWavelet.h:163
static double getInvTableSteps()
Returns the inv_table_steps_ parameter.
Definition: IsotopeWavelet.h:138
static Size getExpTableMaxIndex()
Returns the largest possible index for the pre-sampled exp table.
Definition: IsotopeWavelet.h:169
static double getLambdaL(const double m)
Returns the mass-parameter lambda (linear fit).
IsotopeWavelet()
Default Constructor.
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:77
static void setMaxCharge(const UInt max_charge)
Sets the max_charge parameter.
Definition: IsotopeWavelet.h:118
static Size exp_table_max_index_
Definition: IsotopeWavelet.h:261
static void computeIsotopeDistributionSize_(const double max_m)
Initializes the internally used averagine model; automatically called by the public constructor.
static float myLog2_(float i)
Internally used function uses register shifts for fast computation of the power function....
static double getValueByLambda(const double lambda, const double tz1)
Returns the value of the isotope wavelet at position t via a fast table lookup. Usually,...
static const IsotopeDistribution::ContainerType & getAveragine(const double m, UInt *size=nullptr)
Computes the averagine isotopic distribution we would expect at the de-convoluted mass.
static UInt getNumPeakCutOff(const double mz)
static void setTableSteps(const double table_steps)
Sets the table_steps parameter.
Definition: IsotopeWavelet.h:144
IsotopeWavelet(const double max_m, const UInt max_charge)
Constructor.
static void preComputeExpensiveFunctions_(const double max_m)
Should be called once before values are drawn from the isotope wavelet function. The function is auto...
static CoarseIsotopePatternGenerator solver_
Definition: IsotopeWavelet.h:257
static UInt getMzPeakCutOffAtMonoPos(const double mass, const UInt z)
static IsotopeWavelet * getInstance()
Definition: IsotopeWavelet.h:58
static std::vector< double > sine_table_
Definition: IsotopeWavelet.h:254
static float myPow(float a, float b)
Internally used function; uses register shifts for fast computation of the power function.
static IsotopeWavelet * me_
Definition: IsotopeWavelet.h:188
float f
Definition: IsotopeWavelet.h:236
Internal union for fast computation of the power function.
Definition: IsotopeWavelet.h:234
int Int
Signed integer type.
Definition: Types.h:102
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
const double IW_PROTON_MASS
Definition: IsotopeWaveletConstants.h:68
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48