MSSpectrum.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
//
// This software is released under a three-clause BSD license:
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//    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.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg$
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/KERNEL/Peak1D.h>
#include <OpenMS/KERNEL/StandardDeclarations.h>
#include <OpenMS/METADATA/SpectrumSettings.h>
#include <OpenMS/KERNEL/RangeManager.h>
#include <OpenMS/KERNEL/ComparatorUtils.h>
#include <OpenMS/METADATA/DataArrays.h>
#include <OpenMS/METADATA/MetaInfoDescription.h>

namespace OpenMS
{
  class Peak1D;
  class OPENMS_DLLAPI MSSpectrum :
    private std::vector<Peak1D>,
    public RangeManager<1>,
    public SpectrumSettings
  {
public:

    struct OPENMS_DLLAPI RTLess : public std::binary_function<MSSpectrum, MSSpectrum, bool>
    {
      bool operator()(const MSSpectrum& a, const MSSpectrum& b) const;
    };


    typedef OpenMS::Peak1D PeakType;
    typedef typename PeakType::CoordinateType CoordinateType;
    typedef std::vector<PeakType> ContainerType;
    typedef OpenMS::DataArrays::FloatDataArray FloatDataArray ;
    typedef std::vector<FloatDataArray> FloatDataArrays;
    typedef OpenMS::DataArrays::StringDataArray StringDataArray ;
    typedef std::vector<StringDataArray> StringDataArrays;
    typedef OpenMS::DataArrays::IntegerDataArray IntegerDataArray ;
    typedef std::vector<IntegerDataArray> IntegerDataArrays;


    typedef typename ContainerType::iterator Iterator;
    typedef typename ContainerType::const_iterator ConstIterator;
    typedef typename ContainerType::reverse_iterator ReverseIterator;
    typedef typename ContainerType::const_reverse_iterator ConstReverseIterator;


    using ContainerType::operator[];
    using ContainerType::begin;
    using ContainerType::rbegin;
    using ContainerType::end;
    using ContainerType::rend;
    using ContainerType::resize;
    using ContainerType::size;
    using ContainerType::push_back;
    using ContainerType::emplace_back;
    using ContainerType::pop_back;
    using ContainerType::empty;
    using ContainerType::front;
    using ContainerType::back;
    using ContainerType::reserve;
    using ContainerType::insert;
    using ContainerType::erase;
    using ContainerType::swap;

    using typename ContainerType::iterator;
    using typename ContainerType::const_iterator;
    using typename ContainerType::size_type;
    using typename ContainerType::value_type;
    using typename ContainerType::reference;
    using typename ContainerType::const_reference;
    using typename ContainerType::pointer;
    using typename ContainerType::difference_type;


    MSSpectrum();

    MSSpectrum(const MSSpectrum& source);

    ~MSSpectrum() override
    {}

    MSSpectrum& operator=(const MSSpectrum& source);

    MSSpectrum& operator=(const SpectrumSettings & source);

    bool operator==(const MSSpectrum& rhs) const;

    bool operator!=(const MSSpectrum& rhs) const
    {
      return !(operator==(rhs));
    }

    // Docu in base class (RangeManager)
    void updateRanges() override;

    double getRT() const;

    void setRT(double rt);

    double getDriftTime() const;

    void setDriftTime(double dt);

    UInt getMSLevel() const;

    void setMSLevel(UInt ms_level);

    const String& getName() const;

    void setName(const String& name);


    const FloatDataArrays& getFloatDataArrays() const;

    FloatDataArrays& getFloatDataArrays()
    {
      return float_data_arrays_;
    }

    void setFloatDataArrays(const FloatDataArrays& fda);

    const StringDataArrays& getStringDataArrays() const;

    StringDataArrays& getStringDataArrays();

    void setStringDataArrays(const StringDataArrays& sda);

    const IntegerDataArrays& getIntegerDataArrays() const;

    IntegerDataArrays& getIntegerDataArrays();

    void setIntegerDataArrays(const IntegerDataArrays& ida);

    inline IntegerDataArray& getIntegerDataArrayByName(String name)
    {
      return *std::find_if(integer_data_arrays_.begin(), integer_data_arrays_.end(), 
        [&name](const IntegerDataArray& da) { return da.getName() == name; } );
    }

    inline StringDataArray& getStringDataArrayByName(String name)
    {
      return *std::find_if(string_data_arrays_.begin(), string_data_arrays_.end(), 
        [&name](const StringDataArray& da) { return da.getName() == name; } );
    }

    inline FloatDataArray& getFloatDataArrayByName(String name)
    {
      return *std::find_if(float_data_arrays_.begin(), float_data_arrays_.end(), 
        [&name](const FloatDataArray& da) { return da.getName() == name; } );
    }

    inline const IntegerDataArray& getIntegerDataArrayByName(String name) const
    {
      return *std::find_if(integer_data_arrays_.begin(), integer_data_arrays_.end(), 
        [&name](const IntegerDataArray& da) { return da.getName() == name; } );
    }

    inline const StringDataArray& getStringDataArrayByName(String name) const
    {
      return *std::find_if(string_data_arrays_.begin(), string_data_arrays_.end(), 
        [&name](const StringDataArray& da) { return da.getName() == name; } );
    }

    inline const FloatDataArray& getFloatDataArrayByName(String name) const
    {
      return *std::find_if(float_data_arrays_.begin(), float_data_arrays_.end(), 
        [&name](const FloatDataArray& da) { return da.getName() == name; } );
    }




    void sortByIntensity(bool reverse = false);

    void sortByPosition();

    bool isSorted() const;



    Size findNearest(CoordinateType mz) const;

    Int findNearest(CoordinateType mz, CoordinateType tolerance) const;

    Int findNearest(CoordinateType mz, CoordinateType tolerance_left, CoordinateType tolerance_right) const;

    Iterator MZBegin(CoordinateType mz);

    Iterator MZBegin(Iterator begin, CoordinateType mz, Iterator end);

    Iterator MZEnd(CoordinateType mz);

    Iterator MZEnd(Iterator begin, CoordinateType mz, Iterator end);

    ConstIterator MZBegin(CoordinateType mz) const;

    ConstIterator MZBegin(ConstIterator begin, CoordinateType mz, ConstIterator end) const;

    ConstIterator MZEnd(CoordinateType mz) const;

    ConstIterator MZEnd(ConstIterator begin, CoordinateType mz, ConstIterator end) const;

    Iterator PosBegin(CoordinateType mz);

    Iterator PosBegin(Iterator begin, CoordinateType mz, Iterator end);

    ConstIterator PosBegin(CoordinateType mz) const;

    ConstIterator PosBegin(ConstIterator begin, CoordinateType mz, ConstIterator end) const;

    Iterator PosEnd(CoordinateType mz);

    Iterator PosEnd(Iterator begin, CoordinateType mz, Iterator end);

    ConstIterator PosEnd(CoordinateType mz) const;

    ConstIterator PosEnd(ConstIterator begin, CoordinateType mz, ConstIterator end) const;



    void clear(bool clear_meta_data);

    /*
      @brief Select a (subset of) spectrum and its data_arrays, only retaining the indices given in @p indices

      @param indices Vector of indices to keep
      @return Reference to this MSSpectrum

    */
    MSSpectrum& select(const std::vector<Size>& indices);

protected:

    double retention_time_;

    double drift_time_;

    UInt ms_level_;

    String name_;

    FloatDataArrays float_data_arrays_;

    StringDataArrays string_data_arrays_;

    IntegerDataArrays integer_data_arrays_;
  };

  inline std::ostream& operator<<(std::ostream& os, const MSSpectrum& spec)
  {
    os << "-- MSSPECTRUM BEGIN --" << std::endl;

    // spectrum settings
    os << static_cast<const SpectrumSettings&>(spec);

    // peaklist
    for (MSSpectrum::ConstIterator it = spec.begin(); it != spec.end(); ++it)
    {
      os << *it << std::endl;
    }

    os << "-- MSSPECTRUM END --" << std::endl;
    return os;
  }

} // namespace OpenMS