MSChromatogram.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    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: Andreas Bertsch $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/KERNEL/StandardDeclarations.h>
#include <OpenMS/METADATA/ChromatogramSettings.h>
#include <OpenMS/METADATA/MetaInfoDescription.h>
#include <OpenMS/KERNEL/RangeManager.h>
#include <OpenMS/KERNEL/ComparatorUtils.h>
#include <OpenMS/KERNEL/ChromatogramPeak.h>
#include <OpenMS/METADATA/DataArrays.h>

namespace OpenMS
{
  class ChromatogramPeak;

  class OPENMS_DLLAPI MSChromatogram :
    private std::vector<ChromatogramPeak>,
    public RangeManager<1>,
    public ChromatogramSettings
  {

public:

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

    typedef ChromatogramPeak 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::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;

    MSChromatogram() :
      ContainerType(),
      RangeManager<1>(),
      ChromatogramSettings(),
      name_(),
      float_data_arrays_(),
      string_data_arrays_(),
      integer_data_arrays_()
    {}

    MSChromatogram(const MSChromatogram& source) :
      ContainerType(source),
      RangeManager<1>(source),
      ChromatogramSettings(source),
      name_(source.name_),
      float_data_arrays_(source.float_data_arrays_),
      string_data_arrays_(source.string_data_arrays_),
      integer_data_arrays_(source.integer_data_arrays_)
    {}

    ~MSChromatogram() override
    {}

    MSChromatogram& operator=(const MSChromatogram& source);

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

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

    // Docu in base class (RangeManager)
    void updateRanges() override
    {
      this->clearRanges();
      updateRanges_(ContainerType::begin(), ContainerType::end());
    }

    const String& getName() const;

    void setName(const String& name);


    double getMZ() const;

    const FloatDataArrays& getFloatDataArrays() const;

    FloatDataArrays& getFloatDataArrays();

    void setFloatDataArrays(const FloatDataArrays& fda)
    {
      float_data_arrays_ = fda;
    }

    const StringDataArrays& getStringDataArrays() const;

    StringDataArrays& getStringDataArrays();

    void setStringDataArrays(const StringDataArrays& sda)
    {
      string_data_arrays_ = sda;
    }

    const IntegerDataArrays& getIntegerDataArrays() const;

    IntegerDataArrays& getIntegerDataArrays();

    void setIntegerDataArrays(const IntegerDataArrays& ida)
    {
      integer_data_arrays_ = ida;
    }



    void sortByIntensity(bool reverse = false);

    void sortByPosition();

    bool isSorted() const;



    Size findNearest(CoordinateType rt) const;

    Iterator RTBegin(CoordinateType rt);

    Iterator RTBegin(Iterator begin, CoordinateType rt, Iterator end);

    Iterator RTEnd(CoordinateType rt);

    Iterator RTEnd(Iterator begin, CoordinateType rt, Iterator end);

    ConstIterator RTBegin(CoordinateType rt) const;

    ConstIterator RTBegin(ConstIterator begin, CoordinateType rt, ConstIterator end) const;

    ConstIterator RTEnd(CoordinateType rt) const;

    ConstIterator MZEnd(CoordinateType rt) const;

    ConstIterator RTEnd(ConstIterator begin, CoordinateType rt, ConstIterator end) const;

    Iterator PosBegin(CoordinateType rt);

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

    ConstIterator PosBegin(CoordinateType rt) const;

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

    Iterator PosEnd(CoordinateType rt);

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

    ConstIterator PosEnd(CoordinateType rt) const;

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

    void clear(bool clear_meta_data);


protected:

    String name_;

    FloatDataArrays float_data_arrays_;

    StringDataArrays string_data_arrays_;

    IntegerDataArrays integer_data_arrays_;
  };

  std::ostream& operator<<(std::ostream& os, const MSChromatogram& chrom);

} // namespace OpenMS