IsotopeWavelet.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2021.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg$
// $Authors: $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/IsotopeWaveletConstants.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/CoarseIsotopePatternGenerator.h>
 
namespace OpenMS
{
  class OPENMS_DLLAPI IsotopeWavelet
  {
public:
 
    static IsotopeWavelet * init(const double max_m, const UInt max_charge);
 
    static IsotopeWavelet * getInstance()
    {
      return me_;
    }
 
    static void destroy();
 
 
    static double getValueByMass(const double t, const double m, const UInt z, const Int mode = +1)
    {
      return getValueByLambda(getLambdaL(m * z - z * mode * Constants::IW_PROTON_MASS), t * z + 1);
    }
 
    static double getValueByLambda(const double lambda, const double tz1);
 
    static double getValueByLambdaExtrapol(const double lambda, const double tz1);
 
    static double getValueByLambdaExact(const double lambda, const double tz1);
 
 
    static UInt getMaxCharge()
    {
      return max_charge_;
    }
 
    static void setMaxCharge(const UInt max_charge)
    {
      max_charge_ = max_charge;
    }
 
    static double getTableSteps()
    {
      return table_steps_;
    }
 
    static double getInvTableSteps()
    {
      return inv_table_steps_;
    }
 
    static void setTableSteps(const double table_steps)
    {
      inv_table_steps_ = 1. / table_steps;
      table_steps_ = table_steps;
    }
 
    static double getLambdaL(const double m);
 
 
    static const IsotopeDistribution::ContainerType & getAveragine(const double m, UInt * size = nullptr);
 
 
    static Size getGammaTableMaxIndex()
    {
      return gamma_table_max_index_;
    }
 
    static Size getExpTableMaxIndex()
    {
      return exp_table_max_index_;
    }
 
    static float myPow(float a, float b);
 
    static UInt getMzPeakCutOffAtMonoPos(const double mass, const UInt z);
 
    static UInt getNumPeakCutOff(const double mass, const UInt z);
 
    static UInt getNumPeakCutOff(const double mz);
 
 
protected:
 
    static IsotopeWavelet * me_;
 
    IsotopeWavelet();
 
    IsotopeWavelet(const double max_m, const UInt max_charge);
 
 
    virtual ~IsotopeWavelet();
 
 
    static void preComputeExpensiveFunctions_(const double max_m);
 
 
    static void computeIsotopeDistributionSize_(const double max_m);
 
 
    static float myPow2_(float i);
 
    static float myLog2_(float i);
 
    union fi_
    {
      Int i;
      float f;
    };
 
    static UInt max_charge_;
 
    static double table_steps_;
    static double inv_table_steps_;
 
    static std::vector<double> gamma_table_;
    static std::vector<double> gamma_table_new_;
 
    static std::vector<double> exp_table_;
 
    static std::vector<double> sine_table_;
 
    static CoarseIsotopePatternGenerator solver_;
    static IsotopeDistribution averagine_;
 
    static Size gamma_table_max_index_;
    static Size exp_table_max_index_;
 
  };
 
} //namespace