Sample.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   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:
//  * 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;

  class OPENMS_DLLAPI Sample :
    public MetaInfoInterface
  {
public:
    enum SampleState {SAMPLENULL, SOLID, LIQUID, GAS, SOLUTION, EMULSION, SUSPENSION, SIZE_OF_SAMPLESTATE};
    static const std::string NamesOfSampleState[SIZE_OF_SAMPLESTATE];

    Sample();
    Sample(const Sample & source);
    ~Sample();

    Sample & operator=(const Sample & source);

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

    const String & getName() const;
    void setName(const String & name);

    const String & getOrganism() const;
    void setOrganism(const String & organism);

    const String & getNumber() const;
    void setNumber(const String & number);

    const String & getComment() const;
    void setComment(const String & comment);

    SampleState getState() const;
    void setState(SampleState state);

    double getMass() const;
    void setMass(double mass);

    double getVolume() const;
    void setVolume(double volume);

    double getConcentration() const;
    void setConcentration(double concentration);

    std::vector<Sample> & getSubsamples();
    const std::vector<Sample> & getSubsamples() const;
    void setSubsamples(const std::vector<Sample> & subsamples);

    void addTreatment(const SampleTreatment & treatment, Int before_position = -1);
    SampleTreatment & getTreatment(UInt position);
    const SampleTreatment & getTreatment(UInt position) const;
    void removeTreatment(UInt position);
    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