ParametrizableCollection.h

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//
// File: ParametrizableCollection.h
// Authors:
//   Laurent Guéguen
// Created: 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
  professionals having in-depth computer knowledge. Users are therefore
  encouraged to load and test the software's suitability as regards their
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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 BPP_NUMERIC_PARAMETRIZABLECOLLECTION_H
#define BPP_NUMERIC_PARAMETRIZABLECOLLECTION_H
 
 
#include "AbstractParameterAliasable.h"
#include "Parametrizable.h"
 
// From the STL:
#include <map>
#include <memory>
 
namespace bpp
{
template<class N>
class ParametrizableCollection :
  public AbstractParameterAliasable
{
protected:
  std::map<size_t, std::shared_ptr<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:
 
    for (const auto& it:set.objectsSet_)
    {
      objectsSet_[it.first] = std::shared_ptr<N>(it.second->clone());
    }
  }
 
  ParametrizableCollection<N>& operator=(const ParametrizableCollection<N>& set)
  {
    clear();
 
    AbstractParameterAliasable::operator=(set);
    vChanged_ = set.vChanged_;
 
    // Duplicate all objects:
 
    for (const auto& it:set.objectsSet_)
    {
      objectsSet_[it.first] = std::shared_ptr<N>(it.second->clone());
    }
 
    return *this;
  }
 
  void clear()
  {
    resetParameters_();
 
    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(); }
 
  bool hasObject(size_t objectIndex) const
  {
    return objectsSet_.find(objectIndex) != objectsSet_.end();
  }
 
  bool hasObject(std::shared_ptr<N> object) const
  {
    for (const auto key : objectsSet_)
    {
      if (key.second == object)
        return true;
    }
    return false;
  }
 
  size_t getFirstKey(std::shared_ptr<N> object) const
  {
    for (const auto key:objectsSet_)
    {
      if (key.second == object)
        return key.first;
    }
 
    throw Exception("ParametrizableCollection::getFirstKey: Unknown object");
    return 0;
  }
 
  const std::vector<size_t> keys() const
  {
    std::vector<size_t> vkeys;
 
    for (const auto& it:objectsSet_)
    {
      vkeys.push_back(it.first);
    }
 
    return vkeys;
  }
 
  std::shared_ptr<const N> operator[](size_t objectIndex) const
  {
    const auto it = objectsSet_.find(objectIndex);
    if (it == objectsSet_.end())
      throw BadIntegerException("ParametrizableCollection::getObject().", (int)objectIndex);
 
    return std::dynamic_pointer_cast<const N>(it->second);
  }
 
  std::shared_ptr<N> operator[](size_t objectIndex)
  {
    auto it = objectsSet_.find(objectIndex);
    if (it == objectsSet_.end())
      throw BadIntegerException("ParametrizableCollection::getObject().", (int)objectIndex);
 
    return it->second;
  }
 
  ParameterList getParametersForObject(size_t objectIndex) const
  {
    ParameterList pl;
    const auto it = objectsSet_.find(objectIndex);
 
    if (it != objectsSet_.end())
    {
      if (std::dynamic_pointer_cast<const ParameterAliasable>(it->second) != NULL)
        pl = std::dynamic_pointer_cast<const ParameterAliasable>(it->second)->getIndependentParameters();
      else
        pl = it->second->getParameters();
 
      for (size_t i = 0; i < pl.size(); i++)
      {
        pl[i].setName(pl[i].getName() + "_" + TextTools::toString(objectIndex));
      }
    }
    return pl;
  }
 
  void addObject(std::shared_ptr<N> object, size_t objectIndex)
  {
    auto 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::vector<std::string> nplm;
    nplm = object->getParameters().getParameterNames();
 
    for (const auto& pname:nplm)
    {
      Parameter* p = new Parameter(object->getParameters().getParameter(pname));
      p->setName(pname + "_" + TextTools::toString(objectIndex));
      addParameter_(p);
    }
 
    if (std::dynamic_pointer_cast<ParameterAliasable>(object))
    {
      auto ppa = std::dynamic_pointer_cast<ParameterAliasable>(object);
      for (const auto& name:nplm)
      {
        std::vector<std::string> va = ppa->getAlias(name);
        for (const auto& alias:va)
        {
          aliasParameters(name + "_" + TextTools::toString(objectIndex), alias + "_" + TextTools::toString(objectIndex));
        }
      }
    }
  }
 
  std::shared_ptr<N> removeObject(size_t objectIndex)
  {
    if (objectsSet_.find(objectIndex) == objectsSet_.end())
      throw BadIntegerException("ParametrizableCollection<N>::removeObject. None Object at this objectIndex", (int)objectIndex);
 
    auto 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;
  }
 
  std::shared_ptr<N> replaceObject(std::shared_ptr<N> object, size_t objectIndex)
  {
    auto pm = removeObject(objectIndex);
    addObject(object, objectIndex);
    return pm;
  }
};
} // end of namespace bpp.
#endif // BPP_NUMERIC_PARAMETRIZABLECOLLECTION_H