RangeUtils.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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//  * Redistributions in binary form must reproduce the above copyright
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//    documentation and/or other materials provided with the distribution.
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//    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.
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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
{
  template <class MetaContainer>
  class HasMetaValue :
    std::unary_function<MetaContainer, bool>
  {
public:
    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_;
  };


  template <class SpectrumType>
  class InRTRange :
    std::unary_function<SpectrumType, bool>
  {
public:
    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_;
  };

  template <class SpectrumType>
  class InMSLevelRange :
    std::unary_function<SpectrumType, bool>
  {
public:
    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_;
  };

  template <class SpectrumType>
  class HasScanMode :
    std::unary_function<SpectrumType, bool>
  {
public:
    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_;
  };

  template <class SpectrumType>
  class IsEmptySpectrum :
    std::unary_function<SpectrumType, bool>
  {
public:
    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_;
  };

  template <class SpectrumType>
  class IsZoomSpectrum :
    std::unary_function<SpectrumType, bool>
  {
public:
    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_;
  };


  template <class SpectrumType>
  class HasActivationMethod :
    std::unary_function<SpectrumType, bool>
  {
public:
    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_;
  };

  template <class SpectrumType>
  class InPrecursorMZRange :
    std::unary_function<SpectrumType, bool>
  {
public:
    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_;
  };


  template <class SpectrumType>
  class HasPrecursorCharge :
    std::unary_function<SpectrumType, bool>
  {
public:
    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_;
  };


  template <class PeakType>
  class InMzRange :
    std::unary_function<PeakType, bool>
  {
public:
    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_;
  };

  template <class PeakType>
  class InIntensityRange :
    std::unary_function<PeakType, bool>
  {
public:
    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_;
  };

} // namespace OpenMS

#endif // OPENMS_KERNEL_RANGEUTILS_H