ReactionMonitoringTransition.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// This software is released under a three-clause BSD license:
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//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
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//    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.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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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(ReactionMonitoringTransition&&) noexcept;
 
    ~ReactionMonitoringTransition() override;
 
    ReactionMonitoringTransition & operator=(const ReactionMonitoringTransition & rhs);
 
    ReactionMonitoringTransition & operator=(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);
 
    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;
 
    bool hasPrediction() const;
 
    void setPrediction(const Prediction & prediction);
 
    void addPredictionTerm(const CVTerm & prediction);
 
    const Prediction & getPrediction() const;
 
    DecoyTransitionType getDecoyTransitionType() const;
 
    void setDecoyTransitionType(const DecoyTransitionType & d);
 
    double getLibraryIntensity() const;
 
    void setLibraryIntensity(double intensity);
 
    void setRetentionTime(RetentionTime rt);
 
    const RetentionTime & getRetentionTime() const;
 
 
    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_; 
 
    // attributes to a peptide / compound (optional)
    String peptide_ref_; 
    String compound_ref_; 
 
    double library_intensity_;
 
    DecoyTransitionType decoy_type_;
 
 
    // Precursor
    // Product
    // IntermediateProduct
    // RetentionTime
    // Prediction
    // cvparam / userParam
 
    double precursor_mz_;
 
    CVTermList* precursor_cv_terms_;
 
    Product product_;
 
    std::vector<Product> intermediate_products_;
 
    RetentionTime rts;
 
    Prediction* prediction_;
 
    std::bitset<3> transition_flags_;
  };
}