IncludeExcludeTarget.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 2002-2023.
//
// 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: Hannes Roest $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/METADATA/CVTermList.h>
#include <OpenMS/ANALYSIS/TARGETED/TargetedExperimentHelper.h>
 
#include <vector>
 
namespace OpenMS
{
  class OPENMS_DLLAPI IncludeExcludeTarget :
    public CVTermList
  {
 
public:
 
    typedef TargetedExperimentHelper::Configuration Configuration;
    typedef TargetedExperimentHelper::RetentionTime RetentionTime;
 
    IncludeExcludeTarget();
 
    IncludeExcludeTarget(const IncludeExcludeTarget & rhs);
 
    ~IncludeExcludeTarget() override;
 
    IncludeExcludeTarget & operator=(const IncludeExcludeTarget & rhs);
 
    void setName(const String & name);
 
    const String & getName() const;
 
    void setPeptideRef(const String & peptide_ref);
 
    const String & getPeptideRef() const;
 
    void setCompoundRef(const String & compound_ref);
 
    const String & getCompoundRef() const;
 
    void setPrecursorMZ(double mz);
 
    double getPrecursorMZ() const;
 
    void setPrecursorCVTermList(const CVTermList & list);
 
    void addPrecursorCVTerm(const CVTerm & cv_term);
 
    const CVTermList & getPrecursorCVTermList() const;
 
    void setProductMZ(double mz);
 
    double getProductMZ() const;
 
    void setProductCVTermList(const CVTermList & list);
 
    void addProductCVTerm(const CVTerm & cv_term);
 
    const CVTermList & getProductCVTermList() const;
 
    void setInterpretations(const std::vector<CVTermList> & interpretations);
 
    const std::vector<CVTermList> & getInterpretations() const;
 
    void addInterpretation(const CVTermList & interpretation);
 
    void setConfigurations(const std::vector<Configuration> & configuration);
 
    const std::vector<Configuration> & getConfigurations() const;
 
    void addConfiguration(const Configuration & configuration);
 
    void setPrediction(const CVTermList & prediction);
 
    void addPredictionTerm(const CVTerm & prediction);
 
    const CVTermList & getPrediction() const;
 
    void setRetentionTime(RetentionTime rt);
 
    const RetentionTime & getRetentionTime() const;
 
    bool operator==(const IncludeExcludeTarget & rhs) const;
 
    bool operator!=(const IncludeExcludeTarget & rhs) const;
 
protected:
 
    void updateMembers_();
 
    String name_;
 
    double precursor_mz_;
 
    CVTermList precursor_cv_terms_;
 
    double product_mz_;
 
    CVTermList product_cv_terms_;
 
    std::vector<CVTermList> interpretation_list_;
 
    String peptide_ref_;
 
    String compound_ref_;
 
    std::vector<Configuration> configurations_;
 
    CVTermList prediction_;
 
    RetentionTime rts_;
 
  };
}