ContinuousWaveletTransform.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// This software is released under a three-clause BSD license:
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//    may be used to endorse or promote products derived from this software
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// For a full list of authors, refer to the file AUTHORS.
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Eva Lange $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/Peak1D.h>
 
#include <vector>
 
namespace OpenMS
{
  class OPENMS_DLLAPI ContinuousWaveletTransform
  {
public:
    typedef std::vector<Peak1D>::const_iterator PeakConstIterator;
 
 
    ContinuousWaveletTransform() :
      scale_(0),
      spacing_(0),
      signal_length_(0),
      end_left_padding_(0),
      begin_right_padding_(0)
    {}
 
    virtual ~ContinuousWaveletTransform()
    {}
 
    inline const std::vector<Peak1D> & getSignal() const
    {
      return signal_;
    }
 
    inline std::vector<Peak1D> & getSignal()
    {
      return signal_;
    }
 
    inline void setSignal(const std::vector<Peak1D> & signal)
    {
      signal_ = signal;
    }
 
    inline const std::vector<double> & getWavelet() const
    {
      return wavelet_;
    }
 
    inline std::vector<double> & getWavelet()
    {
      return wavelet_;
    }
 
    inline void setWavelet(const std::vector<double> & wavelet)
    {
      wavelet_ = wavelet;
    }
 
    // Non-mutable access to the scale of the wavelet
    inline double getScale() const
    {
      return scale_;
    }
 
    inline double & getScale()
    {
      return scale_;
    }
 
    inline void setScale(double scale)
    {
      scale_ = scale;
    }
 
    // Non-mutable access to the spacing of raw data
    inline double getSpacing() const
    {
      return spacing_;
    }
 
    inline double & getSpacing()
    {
      return spacing_;
    }
 
    inline void setSpacing(double spacing)
    {
      spacing_ = spacing;
    }
 
    inline SignedSize getLeftPaddingIndex() const
    {
      return end_left_padding_;
    }
 
    inline SignedSize & getLeftPaddingIndex()
    {
      return end_left_padding_;
    }
 
    inline void setLeftPaddingIndex(const SignedSize end_left_padding)
    {
      end_left_padding_ = end_left_padding;
    }
 
    inline SignedSize getRightPaddingIndex() const
    {
      return begin_right_padding_;
    }
 
    inline SignedSize & getRightPaddingIndex()
    {
      return begin_right_padding_;
    }
 
    inline void setRightPaddingIndex(const SignedSize begin_right_padding)
    {
      begin_right_padding_ = begin_right_padding;
    }
 
    inline SignedSize getSignalLength() const
    {
      return signal_length_;
    }
 
    inline SignedSize & getSignalLength()
    {
      return signal_length_;
    }
 
    inline void setSignalLength(const SignedSize signal_length)
    {
      signal_length_ = signal_length;
    }
 
    inline int getSize() const
    {
      return (int) signal_.size();
    }
 
    virtual void init(double scale, double spacing);
 
 
    inline double operator[](unsigned int i)
    {
      return signal_[i].getIntensity();
    }
 
    inline double operator[](unsigned int i) const
    {
      return signal_[i].getIntensity();
    }
 
protected:
    std::vector<Peak1D> signal_;
 
    std::vector<double> wavelet_;
 
    double scale_;
    double spacing_;
    SignedSize signal_length_;
 
    SignedSize end_left_padding_;
    SignedSize begin_right_padding_;
 
    template <typename InputPeakIterator>
    double getInterpolatedValue_(double x, InputPeakIterator it_left)
    {
      // Interpolate between the point to the left and the point to the right.
      double left_position = it_left->getMZ();
      double right_position = (it_left + 1)->getMZ();
      double d = (x - left_position) / (right_position - left_position);
 
      return (it_left + 1)->getIntensity() * d + it_left->getIntensity() * (1 - d);
    }
 
  };
 
} //namespace OpenMS