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 2002-2012.
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// $Maintainer: Alexandra Zerck $
// $Authors: Eva Lange $
// --------------------------------------------------------------------------

#ifndef OPENMS_TRANSFORMATIONS_RAW2PEAK_CONTINUOUSWAVELETTRANSFORM_H
#define OPENMS_TRANSFORMATIONS_RAW2PEAK_CONTINUOUSWAVELETTRANSFORM_H

#include <OpenMS/KERNEL/Peak1D.h>

#include <vector>
#include <iostream>

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 DoubleReal getScale() const
    {
      return scale_;
    }

    inline double & getScale()
    {
      return scale_;
    }

    inline void setScale(DoubleReal scale)
    {
      scale_ = scale;
    }

    // Non-mutable access to the spacing of raw data
    inline DoubleReal 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

#endif