text: // --------------------------------------------------------------------------
  //                   OpenMS -- Open-Source Mass Spectrometry
  // --------------------------------------------------------------------------
  // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
  // ETH Zurich, and Freie Universitaet Berlin 2002-2016.
  //
  // 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.
  // --------------------------------------------------------------------------
  // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
  // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
  // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
  // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
  // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
  // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
  // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
  // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
  // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  //
  // --------------------------------------------------------------------------
  // $Maintainer: Timo Sachsenberg $
  // $Authors: Marc Sturm $
  // --------------------------------------------------------------------------
  
  #ifndef OPENMS_METADATA_SAMPLE_H
  #define OPENMS_METADATA_SAMPLE_H
  
  #include <list>
  
  #include <OpenMS/DATASTRUCTURES/String.h>
  #include <OpenMS/METADATA/MetaInfoInterface.h>
  #include <OpenMS/CONCEPT/Exception.h>
  
  namespace OpenMS
  {
    class SampleTreatment;
  
    /**
        @brief Meta information about the sample
  
        It contains basic descriptions like name, number (i.e. order number), mass,
        volume, concentration, state and a comment.
  
        Additionally sample treatments like Digestion, Modification or Tagging can be added.
  
        A Sample can be composed of other samples.
  
        @ingroup Metadata
    */
    class OPENMS_DLLAPI Sample :
      public MetaInfoInterface
    {
  public:
      ///state of aggregation of the sample
      enum SampleState {SAMPLENULL, SOLID, LIQUID, GAS, SOLUTION, EMULSION, SUSPENSION, SIZE_OF_SAMPLESTATE};
      /// Names of sample states
      static const std::string NamesOfSampleState[SIZE_OF_SAMPLESTATE];
  
      ///default constructor
      Sample();
      ///copy constructor
      Sample(const Sample & source);
      ///destructor
      ~Sample();
  
      ///assignment operator
      Sample & operator=(const Sample & source);
  
      /// Equality operator
      bool operator==(const Sample & rhs) const;
  
      ///returns the sample name (default: "")
      const String & getName() const;
      ///sets the sample name
      void setName(const String & name);
  
      ///returns the sample name (default: "")
      const String & getOrganism() const;
      ///sets the sample name
      void setOrganism(const String & organism);
  
      /// returns the sample number (default: "")
      const String & getNumber() const;
      /// sets the sample number (e.g. sample ID)
      void setNumber(const String & number);
  
      /// returns the comment (default: "")
      const String & getComment() const;
      /// sets the comment (may contain newline characters)
      void setComment(const String & comment);
  
      /// returns the state of aggregation (default: SAMPLENULL)
      SampleState getState() const;
      /// sets the state of aggregation
      void setState(SampleState state);
  
      /// returns the mass (in gram) (default: 0.0)
      double getMass() const;
      /// sets the mass (in gram)
      void setMass(double mass);
  
      /// returns the volume (in ml) (default: 0.0)
      double getVolume() const;
      /// sets the volume (in ml)
      void setVolume(double volume);
  
      /// returns the concentration (in g/l) (default: 0.0)
      double getConcentration() const;
      /// sets the concentration (in g/l)
      void setConcentration(double concentration);
  
      /// returns a mutable reference to the vector of subsamples that were combined to create this sample
      std::vector<Sample> & getSubsamples();
      /// returns a const reference to the vector of subsamples that were combined to create this sample
      const std::vector<Sample> & getSubsamples() const;
      /// sets the vector of subsamples that were combined to create this sample
      void setSubsamples(const std::vector<Sample> & subsamples);
  
      /**
          @brief adds a sample treatment before the given position (default is the end of the list). Sample treatments are ordered in the order of application to the sample. If before_position is smaller than 0, the sample treatment is appended to the list.
  
      @exception Exception::IndexOverflow is thrown if the position is invalid.
    */
      void addTreatment(const SampleTreatment & treatment, Int before_position = -1);
      /**
          @brief returns a mutable reference to the sample treatment at the given position
  
      @exception Exception::IndexOverflow is thrown if the position is invalid.
    */
      SampleTreatment & getTreatment(UInt position);
      /**
          @brief returns a const reference to the sample treatment at the given position
  
      @exception Exception::IndexOverflow is thrown if the position is invalid.
    */
      const SampleTreatment & getTreatment(UInt position) const;
      /**
          @brief removes the sample treatment at the given position
  
      @exception Exception::IndexOverflow is thrown if the position is invalid.
    */
      void removeTreatment(UInt position);
      /// returns the number of sample treatments
      Int countTreatments() const;
  
  protected:
      String name_;
      String number_;
      String comment_;
      String organism_;
      SampleState state_;
      double mass_;
      double volume_;
      double concentration_;
      std::vector<Sample> subsamples_;
      std::list<SampleTreatment *> treatments_;
  
    };
  } // namespace OpenMS
  
  #endif // OPENMS_METADATA_SAMPLE_H
  