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 #ifndef __FASTJET_CLUSTERSEQUENCE_HH__
 #define __FASTJET_CLUSTERSEQUENCE_HH__
 
 //FJSTARTHEADER
 // $Id$
 //
 // Copyright (c) 2005-2021, Matteo Cacciari, Gavin P. Salam and Gregory Soyez
 //
 //----------------------------------------------------------------------
 // This file is part of FastJet.
 //
 //  FastJet is free software; you can redistribute it and/or modify
 //  it under the terms of the GNU General Public License as published by
 //  the Free Software Foundation; either version 2 of the License, or
 //  (at your option) any later version.
 //
 //  The algorithms that underlie FastJet have required considerable
 //  development. They are described in the original FastJet paper,
 //  hep-ph/0512210 and in the manual, arXiv:1111.6097. If you use
 //  FastJet as part of work towards a scientific publication, please
 //  quote the version you use and include a citation to the manual and
 //  optionally also to hep-ph/0512210.
 //
 //  FastJet is distributed in the hope that it will be useful,
 //  but WITHOUT ANY WARRANTY; without even the implied warranty of
 //  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 //  GNU General Public License for more details.
 //
 //  You should have received a copy of the GNU General Public License
 //  along with FastJet. If not, see <http://www.gnu.org/licenses/>.
 //----------------------------------------------------------------------
 //FJENDHEADER
 
 
 #include<vector>
 #include<map>
 #include "fastjet/PseudoJet.hh"
 #include<memory>
 #include<cassert>
 #include<iostream>
 #include<string>
 #include<set>
 #include<cmath> // needed to get double std::abs(double)
 #include "fastjet/Error.hh"
 #include "fastjet/JetDefinition.hh"
 #include "fastjet/SharedPtr.hh"
 #include "fastjet/LimitedWarning.hh"
 #include "fastjet/FunctionOfPseudoJet.hh"
 #include "fastjet/ClusterSequenceStructure.hh"
 #include "fastjet/internal/thread_safety_helpers.hh"  // helpers to write code w&wo thread-safety
 #include "fastjet/internal/deprecated.hh"
 
 FASTJET_BEGIN_NAMESPACE      // defined in fastjet/internal/base.hh
 
 
 // forward declarations
 class ClusterSequenceStructure;
 class DynamicNearestNeighbours;
 
 /// @ingroup basic_classes
 /// \class ClusterSequence
 /// deals with clustering
 class ClusterSequence {
 
 
  public: 
 
   /// default constructor
   ClusterSequence () : _deletes_self_when_unused(false) {}
 
   /// create a ClusterSequence, starting from the supplied set
   /// of PseudoJets and clustering them with jet definition specified
   /// by jet_def (which also specifies the clustering strategy)
   template<class L> ClusterSequence (
                       const std::vector<L> & pseudojets,
                   const JetDefinition & jet_def,
                   const bool & writeout_combinations = false);
   
   /// copy constructor for a ClusterSequence
   ClusterSequence (const ClusterSequence & cs) : _deletes_self_when_unused(false) {
     transfer_from_sequence(cs);
   }
 
   /// explicit assignment operator for a ClusterSequence
   ClusterSequence & operator=(const ClusterSequence & cs);
   
   // virtual ClusterSequence destructor, in case any derived class
   // thinks of needing a destructor at some point
   virtual ~ClusterSequence (); //{}
 
   // NB: in the routines that follow, for extracting lists of jets, a
   //     list structure might be more efficient, if sometimes a little
   //     more awkward to use (at least for old fortran hands).
 
   /// return a vector of all jets (in the sense of the inclusive
   /// algorithm) with pt >= ptmin. Time taken should be of the order
   /// of the number of jets returned.
   std::vector<PseudoJet> inclusive_jets (const double ptmin = 0.0) const;
 
   /// return the number of jets (in the sense of the exclusive
   /// algorithm) that would be obtained when running the algorithm
   /// with the given dcut.
   int n_exclusive_jets (const double dcut) const;
 
   /// return a vector of all jets (in the sense of the exclusive
   /// algorithm) that would be obtained when running the algorithm
   /// with the given dcut.
   std::vector<PseudoJet> exclusive_jets (const double dcut) const;
 
   /// return a vector of all jets when the event is clustered (in the
   /// exclusive sense) to exactly njets. 
   ///
   /// If there are fewer than njets particles in the ClusterSequence
   /// an error is thrown
   std::vector<PseudoJet> exclusive_jets (const int njets) const;
 
   /// return a vector of all jets when the event is clustered (in the
   /// exclusive sense) to exactly njets. 
   ///
   /// If there are fewer than njets particles in the ClusterSequence
   /// the function just returns however many particles there were.
   std::vector<PseudoJet> exclusive_jets_up_to (const int njets) const;
 
   /// return the dmin corresponding to the recombination that went
   /// from n+1 to n jets (sometimes known as d_{n n+1}). If the number
   /// of particles in the event is <= njets, the function returns 0.
   double exclusive_dmerge (const int njets) const;
 
   /// return the maximum of the dmin encountered during all recombinations 
   /// up to the one that led to an n-jet final state; identical to
   /// exclusive_dmerge, except in cases where the dmin do not increase
   /// monotonically.
   double exclusive_dmerge_max (const int njets) const;
 
   /// return the ymin corresponding to the recombination that went from
   /// n+1 to n jets (sometimes known as y_{n n+1}).
   double exclusive_ymerge (int njets) const {return exclusive_dmerge(njets) / Q2();}
 
   /// same as exclusive_dmerge_max, but normalised to squared total energy
   double exclusive_ymerge_max (int njets) const {return exclusive_dmerge_max(njets)/Q2();}
 
   /// the number of exclusive jets at the given ycut
   int n_exclusive_jets_ycut (double ycut) const {return n_exclusive_jets(ycut*Q2());}
 
   /// the exclusive jets obtained at the given ycut
   std::vector<PseudoJet> exclusive_jets_ycut (double ycut) const {
     int njets = n_exclusive_jets_ycut(ycut);
     return exclusive_jets(njets);
   }
 
 
   //int n_exclusive_jets (const PseudoJet & jet, const double dcut) const;
 
   /// return a vector of all subjets of the current jet (in the sense
   /// of the exclusive algorithm) that would be obtained when running
   /// the algorithm with the given dcut. 
   ///
   /// Time taken is O(m ln m), where m is the number of subjets that
   /// are found. If m gets to be of order of the total number of
   /// constituents in the jet, this could be substantially slower than
   /// just getting that list of constituents.
   std::vector<PseudoJet> exclusive_subjets (const PseudoJet & jet, 
                                             const double dcut) const;
 
   /// return the size of exclusive_subjets(...); still n ln n with same
   /// coefficient, but marginally more efficient than manually taking
   /// exclusive_subjets.size()
   int n_exclusive_subjets(const PseudoJet & jet, 
                           const double dcut) const;
 
   /// return the list of subjets obtained by unclustering the supplied
   /// jet down to nsub subjets. Throws an error if there are fewer than
   /// nsub particles in the jet.
   ///
   /// This requires nsub ln nsub time
   std::vector<PseudoJet> exclusive_subjets (const PseudoJet & jet, 
                                             int nsub) const;
 
   /// return the list of subjets obtained by unclustering the supplied
   /// jet down to nsub subjets (or all constituents if there are fewer
   /// than nsub).
   ///
   /// This requires nsub ln nsub time
   std::vector<PseudoJet> exclusive_subjets_up_to (const PseudoJet & jet, 
                           int nsub) const;
 
   /// returns the dij that was present in the merging nsub+1 -> nsub 
   /// subjets inside this jet.
   ///
   /// Returns 0 if there were nsub or fewer constituents in the jet.
   double exclusive_subdmerge(const PseudoJet & jet, int nsub) const;
 
   /// returns the maximum dij that occurred in the whole event at the
   /// stage that the nsub+1 -> nsub merge of subjets occurred inside 
   /// this jet.
   ///
   /// Returns 0 if there were nsub or fewer constituents in the jet.
   double exclusive_subdmerge_max(const PseudoJet & jet, int nsub) const;
 
   //std::vector<PseudoJet> exclusive_jets (const PseudoJet & jet, 
   //                                       const int njets) const;
   //double exclusive_dmerge (const PseudoJet & jet, const int njets) const;
 
   /// returns the sum of all energies in the event (relevant mainly for e+e-)
   double Q() const {return _Qtot;}
   /// return Q()^2
   double Q2() const {return _Qtot*_Qtot;}
 
   /// returns true iff the object is included in the jet. 
   ///
   /// NB: this is only sensible if the object is already registered
   /// within the cluster sequence, so you cannot use it with an input
   /// particle to the CS (since the particle won't have the history
   /// index set properly).
   ///
   /// For nice clustering structures it should run in O(ln(N)) time
   /// but in worst cases (certain cone plugins) it can take O(n) time,
   /// where n is the number of particles in the jet.
   bool object_in_jet(const PseudoJet & object, const PseudoJet & jet) const;
 
   /// if the jet has parents in the clustering, it returns true
   /// and sets parent1 and parent2 equal to them.
   ///
   /// if it has no parents it returns false and sets parent1 and
   /// parent2 to zero
   bool has_parents(const PseudoJet & jet, PseudoJet & parent1, 
                PseudoJet & parent2) const;
 
   /// if the jet has a child then return true and give the child jet
   /// otherwise return false and set the child to zero
   bool has_child(const PseudoJet & jet, PseudoJet & child) const;
 
   /// Version of has_child that sets a pointer to the child if the child
   /// exists;
   bool has_child(const PseudoJet & jet, const PseudoJet * & childp) const;
 
   /// if this jet has a child (and so a partner) return true
   /// and give the partner, otherwise return false and set the
   /// partner to zero
   bool has_partner(const PseudoJet & jet, PseudoJet & partner) const;
 
   
   /// return a vector of the particles that make up jet
   std::vector<PseudoJet> constituents (const PseudoJet & jet) const;
 
 
   /// output the supplied vector of jets in a format that can be read
   /// by an appropriate root script; the format is:
   /// jet-n jet-px jet-py jet-pz jet-E 
   ///   particle-n particle-rap particle-phi particle-pt
   ///   particle-n particle-rap particle-phi particle-pt
   ///   ...
   /// #END
   /// ... [i.e. above repeated]
   void print_jets_for_root(const std::vector<PseudoJet> & jets, 
                            std::ostream & ostr = std::cout) const;
 
   /// print jets for root to the file labelled filename, with an
   /// optional comment at the beginning
   void print_jets_for_root(const std::vector<PseudoJet> & jets, 
                            const std::string & filename,
                const std::string & comment = "") const;
 
 // Not yet. Perhaps in a future release.
 //   /// print out all inclusive jets with pt > ptmin
 //   virtual void print_jets (const double ptmin=0.0) const;
 
   /// add on to subjet_vector the constituents of jet (for internal use mainly)
   void add_constituents (const PseudoJet & jet, 
              std::vector<PseudoJet> & subjet_vector) const;
 
   /// return the enum value of the strategy used to cluster the event
   inline Strategy strategy_used () const {return _strategy;}
 
   /// return the name of the strategy used to cluster the event
   std::string strategy_string () const {return strategy_string(_strategy);}
 
   /// return the name of the strategy associated with the enum strategy_in
   std::string strategy_string (Strategy strategy_in) const;
 
 
   /// return a reference to the jet definition
   const JetDefinition & jet_def() const {return _jet_def;}
 
   /// by calling this routine you tell the ClusterSequence to delete
   /// itself when all the Pseudojets associated with it have gone out
   /// of scope. 
   ///
   /// At the time you call this, there must be at least one jet or
   /// other object outside the CS that is associated with the CS
   /// (e.g. the result of inclusive_jets()).
   ///
   /// NB: after having made this call, the user is still allowed to
   /// delete the CS. Jets associated with it will then simply not be
   /// able to access their substructure after that point.
   void delete_self_when_unused();
 
   /// return true if the object has been told to delete itself
   /// when unused
   bool will_delete_self_when_unused() const {return _deletes_self_when_unused;}
 
 //std::shared_ptr: #ifdef FASTJET_HAVE_THREAD_SAFETY
 //std::shared_ptr:   /// signals that a jet will no longer use the current CS (internal use only)
 //std::shared_ptr:   void release_pseudojet(PseudoJet &jet) const;
 //std::shared_ptr: #else
   /// tell the ClusterSequence it's about to be self deleted (internal use only)
   void signal_imminent_self_deletion() const;
 //std::shared_ptr: #endif
 
   /// returns the scale associated with a jet as required for this
   /// clustering algorithm (kt^2 for the kt-algorithm, 1 for the
   /// Cambridge algorithm). Intended mainly for internal use and not
   /// valid for plugin algorithms.
   double jet_scale_for_algorithm(const PseudoJet & jet) const;
 
   ///
 
   //----- next follow functions designed specifically for plugins, which
   //      may only be called when plugin_activated() returns true
 
   /// record the fact that there has been a recombination between
   /// jets()[jet_i] and jets()[jet_k], with the specified dij, and
   /// return the index (newjet_k) allocated to the new jet, whose
   /// momentum is assumed to be the 4-vector sum of that of jet_i and
   /// jet_j
   void plugin_record_ij_recombination(int jet_i, int jet_j, double dij, 
                       int & newjet_k) {
     assert(plugin_activated());
     _do_ij_recombination_step(jet_i, jet_j, dij, newjet_k);
   }
 
   /// as for the simpler variant of plugin_record_ij_recombination,
   /// except that the new jet is attributed the momentum and
   /// user_index of newjet
   void plugin_record_ij_recombination(int jet_i, int jet_j, double dij, 
                       const PseudoJet & newjet, 
                       int & newjet_k);
 
   /// record the fact that there has been a recombination between
   /// jets()[jet_i] and the beam, with the specified diB; when looking
   /// for inclusive jets, any iB recombination will returned to the user 
   /// as a jet.
   void plugin_record_iB_recombination(int jet_i, double diB) {
     assert(plugin_activated());
     _do_iB_recombination_step(jet_i, diB);
   }
 
   /// @ingroup extra_info
   /// \class Extras
   /// base class to store extra information that plugins may provide
   /// 
   /// a class intended to serve as a base in case a plugin needs to
   /// associate extra information with a ClusterSequence (see
   /// SISConePlugin.* for an example).
   class Extras {
   public:
     virtual ~Extras() {}
     virtual std::string description() const {return "This is a dummy extras class that contains no extra information! Derive from it if you want to use it to provide extra information from a plugin jet finder";}
   };
 
   /// the plugin can associate some extra information with the
   /// ClusterSequence object by calling this function. The
   /// ClusterSequence takes ownership of the pointer (and
   /// responsibility for deleting it when the CS gets deleted).
   inline void plugin_associate_extras(Extras * extras_in) {
     _extras.reset(extras_in);
   }
 
   /// the plugin can associate some extra information with the
   /// ClusterSequence object by calling this function
   /// 
   /// As of FJ v3.1, this is deprecated, in line with the deprecation
   /// of auto_ptr in C++11
 #ifndef SWIG
 #ifdef FASTJET_HAVE_AUTO_PTR_INTERFACE
   FASTJET_DEPRECATED_MSG("Please use ClusterSequence::plugin_associate_extras(Extras * extras_in)) instead",
   inline void plugin_associate_extras(std::auto_ptr<Extras> extras_in)){
     _extras.reset(extras_in.release());
   }
 #endif
 #endif //SWIG
 
   /// returns true when the plugin is allowed to run the show.
   inline bool plugin_activated() const {return _plugin_activated;}
 
   /// returns a pointer to the extras object (may be null)
   const Extras * extras() const {return _extras.get();}
 
   /// allows a plugin to run a templated clustering (nearest-neighbour heuristic)
   ///
   /// This has N^2 behaviour on "good" distance, but a worst case behaviour
   /// of N^3 (and many algs trigger the worst case behaviour)
   ///
   /// 
   /// For more details on how this works, see GenBriefJet below
   template<class GBJ> void plugin_simple_N2_cluster () {
     assert(plugin_activated());
     _simple_N2_cluster<GBJ>();
   }
 
 
 public:
 //DEP   /// set the default (static) jet finder across all current and future
 //DEP   /// ClusterSequence objects -- deprecated and obsolescent (i.e. may be
 //DEP   /// suppressed in a future release).
 //DEP   static void set_jet_algorithm (JetAlgorithm jet_algorithm) {_default_jet_algorithm = jet_algorithm;}
 //DEP   /// same as above for backward compatibility
 //DEP   static void set_jet_finder (JetAlgorithm jet_algorithm)    {_default_jet_algorithm = jet_algorithm;}
 
 
   /// \ingroup extra_info
   /// \struct history_element
   /// a single element in the clustering history
   /// 
   /// (see vector _history below).
   struct history_element{
     int parent1; /// index in _history where first parent of this jet
                  /// was created (InexistentParent if this jet is an
                  /// original particle)
 
     int parent2; /// index in _history where second parent of this jet
                  /// was created (InexistentParent if this jet is an
                  /// original particle); BeamJet if this history entry
                  /// just labels the fact that the jet has recombined
                  /// with the beam)
 
     int child;   /// index in _history where the current jet is
          /// recombined with another jet to form its child. It
          /// is Invalid if this jet does not further
          /// recombine.
 
     int jetp_index; /// index in the _jets vector where we will find the
                  /// PseudoJet object corresponding to this jet
                  /// (i.e. the jet created at this entry of the
                  /// history). NB: if this element of the history
                  /// corresponds to a beam recombination, then
                  /// jetp_index=Invalid.
 
     double dij;  /// the distance corresponding to the recombination
          /// at this stage of the clustering.
 
     double max_dij_so_far; /// the largest recombination distance seen
                /// so far in the clustering history.
   };
 
   enum JetType {Invalid=-3, InexistentParent = -2, BeamJet = -1};
 
   /// allow the user to access the internally stored _jets() array,
   /// which contains both the initial particles and the various
   /// intermediate and final stages of recombination.
   ///
   /// The first n_particles() entries are the original particles,
   /// in the order in which they were supplied to the ClusterSequence
   /// constructor. It can be useful to access them for example when
   /// examining whether a given input object is part of a specific
   /// jet, via the objects_in_jet(...) member function (which only takes
   /// PseudoJets that are registered in the ClusterSequence).
   ///
   /// One of the other (internal uses) is related to the fact
   /// because we don't seem to be able to access protected elements of
   /// the class for an object that is not "this" (at least in case where
   /// "this" is of a slightly different kind from the object, both
   /// derived from ClusterSequence).
   const std::vector<PseudoJet> & jets()    const;
 
   /// allow the user to access the raw internal history.
   ///
   /// This is present (as for jets()) in part so that protected
   /// derived classes can access this information about other
   /// ClusterSequences.
   ///
   /// A user who wishes to follow the details of the ClusterSequence
   /// can also make use of this information (and should consult the
   /// history_element documentation for more information), but should
   /// be aware that these internal structures may evolve in future
   /// FastJet versions.
   const std::vector<history_element> & history() const;
 
   /// returns the number of particles that were provided to the
   /// clustering algorithm (helps the user find their way around the
   /// history and jets objects if they weren't paying attention
   /// beforehand).
   unsigned int n_particles() const;
 
   /// returns a vector of size n_particles() which indicates, for 
   /// each of the initial particles (in the order in which they were
   /// supplied), which of the supplied jets it belongs to; if it does
   /// not belong to any of the supplied jets, the index is set to -1;
   std::vector<int> particle_jet_indices(const std::vector<PseudoJet> &) const;
 
   /// routine that returns an order in which to read the history
   /// such that clusterings that lead to identical jet compositions
   /// but different histories (because of degeneracies in the
   /// clustering order) will have matching constituents for each
   /// matching entry in the unique_history_order.
   ///
   /// The order has the property that an entry's parents will always
   /// appear prior to that entry itself. 
   ///
   /// Roughly speaking the order is such that we first provide all
   /// steps that lead to the final jet containing particle 1; then we
   /// have the steps that lead to reconstruction of the jet containing
   /// the next-lowest-numbered unclustered particle, etc...
   /// [see GPS CCN28-12 for more info -- of course a full explanation
   /// here would be better...]
   std::vector<int> unique_history_order() const;
 
   /// return the set of particles that have not been clustered. For 
   /// kt and cam/aachen algorithms this should always be null, but for
   /// cone type algorithms it can be non-null;
   std::vector<PseudoJet> unclustered_particles() const;
 
   /// Return the list of pseudojets in the ClusterSequence that do not
   /// have children (and are not among the inclusive jets). They may
   /// result from a clustering step or may be one of the pseudojets
   /// returned by unclustered_particles().
   std::vector<PseudoJet> childless_pseudojets() const;
 
   /// returns true if the object (jet or particle) is contained by (ie
   /// belongs to) this cluster sequence.
   ///
   /// Tests performed: if thejet's interface is this cluster sequence
   /// and its cluster history index is in a consistent range.
   bool contains(const PseudoJet & object) const;
 
   /// transfer the sequence contained in other_seq into our own;
   /// any plugin "extras" contained in the from_seq will be lost
   /// from there.
   ///
   /// It also sets the ClusterSequence pointers of the PseudoJets in
   /// the history to point to this ClusterSequence
   ///
   /// When specified, the second argument is an action that will be
   /// applied on every jets in the resulting ClusterSequence
   void transfer_from_sequence(const ClusterSequence & from_seq,
                   const FunctionOfPseudoJet<PseudoJet> * action_on_jets = 0);
 
   /// retrieve a shared pointer to the wrapper to this ClusterSequence
   ///
   /// this may turn useful if you want to track when this
   /// ClusterSequence goes out of scope
   const SharedPtr<PseudoJetStructureBase> & structure_shared_ptr() const{
     return _structure_shared_ptr;
   }
 
   /// the structure type associated with a jet belonging to a ClusterSequence
   typedef ClusterSequenceStructure StructureType;
 
   /// This is the function that is automatically called during
   /// clustering to print the FastJet banner. Only the first call to
   /// this function will result in the printout of the banner. Users
   /// may wish to call this function themselves, during the
   /// initialization phase of their program, in order to ensure that
   /// the banner appears before other output. This call will not
   /// affect 3rd-party banners, e.g. those from plugins.
   static void print_banner();
 
   /// \cond internal_doc
   //  [this line must be left as is to hide the doxygen comment]
   /// A call to this function modifies the stream used to print
   /// banners (by default cout). If a null pointer is passed, banner
   /// printout is suppressed. This affects all banners, including
   /// those from plugins.
   ///
   /// Please note that if you distribute 3rd party code
   /// that links with FastJet, that 3rd party code must not
   /// use this call turn off the printing of FastJet banners
   /// by default. This requirement reflects the spirit of
   /// clause 2c of the GNU Public License (v2), under which
   /// FastJet and its plugins are distributed.
   static void set_fastjet_banner_stream(std::ostream * ostr) {_fastjet_banner_ostr = ostr;}
   //  [this line must be left as is to hide the doxygen comment]
   /// \endcond
 
   /// returns a pointer to the stream to be used to print banners
   /// (cout by default). This function is used by plugins to determine
   /// where to direct their banners. Plugins should properly handle
   /// the case where the pointer is null.
   static std::ostream * fastjet_banner_stream() {return _fastjet_banner_ostr;}
 
 private:
   
   /// \cond internal_doc
   /// contains the actual stream to use for banners 
 #ifdef FASTJET_HAVE_LIMITED_THREAD_SAFETY
   static std::atomic<std::ostream*> _fastjet_banner_ostr;
 #else
   static std::ostream * _fastjet_banner_ostr;
 #endif // FASTJET_HAVE_LIMITED_THREAD_SAFETY
   /// \endcond
 
 protected:
 //DEP  static JetAlgorithm _default_jet_algorithm;
   JetDefinition _jet_def;
 
   /// transfer the vector<L> of input jets into our own vector<PseudoJet>
   /// _jets (with some reserved space for future growth).
   template<class L> void _transfer_input_jets(
                                      const std::vector<L> & pseudojets);
 
   /// This is what is called to do all the initialisation and
   /// then run the clustering (may be called by various constructors).
   /// It assumes _jets contains the momenta to be clustered.
   void _initialise_and_run (const JetDefinition & jet_def,
                 const bool & writeout_combinations);
 
   //// this performs the initialisation, minus the option-decanting
   //// stage; for low multiplicity, initialising a few things in the
   //// constructor, calling the decant_options_partial() and then this
   //// is faster than going through _initialise_and_run.
   void _initialise_and_run_no_decant();
 
 //DEP   /// This is an alternative routine for initialising and running the
 //DEP   /// clustering, provided for legacy purposes. The jet finder is that
 //DEP   /// specified in the static member _default_jet_algorithm.
 //DEP   void _initialise_and_run (const double R,
 //DEP               const Strategy & strategy,
 //DEP               const bool & writeout_combinations);
 
   /// fills in the various member variables with "decanted" options from
   /// the jet_definition and writeout_combinations variables
   void _decant_options(const JetDefinition & jet_def,
                        const bool & writeout_combinations);
 
   /// assuming that the jet definition, writeout_combinations and
   /// _structure_shared_ptr have been set (e.g. in an initialiser list
   /// in the constructor), it handles the remaining decanting of
   /// options.
   void _decant_options_partial();
 
   /// fill out the history (and jet cross refs) related to the initial
   /// set of jets (assumed already to have been "transferred"),
   /// without any clustering
   void _fill_initial_history();
 
   /// carry out the recombination between the jets numbered jet_i and
   /// jet_j, at distance scale dij; return the index newjet_k of the
   /// result of the recombination of i and j.
   void _do_ij_recombination_step(const int jet_i, const int jet_j, 
                  const double dij, int & newjet_k);
 
   /// carry out an recombination step in which _jets[jet_i] merges with
   /// the beam, 
   void _do_iB_recombination_step(const int jet_i, const double diB);
 
   /// every time a jet is added internally during clustering, this
   /// should be called to set the jet's structure shared ptr to point
   /// to the CS (and the count of internally associated objects is
   /// also updated). This should not be called outside construction of
   /// a CS object.
   void _set_structure_shared_ptr(PseudoJet & j);
 
   /// make sure that the CS's internal tally of the use count matches
   /// that of the _structure_shared_ptr
   void _update_structure_use_count();
   
   /// returns a suggestion for the best strategy to use on event
   /// multiplicity, algorithm, R, etc.
   Strategy _best_strategy() const;
   
   /// \if internal_doc
   /// \class _Parabola
   /// returns c*(a*R**2 + b*R + 1);
   /// Written as a class in case we want to give names to different
   /// parabolas
   /// \endif
   class _Parabola {
   public:
     _Parabola(double a, double b, double c) : _a(a), _b(b), _c(c) {}
     inline double operator()(const double R) const {return _c*(_a*R*R + _b*R + 1);}
   private:
     double _a, _b, _c;
   };
 
   /// \if internal_doc
   /// \class _Line
   /// operator()(R) returns a*R+b;
   /// \endif
   class _Line {
   public:
     _Line(double a, double b) : _a(a), _b(b) {}
     inline double operator()(const double R) const {return _a*R + _b;}
   private:
     double _a, _b;
   };
 
   /// This contains the physical PseudoJets; for each PseudoJet one
   /// can find the corresponding position in the _history by looking
   /// at _jets[i].cluster_hist_index().
   std::vector<PseudoJet> _jets;
 
 
   /// this vector will contain the branching history; for each stage,
   /// _history[i].jetp_index indicates where to look in the _jets
   /// vector to get the physical PseudoJet.
   std::vector<history_element> _history;
 
   /// set subhist to be a set pointers to history entries corresponding to the
   /// subjets of this jet; one stops going working down through the
   /// subjets either when 
   ///   - there is no further to go
   ///   - one has found maxjet entries
   ///   - max_dij_so_far <= dcut
   /// By setting maxjet=0 one can use just dcut; by setting dcut<0
   /// one can use jet maxjet
   void get_subhist_set(std::set<const history_element*> & subhist,
                        const  PseudoJet & jet, double dcut, int maxjet) const;
 
   bool _writeout_combinations;
   int  _initial_n;
   double _Rparam, _R2, _invR2;
   double _Qtot;
   Strategy    _strategy;
   JetAlgorithm  _jet_algorithm;
 
   SharedPtr<PseudoJetStructureBase> _structure_shared_ptr; //< will actually be of type ClusterSequenceStructure
   int _structure_use_count_after_construction; //< info of use when CS handles its own memory
   /// if true then the CS will delete itself when the last external
   /// object referring to it disappears. It is mutable so as to ensure
   /// that signal_imminent_self_deletion() [const] can make relevant
   /// changes.
 #ifdef FASTJET_HAVE_THREAD_SAFETY
   mutable std::atomic<bool> _deletes_self_when_unused;
 #else
   mutable bool _deletes_self_when_unused;
 #endif
 
  private:
 
   bool _plugin_activated;
   SharedPtr<Extras> _extras; // things the plugin might want to add
 
   void _really_dumb_cluster ();
   void _delaunay_cluster ();
   //void _simple_N2_cluster ();
   template<class BJ> void _simple_N2_cluster ();
   void _tiled_N2_cluster ();
   void _faster_tiled_N2_cluster ();
 
   //
   void _minheap_faster_tiled_N2_cluster();
 
   // things needed specifically for Cambridge with Chan's 2D closest
   // pairs method
   void _CP2DChan_cluster();
   void _CP2DChan_cluster_2pi2R ();
   void _CP2DChan_cluster_2piMultD ();
   void _CP2DChan_limited_cluster(double D);
   void _do_Cambridge_inclusive_jets();
 
   // NSqrtN method for C/A
   void _fast_NsqrtN_cluster();
 
   void _add_step_to_history( //const int step_number,
                             const int parent1, 
                 const int parent2, const int jetp_index,
                 const double dij);
 
   /// internal routine associated with the construction of the unique
   /// history order (following children in the tree)
   void _extract_tree_children(int pos, std::valarray<bool> &, 
         const std::valarray<int> &, std::vector<int> &) const;
 
   /// internal routine associated with the construction of the unique
   /// history order (following parents in the tree)
   void _extract_tree_parents (int pos, std::valarray<bool> &, 
                 const std::valarray<int> &,  std::vector<int> &) const;
 
 
   // these will be useful shorthands in the Voronoi-based code
   typedef std::pair<int,int> TwoVertices;
   typedef std::pair<double,TwoVertices> DijEntry;
   typedef std::multimap<double,TwoVertices> DistMap;
 
   /// currently used only in the Voronoi based code
   void _add_ktdistance_to_map(const int ii, 
                   DistMap & DijMap,
                   const DynamicNearestNeighbours * DNN);
 
 
   /// will be set by default to be true for the first run
   static thread_safety_helpers::FirstTimeTrue _first_time;
 
   /// manage warnings related to exclusive jets access
   static LimitedWarning _exclusive_warnings;
 
   /// the limited warning member for notification of user that 
   /// their requested strategy has been overridden (usually because
   /// they have R>2pi and not all strategies work then)
   static LimitedWarning _changed_strategy_warning;
 
   //----------------------------------------------------------------------
   /// the fundamental structure which contains the minimal info about
   /// a jet, as needed for our plain N^2 algorithm -- the idea is to
   /// put all info that will be accessed N^2 times into an array of
   /// BriefJets...
   struct BriefJet {
     double     eta, phi, kt2, NN_dist;
     BriefJet * NN;
     int        _jets_index;
   };
 
   /// structure analogous to BriefJet, but with the extra information
   /// needed for dealing with tiles
   class TiledJet {
   public:
     double     eta, phi, kt2, NN_dist;
     TiledJet * NN, *previous, * next; 
     int        _jets_index, tile_index, diJ_posn;
     // routines that are useful in the minheap version of tiled
     // clustering ("misuse" the otherwise unused diJ_posn, so as
     // to indicate whether jets need to have their minheap entries
     // updated).
     inline void label_minheap_update_needed() {diJ_posn = 1;}
     inline void label_minheap_update_done()   {diJ_posn = 0;}
     inline bool minheap_update_needed() const {return diJ_posn==1;}
   };
 
   //-- some of the functions that follow are templates and will work
   //as well for briefjet and tiled jets
 
   /// set the kinematic and labelling info for jeta so that it corresponds
   /// to _jets[_jets_index]
   template <class J> void _bj_set_jetinfo( J * const jet, 
                          const int _jets_index) const;
 
   /// "remove" this jet, which implies updating links of neighbours and
   /// perhaps modifying the tile structure
   void _bj_remove_from_tiles( TiledJet * const jet) const;
 
   /// return the distance between two BriefJet objects
   template <class J> double _bj_dist(const J * const jeta, 
             const J * const jetb) const;
 
   // return the diJ (multiplied by _R2) for this jet assuming its NN
   // info is correct
   template <class J> double _bj_diJ(const J * const jeta) const;
 
   /// for testing purposes only: if in the range head--tail-1 there is a
   /// a jet which corresponds to hist_index in the history, then
   /// return a pointer to that jet; otherwise return tail.
   template <class J> inline J * _bj_of_hindex(
                           const int hist_index, 
               J * const head, J * const tail) 
     const {
     J * res;
     for(res = head; res<tail; res++) {
       if (_jets[res->_jets_index].cluster_hist_index() == hist_index) {break;}
     }
     return res;
   }
 
 
   //-- remaining functions are different in various cases, so we
   //   will use templates but are not sure if they're useful...
 
   /// updates (only towards smaller distances) the NN for jeta without checking
   /// whether in the process jeta itself might be a new NN of one of
   /// the jets being scanned -- span the range head to tail-1 with
   /// assumption that jeta is not contained in that range
   template <class J> void _bj_set_NN_nocross(J * const jeta, 
             J * const head, const J * const tail) const;
 
   /// reset the NN for jeta and DO check whether in the process jeta
   /// itself might be a new NN of one of the jets being scanned --
   /// span the range head to tail-1 with assumption that jeta is not
   /// contained in that range
   template <class J> void _bj_set_NN_crosscheck(J * const jeta, 
             J * const head, const J * const tail) const;
   
 
 
   /// number of neighbours that a tile will have (rectangular geometry
   /// gives 9 neighbours).
   static const int n_tile_neighbours = 9;
   //----------------------------------------------------------------------
   /// The fundamental structures to be used for the tiled N^2 algorithm
   /// (see CCN27-44 for some discussion of pattern of tiling)
   struct Tile {
     /// pointers to neighbouring tiles, including self
     Tile *   begin_tiles[n_tile_neighbours]; 
     /// neighbouring tiles, excluding self
     Tile **  surrounding_tiles; 
     /// half of neighbouring tiles, no self
     Tile **  RH_tiles;  
     /// just beyond end of tiles
     Tile **  end_tiles; 
     /// start of list of BriefJets contained in this tile
     TiledJet * head;    
     /// sometimes useful to be able to tag a tile
     bool     tagged;    
   };
   std::vector<Tile> _tiles;
   double _tiles_eta_min, _tiles_eta_max;
   double _tile_size_eta, _tile_size_phi;
   int    _n_tiles_phi,_tiles_ieta_min,_tiles_ieta_max;
 
   // reasonably robust return of tile index given ieta and iphi, in particular
   // it works even if iphi is negative
   inline int _tile_index (int ieta, int iphi) const {
     // note that (-1)%n = -1 so that we have to add _n_tiles_phi
     // before performing modulo operation
     return (ieta-_tiles_ieta_min)*_n_tiles_phi
                   + (iphi+_n_tiles_phi) % _n_tiles_phi;
   }
 
   // routines for tiled case, including some overloads of the plain
   // BriefJet cases
   int  _tile_index(const double eta, const double phi) const;
   void _tj_set_jetinfo ( TiledJet * const jet, const int _jets_index);
   void  _bj_remove_from_tiles(TiledJet * const jet);
   void _initialise_tiles();
   void _print_tiles(TiledJet * briefjets ) const;
   void _add_neighbours_to_tile_union(const int tile_index, 
          std::vector<int> & tile_union, int & n_near_tiles) const;
   void _add_untagged_neighbours_to_tile_union(const int tile_index, 
          std::vector<int> & tile_union, int & n_near_tiles);
 
   //----------------------------------------------------------------------
   /// fundamental structure for e+e- clustering
   struct EEBriefJet {
     double NN_dist;  // obligatorily present
     double kt2;      // obligatorily present == E^2 in general
     EEBriefJet * NN; // must be present too
     int    _jets_index; // must also be present!
     //...........................................................
     double nx, ny, nz;  // our internal storage for fast distance calcs
   };
 
   /// to help instantiation (fj 2.4.0; did not quite work on gcc 33 and os x 10.3?)
   //void _dummy_N2_cluster_instantiation();
 
 
   /// to avoid issues with template instantiation (OS X 10.3, gcc 3.3)
   void _simple_N2_cluster_BriefJet();
   /// to avoid issues with template instantiation (OS X 10.3, gcc 3.3)
   void _simple_N2_cluster_EEBriefJet();
 };
 
 
 //**********************************************************************
 //**************    START   OF   INLINE   MATERIAL    ******************
 //**********************************************************************
 
 
 //----------------------------------------------------------------------
 // Transfer the initial jets into our internal structure
 template<class L> void ClusterSequence::_transfer_input_jets(
                                        const std::vector<L> & pseudojets) {
 
   // this will ensure that we can point to jets without difficulties
   // arising.
   _jets.reserve(pseudojets.size()*2);
 
   // insert initial jets this way so that any type L that can be
   // converted to a pseudojet will work fine (basically PseudoJet
   // and any type that has [] subscript access to the momentum
   // components, such as CLHEP HepLorentzVector).
   for (unsigned int i = 0; i < pseudojets.size(); i++) {
     _jets.push_back(pseudojets[i]);}
   
 }
 
 // //----------------------------------------------------------------------
 // // initialise from some generic type... Has to be made available
 // // here in order for it the template aspect of it to work...
 // template<class L> ClusterSequence::ClusterSequence (
 //                    const std::vector<L> & pseudojets,
 //                const double R,
 //                const Strategy & strategy,
 //                const bool & writeout_combinations) {
 // 
 //   // transfer the initial jets (type L) into our own array
 //   _transfer_input_jets(pseudojets);
 // 
 //   // run the clustering
 //   _initialise_and_run(R,strategy,writeout_combinations);
 // }
 
 
 //----------------------------------------------------------------------
 /// constructor of a jet-clustering sequence from a vector of
 /// four-momenta, with the jet definition specified by jet_def
 template<class L> ClusterSequence::ClusterSequence (
                       const std::vector<L> & pseudojets,
                   const JetDefinition & jet_def_in,
                   const bool & writeout_combinations) :
   _jet_def(jet_def_in), _writeout_combinations(writeout_combinations),
   _structure_shared_ptr(new ClusterSequenceStructure(this))
 {
 
   // transfer the initial jets (type L) into our own array
   _transfer_input_jets(pseudojets);
 
   // transfer the remaining options
   _decant_options_partial();
 
   // run the clustering
   _initialise_and_run_no_decant();
 }
 
 
 inline const std::vector<PseudoJet> & ClusterSequence::jets () const {
   return _jets;
 }
 
 inline const std::vector<ClusterSequence::history_element> & ClusterSequence::history () const {
   return _history;
 }
 
 inline unsigned int ClusterSequence::n_particles() const {return _initial_n;}
 
 //----------------------------------------------------------------------
 // implementation of JetDefinition::operator() is here to avoid nasty
 // issues of order of implementations and includes
 #ifndef __CINT__
 template<class L>
 std::vector<PseudoJet> JetDefinition::operator()(const std::vector<L> & particles) const {
   // create a new cluster sequence
   ClusterSequence * cs = new ClusterSequence(particles, *this);
 
   // get the jets, and sort them according to whether the algorithm
   // is spherical or not
   std::vector<PseudoJet> jets;
   if (is_spherical()) {
     jets = sorted_by_E(cs->inclusive_jets());
   } else {
     jets = sorted_by_pt(cs->inclusive_jets());
   }
   
   // make sure the ClusterSequence gets deleted once it's no longer
   // needed
   if (jets.size() != 0) {
     cs->delete_self_when_unused();
   } else {
     delete cs;
   }
 
   return jets;
 }
 #endif // __CINT__
 
 
 //----------------------------------------------------------------------
 template <class J> inline void ClusterSequence::_bj_set_jetinfo(
                             J * const jetA, const int _jets_index) const {
     jetA->eta  = _jets[_jets_index].rap();
     jetA->phi  = _jets[_jets_index].phi_02pi();
     jetA->kt2  = jet_scale_for_algorithm(_jets[_jets_index]);
     jetA->_jets_index = _jets_index;
     // initialise NN info as well
     jetA->NN_dist = _R2;
     jetA->NN      = NULL;
 }
 
 
 
 
 //----------------------------------------------------------------------
 template <class J> inline double ClusterSequence::_bj_dist(
                 const J * const jetA, const J * const jetB) const {
   //#define FASTJET_NEW_DELTA_PHI
 #ifndef FASTJET_NEW_DELTA_PHI
   //GPS+MC old version of Delta phi calculation
   double dphi = std::abs(jetA->phi - jetB->phi);
   double deta = (jetA->eta - jetB->eta);
   if (dphi > pi) {dphi = twopi - dphi;}
 #else 
   //GPS+MC testing for 2015-02-faster-deltaR2
   double dphi = pi-std::abs(pi-std::abs(jetA->phi - jetB->phi));
   double deta = (jetA->eta - jetB->eta);
 #endif 
   return dphi*dphi + deta*deta;
 }
 
 //----------------------------------------------------------------------
 template <class J> inline double ClusterSequence::_bj_diJ(const J * const jet) const {
   double kt2 = jet->kt2;
   if (jet->NN != NULL) {if (jet->NN->kt2 < kt2) {kt2 = jet->NN->kt2;}}
   return jet->NN_dist * kt2;
 }
 
 
 //----------------------------------------------------------------------
 // set the NN for jet without checking whether in the process you might
 // have discovered a new nearest neighbour for another jet
 template <class J> inline void ClusterSequence::_bj_set_NN_nocross(
                  J * const jet, J * const head, const J * const tail) const {
   double NN_dist = _R2;
   J * NN  = NULL;
   if (head < jet) {
     for (J * jetB = head; jetB != jet; jetB++) {
       double dist = _bj_dist(jet,jetB);
       if (dist < NN_dist) {
     NN_dist = dist;
     NN = jetB;
       }
     }
   }
   if (tail > jet) {
     for (J * jetB = jet+1; jetB != tail; jetB++) {
       double dist = _bj_dist(jet,jetB);
       if (dist < NN_dist) {
     NN_dist = dist;
     NN = jetB;
       }
     }
   }
   jet->NN = NN;
   jet->NN_dist = NN_dist;
 }
 
 
 //----------------------------------------------------------------------
 template <class J> inline void ClusterSequence::_bj_set_NN_crosscheck(J * const jet, 
             J * const head, const J * const tail) const {
   double NN_dist = _R2;
   J * NN  = NULL;
   for (J * jetB = head; jetB != tail; jetB++) {
     double dist = _bj_dist(jet,jetB);
     if (dist < NN_dist) {
       NN_dist = dist;
       NN = jetB;
     }
     if (dist < jetB->NN_dist) {
       jetB->NN_dist = dist;
       jetB->NN = jet;
     }
   }
   jet->NN = NN;
   jet->NN_dist = NN_dist;
 }
 
 FASTJET_END_NAMESPACE
 
 #endif // __FASTJET_CLUSTERSEQUENCE_HH__

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