ParametrizableCollection.h

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//
// File: ParametrizableCollection.h
// Created by: Laurent Guéguen
// Created on: mercredi 12 juin 2013, à 14h 24
//

/*
  Copyright or (c) or Copr. Bio++ Development Team, (November 16, 2004)

  This software is a computer program whose purpose is to provide classes
  for phylogenetic data analysis.

  This software is governed by the CeCILL  license under French law and
  abiding by the rules of distribution of free software.  You can  use,
  modify and/ or redistribute the software under the terms of the CeCILL
  license as circulated by CEA, CNRS and INRIA at the following URL
  "http://www.cecill.info".

  As a counterpart to the access to the source code and  rights to copy,
  modify and redistribute granted by the license, users are provided only
  with a limited warranty  and the software's author,  the holder of the
  economic rights,  and the successive licensors  have only  limited
  liability.

  In this respect, the user's attention is drawn to the risks associated
  with loading,  using,  modifying and/or developing or reproducing the
  software by the user in light of its specific status of free software,
  that may mean  that it is complicated to manipulate,  and  that  also
  therefore means  that it is reserved for developers  and  experienced
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  The fact that you are presently reading this means that you have had
  knowledge of the CeCILL license and that you accept its terms.
*/

#ifndef _PARAMETRIZABLECOLLECTION_H_
#define _PARAMETRIZABLECOLLECTION_H_

#include "Parametrizable.h"
#include "AbstractParameterAliasable.h"

// From the STL:
#include <map>
#include <memory>

namespace bpp
{
  template <class N>
  class ParametrizableCollection :
    public AbstractParameterAliasable
  {
  protected:
    std::map<size_t, N* > objectsSet_;

    std::vector<size_t> vChanged_;
    
  public:
    ParametrizableCollection():
      AbstractParameterAliasable(""),
      objectsSet_(),
      vChanged_()
    {
    }

    ParametrizableCollection(const ParametrizableCollection<N>& set) :
      AbstractParameterAliasable(set),
      objectsSet_(),
      vChanged_(set.vChanged_)
    {
      // Duplicate all objects:
      typename std::map<size_t, N* >::const_iterator it;
      for (it=set.objectsSet_.begin(); it!=set.objectsSet_.end(); it++)
        objectsSet_[it->first]=it->second->clone();
    }

    ParametrizableCollection<N>& operator=(const ParametrizableCollection<N>& set)
    {
      clear();

      AbstractParameterAliasable::operator=(set);
      vChanged_ = set.vChanged_;
      
      // Duplicate all objects:
      typename std::map<size_t, N* >::const_iterator it;
      for (it=set.objectsSet_.begin(); it!=set.objectsSet_.end(); it++)
        objectsSet_[it->first]=it->second->clone();

      return *this;
    }

    void clear()
    {
      resetParameters_();
      
      typename std::map<size_t, N*>::const_iterator it;
      for (it=objectsSet_.begin(); it!=objectsSet_.end(); it++)
        delete it->second;
      objectsSet_.clear();
      vChanged_.empty();
    }

    ~ParametrizableCollection()
    {
      clear();
    }

    ParametrizableCollection<N>* clone() const { return new ParametrizableCollection<N>(*this); }

  public:
    void fireParameterChanged(const ParameterList& parameters)
    {
      vChanged_.clear();
      
      std::vector<size_t> vCh;

      std::map<size_t, ParameterList > mNumPl;
      
      for (size_t i=0; i<parameters.size(); i++)
        {
          std::string n=parameters[i].getName();
          size_t t=n.rfind("_");
          if (t==std::string::npos)
            continue;
          size_t num=(size_t)atoi(n.substr(t+1).c_str());
          mNumPl[num].addParameter(Parameter(n.substr(0,t),parameters[i].getValue()));
        }

      std::map<size_t, ParameterList >::iterator it;
      
      // Then we update all objects in the set:
      for (it=mNumPl.begin(); it!=mNumPl.end(); it++){
        if (hasObject(it->first) && objectsSet_[it->first]->matchParametersValues(it->second))
          vChanged_.push_back(it->first);
      }
    }

    std::vector<size_t> hasChanged() const
    {
      return vChanged_;
    }

    void clearChanged()
    {
      vChanged_.clear();
    }

    size_t getNumberOfObjects() const { return objectsSet_.size(); }

    const bool hasObject(size_t objectIndex) const
    {
      return (objectsSet_.find(objectIndex)!=objectsSet_.end());
    }

    const std::vector<size_t> keys() const
    {
      std::vector<size_t> vkeys;
      typename std::map<size_t, N*>::const_iterator it;

      for (it=objectsSet_.begin(); it!=objectsSet_.end(); it++)
        vkeys.push_back(it->first);
            
      return vkeys;
    }

  
    const N* operator[](size_t objectIndex) const
    {
      typename std::map<size_t, N*>::const_iterator it=objectsSet_.find(objectIndex);
      if (it==objectsSet_.end())
        throw BadIntegerException("ParametrizableCollection::getObject().", (int)objectIndex);
    
      return dynamic_cast<const N*>(it->second);
    }

    N* operator[](size_t objectIndex)
    {
      typename std::map<size_t, N*>::iterator it=objectsSet_.find(objectIndex);
      if (it==objectsSet_.end())
        throw BadIntegerException("ParametrizableCollection::getObject().", (int)objectIndex);
    
      return it->second;
    }
  
    void addObject(N* object, size_t objectIndex)
    {
      typename std::map<size_t, N*>::iterator it=objectsSet_.find(objectIndex);
      if (it!=objectsSet_.end())
        throw BadIntegerException("ParametrizableCollection<N>::addObject. Object objectIndex already used", (int)objectIndex);

      objectsSet_[objectIndex]=object;

      // Associate parameters:
      std::string pname;
      std::vector<std::string> nplm;
      nplm=object->getParameters().getParameterNames();

      for (size_t i  = 0; i < nplm.size(); i++)
        {
          pname = nplm[i];
          Parameter* p = new Parameter(object->getParameters().getParameter(pname));
          p->setName(pname + "_" + TextTools::toString(objectIndex));
          addParameter_(p);
        }

      if (dynamic_cast<ParameterAliasable*>(object)){
        ParameterAliasable* ppa=dynamic_cast<ParameterAliasable*>(object);
        for (size_t i  = 0; i < nplm.size(); i++)
          {
            std::vector<std::string> va=ppa->getAlias(nplm[i]);
            for (size_t j=0;j<va.size();j++)
              aliasParameters(nplm[i] + "_" + TextTools::toString(objectIndex), va[j] + "_" + TextTools::toString(objectIndex));
          }
      }
    }

    N* removeObject(size_t objectIndex)
    {
      if (objectsSet_.find(objectIndex)==objectsSet_.end())
        throw BadIntegerException("ParametrizableCollection<N>::removeObject. None Object at this objectIndex", (int)objectIndex);

      N* pm=objectsSet_[objectIndex];
      objectsSet_.erase(objectIndex);
      
      // Erase all parameter references to this object and translate other indices...
      
      ParameterList pl=getParameters();
      
      for (size_t i = pl.size(); i>0; i--)
        {
          std::string pn=pl[i-1].getName();
          
          size_t pu=pn.rfind("_");
          int nm=atoi(pn.substr(pu+1).c_str());
          if (nm==(int)objectIndex){
            std::vector<std::string> alpn=getAlias(pn);
            for (unsigned j=0; j<alpn.size(); j++)
              try {
                unaliasParameters(alpn[j],pn);
              }
              catch (Exception& e)
                {
                  continue;
                }
            deleteParameter_(i-1);
          }
        }
      
      return pm;
    }

    N* replaceObject(N* object, size_t objectIndex)
    {
      N* pm=removeObject(objectIndex);
      addObject(object, objectIndex);
      return pm;
    }


  };
} // end of namespace bpp.

#endif // _PARAMETRIZABLECOLLECTION_H_