ReactionMonitoringTransition.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/ANALYSIS/TARGETED/TargetedExperimentHelper.h>
#include <OpenMS/CONCEPT/HashUtils.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/METADATA/CVTermList.h>
 
#include <functional>
#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) noexcept ;
 
    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(const 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
    {
      bool operator()(ReactionMonitoringTransition const & left, ReactionMonitoringTransition const & right) const;
    };
 
    struct NameLess
    {
      bool operator()(ReactionMonitoringTransition const & left, ReactionMonitoringTransition const & right) const;
    };
 
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_;
  };
} // namespace OpenMS
 
namespace std
{
  template<>
  struct hash<OpenMS::ReactionMonitoringTransition>
  {
    std::size_t operator()(const OpenMS::ReactionMonitoringTransition& rmt) const noexcept
    {
      std::size_t seed = 0;
 
      // Hash base class CVTermList - use the CV terms map
      for (const auto& [accession, terms] : rmt.getCVTerms())
      {
        OpenMS::hash_combine(seed, OpenMS::fnv1a_hash_string(accession));
        OpenMS::hash_combine(seed, OpenMS::hash_int(terms.size()));
        for (const auto& term : terms)
        {
          OpenMS::hash_combine(seed, OpenMS::fnv1a_hash_string(term.getAccession()));
          OpenMS::hash_combine(seed, OpenMS::fnv1a_hash_string(term.getName()));
        }
      }
 
      // Hash name_
      OpenMS::hash_combine(seed, OpenMS::fnv1a_hash_string(rmt.getName()));
 
      // Hash peptide_ref_
      OpenMS::hash_combine(seed, OpenMS::fnv1a_hash_string(rmt.getPeptideRef()));
 
      // Hash compound_ref_
      OpenMS::hash_combine(seed, OpenMS::fnv1a_hash_string(rmt.getCompoundRef()));
 
      // Hash precursor_mz_
      OpenMS::hash_combine(seed, OpenMS::hash_float(rmt.getPrecursorMZ()));
 
      // Hash precursor_cv_terms_ (pointer - check if present)
      if (rmt.hasPrecursorCVTerms())
      {
        const auto& precursorTerms = rmt.getPrecursorCVTermList();
        for (const auto& [accession, terms] : precursorTerms.getCVTerms())
        {
          OpenMS::hash_combine(seed, OpenMS::fnv1a_hash_string(accession));
          OpenMS::hash_combine(seed, OpenMS::hash_int(terms.size()));
        }
      }
      else
      {
        OpenMS::hash_combine(seed, OpenMS::hash_int(0));
      }
 
      // Hash product_ - use getMZ and charge state
      const auto& product = rmt.getProduct();
      OpenMS::hash_combine(seed, OpenMS::hash_float(product.getMZ()));
      if (product.hasCharge())
      {
        OpenMS::hash_combine(seed, OpenMS::hash_int(product.getChargeState()));
      }
      // Hash product CV terms
      for (const auto& [accession, terms] : product.getCVTerms())
      {
        OpenMS::hash_combine(seed, OpenMS::fnv1a_hash_string(accession));
        OpenMS::hash_combine(seed, OpenMS::hash_int(terms.size()));
      }
      // Hash configuration list size and interpretation list size
      OpenMS::hash_combine(seed, OpenMS::hash_int(product.getConfigurationList().size()));
      OpenMS::hash_combine(seed, OpenMS::hash_int(product.getInterpretationList().size()));
 
      // Hash intermediate_products_ - use size and individual product m/z values
      const auto& intermediates = rmt.getIntermediateProducts();
      OpenMS::hash_combine(seed, OpenMS::hash_int(intermediates.size()));
      for (const auto& ip : intermediates)
      {
        OpenMS::hash_combine(seed, OpenMS::hash_float(ip.getMZ()));
        if (ip.hasCharge())
        {
          OpenMS::hash_combine(seed, OpenMS::hash_int(ip.getChargeState()));
        }
      }
 
      // Hash rts (RetentionTime)
      const auto& rt = rmt.getRetentionTime();
      OpenMS::hash_combine(seed, OpenMS::fnv1a_hash_string(rt.software_ref));
      OpenMS::hash_combine(seed, OpenMS::hash_int(static_cast<int>(rt.retention_time_unit)));
      OpenMS::hash_combine(seed, OpenMS::hash_int(static_cast<int>(rt.retention_time_type)));
      OpenMS::hash_combine(seed, OpenMS::hash_int(rt.isRTset() ? 1 : 0));
      if (rt.isRTset())
      {
        OpenMS::hash_combine(seed, OpenMS::hash_float(rt.getRT()));
      }
      // Hash RetentionTime CV terms
      for (const auto& [accession, terms] : rt.getCVTerms())
      {
        OpenMS::hash_combine(seed, OpenMS::fnv1a_hash_string(accession));
        OpenMS::hash_combine(seed, OpenMS::hash_int(terms.size()));
      }
 
      // Hash prediction_ (pointer - check if present)
      if (rmt.hasPrediction())
      {
        const auto& pred = rmt.getPrediction();
        OpenMS::hash_combine(seed, OpenMS::fnv1a_hash_string(pred.software_ref));
        OpenMS::hash_combine(seed, OpenMS::fnv1a_hash_string(pred.contact_ref));
        for (const auto& [accession, terms] : pred.getCVTerms())
        {
          OpenMS::hash_combine(seed, OpenMS::fnv1a_hash_string(accession));
          OpenMS::hash_combine(seed, OpenMS::hash_int(terms.size()));
        }
      }
      else
      {
        OpenMS::hash_combine(seed, OpenMS::hash_int(0));
      }
 
      // Hash library_intensity_
      OpenMS::hash_combine(seed, OpenMS::hash_float(rmt.getLibraryIntensity()));
 
      // Hash decoy_type_
      OpenMS::hash_combine(seed, OpenMS::hash_int(static_cast<int>(rmt.getDecoyTransitionType())));
 
      // Hash transition_flags_ (bitset<3>) - use the boolean accessors
      OpenMS::hash_combine(seed, OpenMS::hash_int(rmt.isDetectingTransition() ? 1 : 0));
      OpenMS::hash_combine(seed, OpenMS::hash_int(rmt.isIdentifyingTransition() ? 1 : 0));
      OpenMS::hash_combine(seed, OpenMS::hash_int(rmt.isQuantifyingTransition() ? 1 : 0));
 
      return seed;
    }
  };
} // namespace std