libopenms-dev 1.11.1-5 / usr / include / OpenMS / KERNEL / RangeUtils.h

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Stephan Aiche$
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------

#ifndef OPENMS_KERNEL_RANGEUTILS_H
#define OPENMS_KERNEL_RANGEUTILS_H

#include <functional>
#include <algorithm>
#include <vector>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/DATASTRUCTURES/IntList.h>
#include <OpenMS/METADATA/Precursor.h>

namespace OpenMS
{
  /**
    @defgroup RangeUtils RangeUtils

    @brief Predicates for range operations

    @ingroup Kernel
    A group of predicates that can be used to perform range operations on MS data.
    They operate on classes that have the save interface as Spectrum or Peak1D or Peak2D, respectively.
    <BR>
    <BR>
    The code for the removal of spectra in a certain retention time range from a vector of spectra might look like this:

    @code
    //data
    std::vector< MSSpectrum<> > spectra;

    //... spectra are added to the vector ...

    //range from 0.0 to 36.0 s
    InRTRange< MSSpectrum<> > range(0.0, 36.0);

    //remove the range
    spectra.erase(remove_if(spectra.begin(), spectra.end(), range), spectra.end());
    @endcode

    The code for the removal of peaks within certain intensity range from a spectrum might look like this:

    @code
    //data
    MSSpectrum<> spectrum;

    //... peaks are added to the spectrum ...

    //range from 0.0 to 5000.0 intensity
    InIntensityRange range< Peak1D >(0.0, 5000.0);

    //remove the range
    spectrum.erase(remove_if(spectrum.begin(), spectrum.end(), range), spectrum.end());
    @endcode
  */

  /**
    @brief Predicate that determines if a class has a certain metavalue

    MetaContainer must be a MetaInfoInterface or have the same interface

    @ingroup RangeUtils
  */
  template <class MetaContainer>
  class HasMetaValue :
    std::unary_function<MetaContainer, bool>
  {
public:
    /**
      @brief Constructor

      @param metavalue MetaValue that needs to be present.
      @param reverse if @p reverse is true, operator() returns true if the metavalue does not exist.
    */
    HasMetaValue(String metavalue, bool reverse = false) :
      metavalue_key_(metavalue),
      reverse_(reverse)
    {}

    inline bool operator()(const MetaContainer& s) const
    {
      bool has_meta_value = s.metaValueExists(metavalue_key_);
      if (reverse_)
      {
        return !has_meta_value;
      }
      return has_meta_value;
    }

protected:
    String metavalue_key_;
    bool reverse_;
  };


  /**
    @brief Predicate that determines if a spectrum lies inside/outside a specific retention time range

    SpectrumType must be a Spectrum or have the same interface

    @ingroup RangeUtils
  */
  template <class SpectrumType>
  class InRTRange :
    std::unary_function<SpectrumType, bool>
  {
public:
    /**
      @brief Constructor

      @param min lower boundary
      @param max upper boundary
      @param reverse if @p reverse is true, operator() returns true if the spectrum lies outside the
      range
    */
    InRTRange(DoubleReal min, DoubleReal max, bool reverse = false) :
      min_(min),
      max_(max),
      reverse_(reverse)
    {}

    inline bool operator()(const SpectrumType& s) const
    {
      DoubleReal tmp = s.getRT();
      if (reverse_)
      {
        return min_ > tmp || max_ < tmp;
      }
      return min_ <= tmp && max_ >= tmp;
    }

protected:
    DoubleReal min_, max_;
    bool reverse_;
  };

  /**
    @brief Predicate that determines if a spectrum lies inside/outside a specific MS level set

    SpectrumType must be a Spectrum or have the same interface

    @ingroup RangeUtils
  */
  template <class SpectrumType>
  class InMSLevelRange :
    std::unary_function<SpectrumType, bool>
  {
public:
    /**
      @brief Constructor

      @param levels an array of MS levels
      @param reverse if @p reverse is true, operator() returns true if the spectrum lies outside the
      set
    */
    InMSLevelRange(const IntList& levels, bool reverse = false) :
      levels_(levels),
      reverse_(reverse)
    {}

    inline bool operator()(const SpectrumType& s) const
    {
      Int tmp = s.getMSLevel();
      if (reverse_)
      {
        return std::find(levels_.begin(), levels_.end(), tmp) == levels_.end();
      }
      return std::find(levels_.begin(), levels_.end(), tmp) != levels_.end();
    }

protected:
    IntList levels_;
    bool reverse_;
  };

  /**
    @brief Predicate that determines if a spectrum has a certain scan mode

    SpectrumType must be a Spectrum or have the same interface (SpectrumSettings)

    @ingroup RangeUtils
  */
  template <class SpectrumType>
  class HasScanMode :
    std::unary_function<SpectrumType, bool>
  {
public:
    /**
      @brief Constructor

      @param mode scan mode
      @param reverse if @p reverse is true, operator() returns true if the spectrum has a different
      scan mode
    */
    HasScanMode(Int mode, bool reverse = false) :
      mode_(mode),
      reverse_(reverse)
    {}

    inline bool operator()(const SpectrumType& s) const
    {
      if (reverse_)
      {
        return s.getInstrumentSettings().getScanMode() != mode_;
      }
      return s.getInstrumentSettings().getScanMode() == mode_;
    }

protected:
    Int mode_;
    bool reverse_;
  };

  /**
    @brief Predicate that determines if a spectrum is empty.

    SpectrumType must have a empty() method

    @ingroup RangeUtils
  */
  template <class SpectrumType>
  class IsEmptySpectrum :
    std::unary_function<SpectrumType, bool>
  {
public:
    /**
      @brief Constructor

      @param reverse if @p reverse is true, operator() returns true if the spectrum is not empty
    */
    explicit IsEmptySpectrum(bool reverse = false) :
      reverse_(reverse)
    {}

    inline bool operator()(const SpectrumType& s) const
    {
      if (reverse_)
      {
        return !s.empty();
      }
      return s.empty();
    }

protected:
    bool reverse_;
  };

  /**
    @brief Predicate that determines if a spectrum is a zoom (enhanced resolution) spectrum.

    SpectrumType must have a getInstrumentSettings() method

    @ingroup RangeUtils
  */
  template <class SpectrumType>
  class IsZoomSpectrum :
    std::unary_function<SpectrumType, bool>
  {
public:
    /**
      @brief Constructor

      @param reverse if @p reverse is true, operator() returns true if the spectrum is not a zoom
      spectrum
    */
    explicit IsZoomSpectrum(bool reverse = false) :
      reverse_(reverse)
    {}

    inline bool operator()(const SpectrumType& s) const
    {
      if (reverse_)
      {
        return !s.getInstrumentSettings().getZoomScan();
      }
      return s.getInstrumentSettings().getZoomScan();
    }

protected:
    bool reverse_;
  };


  /**
    @brief Predicate that determines if a spectrum was generated using any activation method given
    in the constructor list.

    SpectrumType must have a getPrecursors() method

    @ingroup RangeUtils
  */
  template <class SpectrumType>
  class HasActivationMethod :
    std::unary_function<SpectrumType, bool>
  {
public:
    /**
      @brief Constructor

      @param methods List of methods that is compared against precursor activation methods.
      @param reverse if @p reverse is true, operator() returns true if the spectrum is not using one
      of the specified activation methods.
    */
    HasActivationMethod(const StringList& methods, bool reverse = false) :
      methods_(methods),
      reverse_(reverse)
    {}

    inline bool operator()(const SpectrumType& s) const
    {
      for (std::vector<Precursor>::const_iterator it = s.getPrecursors().begin(); it != s.getPrecursors().end(); ++it)
      {
        for (std::set<Precursor::ActivationMethod>::const_iterator it_a = it->getActivationMethods().begin();
             it_a != it->getActivationMethods().end();
             ++it_a)
        {
          if (methods_.contains(Precursor::NamesOfActivationMethod[*it_a]))
          {
            // found matching activation method
            if (reverse_) return false;
            else return true;
          }
        }
      }

      if (reverse_) return true;
      else return false;
    }

protected:
    StringList methods_;
    bool reverse_;
  };

  /**
    @brief Predicate that determines if a spectrum's precursor is within a certain m/z range.

    SpectrumType must have a getPrecursors() method

    If multiple precursors are present, all must fulfill the range criterium.

    @ingroup RangeUtils
  */
  template <class SpectrumType>
  class InPrecursorMZRange :
    std::unary_function<SpectrumType, bool>
  {
public:
    /**
      @brief Constructor

      @param mz_left left m/z boundary (closed interval)
      @param mz_right right m/z boundary (closed interval)
      @param reverse if @p reverse is true, operator() returns true if the precursor's m/z is outside of the given interval.
    */
    InPrecursorMZRange(const DoubleReal& mz_left, const DoubleReal& mz_right, bool reverse = false) :
      mz_left_(mz_left),
      mz_right_(mz_right),
      reverse_(reverse)
    {}

    inline bool operator()(const SpectrumType& s) const
    {
      for (std::vector<Precursor>::const_iterator it = s.getPrecursors().begin(); it != s.getPrecursors().end(); ++it)
      {
        //std::cerr << mz_left_ << " " << mz_right_ << " " << it->getMZ() << "\n";
        if (!(mz_left_ <= it->getMZ() && it->getMZ() <= mz_right_))
        { // found PC outside of allowed window
          if (reverse_) return true;
          else return false;
        }
      }

      if (reverse_) return false;
      else return true;
    }

protected:
    DoubleReal mz_left_;
    DoubleReal mz_right_;
    bool reverse_;
  };


  /**
    @brief Predicate that determines if a spectrum has a certain precursor charge as given in the
    constructor list.

    SpectrumType must have a getPrecursors() method

    @ingroup RangeUtils
  */
  template <class SpectrumType>
  class HasPrecursorCharge :
    std::unary_function<SpectrumType, bool>
  {
public:
    /**
      @brief Constructor

      @param charges List of charges that is compared against precursor charge.
      @param reverse if @p reverse is true, operator() returns true if the spectrum has not one of
      the specified precursor charges.
    */
    HasPrecursorCharge(const IntList& charges, bool reverse = false) :
      charges_(charges),
      reverse_(reverse)
    {}

    inline bool operator()(const SpectrumType& s) const
    {
      bool match = false;
      for (std::vector<Precursor>::const_iterator it = s.getPrecursors().begin(); it != s.getPrecursors().end(); ++it)
      {
        Int tmp = it->getCharge();
        match = match || (std::find(charges_.begin(), charges_.end(), tmp) != charges_.end());
      }

      if (reverse_) return !match;
      else return match;
    }

protected:
    IntList charges_;
    bool reverse_;
  };


  /**
    @brief Predicate that determines if a peak lies inside/outside a specific m/z range

    PeakType must have a getPosition() method.

    @note It is assumed that the m/z dimension is dimension 0!

    @ingroup RangeUtils
  */
  template <class PeakType>
  class InMzRange :
    std::unary_function<PeakType, bool>
  {
public:
    /**
      @brief Constructor

      @param min lower boundary
      @param max upper boundary
      @param reverse if @p reverse is true, operator() returns true if the peak lies outside the
      range
    */
    InMzRange(DoubleReal min, DoubleReal max, bool reverse = false) :
      min_(min),
      max_(max),
      reverse_(reverse)
    {}

    inline bool operator()(const PeakType& p) const
    {
      DoubleReal tmp = p.getPosition()[0];
      if (reverse_)
      {
        return min_ > tmp || max_ < tmp;
      }
      return min_ <= tmp && max_ >= tmp;
    }

protected:
    DoubleReal min_, max_;
    bool reverse_;
  };

  /**
    @brief Predicate that determines if a peak lies inside/outside a specific intensity range

    PeakType must have a getIntensity() method.

    @ingroup RangeUtils
  */
  template <class PeakType>
  class InIntensityRange :
    std::unary_function<PeakType, bool>
  {
public:
    /**
      @brief Constructor

      @param min lower boundary
      @param max upper boundary
      @param reverse if @p reverse is true, operator() returns true if the peak lies outside the set
    */
    InIntensityRange(DoubleReal min, DoubleReal max, bool reverse = false) :
      min_(min),
      max_(max),
      reverse_(reverse)
    {}

    inline bool operator()(const PeakType& p) const
    {
      DoubleReal tmp = p.getIntensity();
      if (reverse_)
      {
        return min_ > tmp || max_ < tmp;
      }
      return min_ <= tmp && max_ >= tmp;
    }

protected:
    DoubleReal min_, max_;
    bool reverse_;
  };

  /**
    @brief Predicate that determines if an MSn spectrum was generated with a collision energy in the given range.
    @note This applies only to CID and HCD spectra. For spectra that do not have a collision energy, the predicate will return true.
    @note This predicate will return always true for spectra with getMSLevel() = 1.

    @ingroup RangeUtils
  */
  template <class SpectrumType>
  class IsInCollisionEnergyRange :
    std::unary_function<SpectrumType, bool>
  {
public:
    /**
      @brief Constructor

      @param min minimum collision energy to be included in the range.
      @param max maximum collision energy to be included in the range.
      @param reverse if @p reverse is true, operator() returns true if the collision energy lies outside the range.
    */
    IsInCollisionEnergyRange(DoubleReal min, DoubleReal max, bool reverse = false) :
      min_energy_(min),
      max_energy_(max),
      reverse_(reverse)
    {}

    inline bool operator()(const SpectrumType& s) const
    {
      // leave non-fragmentation spectra untouched
      if (s.getMSLevel() == 1) return false;

      bool isIn = false;
      bool hasCollisionEnergy = false;
      for (std::vector<Precursor>::const_iterator it = s.getPrecursors().begin(); it != s.getPrecursors().end(); ++it)
      {
        if (it->metaValueExists("collision energy"))
        {
          hasCollisionEnergy = true;
          DoubleReal cE = it->getMetaValue("collision energy");
          isIn |= !(cE > max_energy_ || cE < min_energy_);
        }
      }

      // we accept all spectra that have no collision energy value
      if (!hasCollisionEnergy) return false;

      if (reverse_) return !isIn;
      else return isIn;
    }

private:
    DoubleReal min_energy_, max_energy_;
    bool reverse_;
  };

  /**
    @brief Predicate that determines if the width of the isolation window of an MSn spectrum is in the given range.
    @note This predicate will return always true for spectra with getMSLevel() = 1.

    @ingroup RangeUtils
  */
  template <class SpectrumType>
  class IsInIsolationWindowSizeRange :
    std::unary_function<SpectrumType, bool>
  {

public:
    /**
      @brief Constructor

      @param min_size minimum width of the isolation window.
      @param max_size maximum width of the isolation window.
      @param reverse if @p reverse is true, operator() returns true if the width of the isolation window lies outside the range.
    */
    IsInIsolationWindowSizeRange(DoubleReal min_size, DoubleReal max_size, bool reverse = false) :
      min_size_(min_size),
      max_size_(max_size),
      reverse_(reverse)
    {}

    inline bool operator()(const SpectrumType& s) const
    {
      // leave non-fragmentation spectra untouched
      if (s.getMSLevel() == 1) return false;

      bool isIn = false;
      for (std::vector<Precursor>::const_iterator it = s.getPrecursors().begin(); it != s.getPrecursors().end(); ++it)
      {
        const DoubleReal isolationWindowSize = it->getIsolationWindowUpperOffset() + it->getIsolationWindowLowerOffset();
        isIn |= !(isolationWindowSize > max_size_ || isolationWindowSize < min_size_);
      }

      if (reverse_) return !isIn;
      else return isIn;
    }

private:
    DoubleReal min_size_, max_size_;
    bool reverse_;
  };

} // namespace OpenMS

#endif // OPENMS_KERNEL_RANGEUTILS_H