libopenms-dev 1.11.1-5 / usr / include / OpenMS / ANALYSIS / TARGETED / IncludeExcludeTarget.h

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
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// $Maintainer: Hannes Roest $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------

#ifndef OPENMS_ANALYSIS_TARGETED_INCLUDEEXCLUDETARGET_H
#define OPENMS_ANALYSIS_TARGETED_INCLUDEEXCLUDETARGET_H

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/METADATA/CVTermList.h>
#include <OpenMS/ANALYSIS/TARGETED/TargetedExperimentHelper.h>

#include <vector>

namespace OpenMS
{
  /**
    @brief This class stores a SRM/MRM transition

    The default values for precursor and product m/z values are
    set to numeric_limits<DoubleReal>::max(). Default values for
    precursor an product charge is set to numeric_limits<Int>::max().
  */
  class OPENMS_DLLAPI IncludeExcludeTarget :
    public CVTermList
  {

public:

    typedef TargetedExperimentHelper::Configuration Configuration;
    typedef TargetedExperimentHelper::RetentionTime RetentionTime;

    /** @name Constructors and destructors
    */
    //@{
    /// default constructor
    IncludeExcludeTarget();

    /// copy constructor
    IncludeExcludeTarget(const IncludeExcludeTarget & rhs);

    /// destructor
    virtual ~IncludeExcludeTarget();
    //@}

    /// assignment operator
    IncludeExcludeTarget & operator=(const IncludeExcludeTarget & rhs);

    /** @name Accessors
    */
    //@{
    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;

    /// sets the precursor mz (Q1 value)
    void setPrecursorMZ(DoubleReal mz);

    DoubleReal getPrecursorMZ() const;

    void setPrecursorCVTermList(const CVTermList & list);

    void addPrecursorCVTerm(const CVTerm & cv_term);

    const CVTermList & getPrecursorCVTermList() const;

    void setProductMZ(DoubleReal mz);

    DoubleReal 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;
    //@}

    /** @name Predicates
    */
    //@{
    /// equality operator
    bool operator==(const IncludeExcludeTarget & rhs) const;

    /// inequality operator
    bool operator!=(const IncludeExcludeTarget & rhs) const;
    //@}

protected:

    void updateMembers_();

    String name_;

    DoubleReal precursor_mz_;

    CVTermList precursor_cv_terms_;

    DoubleReal 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_;

  };
}

#endif // OPENMS_ANALYSIS_TARGETED_INCLUDEEXCLUDETARGET_H