ReactionMonitoringTransition.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------

#pragma once

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

#include <vector>
#include <bitset>

namespace OpenMS
{
  class OPENMS_DLLAPI ReactionMonitoringTransition :
    public CVTermList
  {

public:

    typedef TargetedExperimentHelper::Configuration Configuration;
    typedef TargetedExperimentHelper::RetentionTime RetentionTime;
    typedef TargetedExperimentHelper::TraMLProduct Product;
    typedef TargetedExperimentHelper::Prediction Prediction;

    enum DecoyTransitionType
    {
      UNKNOWN,
      TARGET,
      DECOY
    };

    ReactionMonitoringTransition();

    ReactionMonitoringTransition(const ReactionMonitoringTransition & rhs);

    ~ReactionMonitoringTransition() override;

    ReactionMonitoringTransition & operator=(const ReactionMonitoringTransition & rhs);

    void setName(const String & name);

    const String & getName() const;

    void setNativeID(const String & name);

    const String & getNativeID() 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;

    bool hasPrecursorCVTerms() const;

    void setPrecursorCVTermList(const CVTermList & list);

    void addPrecursorCVTerm(const CVTerm & cv_term);

    /* @brief Obtain the list of CV Terms for the precursor
     *
     * @note You first need to check whether they exist using hasPrecursorCVTerms() 
    */
    const CVTermList & getPrecursorCVTermList() const;

    void setProductMZ(double mz);

    double getProductMZ() const;

    int getProductChargeState() const;

    bool isProductChargeStateSet() const;

    void addProductCVTerm(const CVTerm & cv_term);

    const std::vector<Product> & getIntermediateProducts() const;

    void addIntermediateProduct(Product product);

    void setIntermediateProducts(const std::vector<Product> & products);

    void setProduct(Product product);

    const Product & getProduct() const;

    void setRetentionTime(RetentionTime rt);

    const RetentionTime & getRetentionTime() const;

    bool hasPrediction() const;

    void setPrediction(const Prediction & prediction);

    void addPredictionTerm(const CVTerm & prediction);

    /* @brief Obtain the Prediction object 
     *
     * @note You first need to check whether the object is accessible using hasPrediction() 
    */
    const Prediction & getPrediction() const;

    DecoyTransitionType getDecoyTransitionType() const;

    void setDecoyTransitionType(const DecoyTransitionType & d);

    double getLibraryIntensity() const;

    void setLibraryIntensity(double intensity);

    bool isDetectingTransition() const;

    void setDetectingTransition(bool val);

    bool isIdentifyingTransition() const;

    void setIdentifyingTransition(bool val);

    bool isQuantifyingTransition() const;

    void setQuantifyingTransition(bool val);


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

    bool operator!=(const ReactionMonitoringTransition & rhs) const;

    struct ProductMZLess :
      std::binary_function<ReactionMonitoringTransition, ReactionMonitoringTransition, bool>
    {
      inline bool operator()(ReactionMonitoringTransition const & left, ReactionMonitoringTransition const & right) const
      {
        return left.getProductMZ() < right.getProductMZ();
      }

    };

protected:

    void updateMembers_();


    String name_; // id, required attribute

    // attributes to a peptide / compound (optional)
    String peptide_ref_;
    String compound_ref_;


    // Precursor
    // Product
    // IntermediateProduct
    // RetentionTime
    // Prediction
    // cvparam / userParam

    double precursor_mz_;

    double library_intensity_;

    DecoyTransitionType decoy_type_;

    CVTermList* precursor_cv_terms_;

    Product product_;

    std::vector<Product> intermediate_products_;

    RetentionTime rts;

    Prediction* prediction_;

    // (currently: detecting, identifying and quantifying)
    std::bitset<3> transition_flags_;
  };
}