AbstractParameterAliasable.cpp

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//
// File: AbstractParameterAliasable.cpp
// Authors:
//   Julien Dutheil
// Created: 2009-03-29 09:10:00
//
 
/*
  Copyright or © or Copr. Bio++ Development Team, (November 19, 2004)
  
  This software is a computer program whose purpose is to provide classes
  for numerical calculus.
  
  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.
  
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  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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  knowledge of the CeCILL license and that you accept its terms.
*/
 
 
#include "AbstractParameterAliasable.h"
#include "VectorTools.h"
 
using namespace bpp;
using namespace std;
 
AbstractParameterAliasable::AbstractParameterAliasable(const AbstractParameterAliasable& ap) :
  AbstractParametrizable(ap),
  independentParameters_(),
  aliasListenersRegister_()
{
  for (size_t i = 0; i < ap.independentParameters_.size(); i++)
  {
    independentParameters_.shareParameter(getSharedParameter(getParameterNameWithoutNamespace(ap.independentParameters_[i].getName())));
  }
 
  // Actualize the register with adequate pointers:
  for (map<string, AliasParameterListener*>::const_iterator it = ap.aliasListenersRegister_.begin();
       it != ap.aliasListenersRegister_.end();
       it++)
  {
    AliasParameterListener* listener = it->second->clone();
    listener->setParameterList(&getParameters_());
    aliasListenersRegister_[it->first] = listener;
    // Now correct parameters with appropriate pointers:
    for (unsigned int i = 0; i < getNumberOfParameters(); ++i)
    {
      if (getParameters_()[i].hasParameterListener(it->first))
      {
        getParameters_()[i].removeParameterListener(it->first);
        getParameters_()[i].addParameterListener(listener, false);
      }
    }
  }
}
 
AbstractParameterAliasable& AbstractParameterAliasable::operator=(const AbstractParameterAliasable& ap)
{
  AbstractParametrizable::operator=(ap);
 
  for (size_t i = 0; i < ap.independentParameters_.size(); i++)
  {
    independentParameters_.shareParameter(getSharedParameter(getParameterNameWithoutNamespace(ap.independentParameters_[i].getName())));
  }
 
  // Actualize the register with adequate pointers:
  for (map<string, AliasParameterListener*>::const_iterator it = ap.aliasListenersRegister_.begin();
       it != ap.aliasListenersRegister_.end();
       it++)
  {
    AliasParameterListener* listener = it->second->clone();
    listener->setParameterList(&getParameters_());
    aliasListenersRegister_[it->first] = listener;
    // Now correct parameters with appropriate pointers:
    for (unsigned int i = 0; i < getNumberOfParameters(); ++i)
    {
      if (getParameters_()[i].hasParameterListener(it->first))
      {
        getParameters_()[i].removeParameterListener(it->first);
        getParameters_()[i].addParameterListener(listener, false);
      }
    }
  }
  return *this;
}
 
AbstractParameterAliasable::~AbstractParameterAliasable()
{
  // Delete the registry content:
  for (map<string, AliasParameterListener*>::iterator it = aliasListenersRegister_.begin();
       it != aliasListenersRegister_.end();
       it++)
  {
    delete it->second;
  }
}
 
void AbstractParameterAliasable::aliasParameters(const std::string& p1, const std::string& p2)
{
  // In case this is the first time we call this method:
  if (getNumberOfParameters() > 0 && independentParameters_.size() == 0)
    independentParameters_.shareParameters(getParameters());
 
  if (!hasParameter(p1))
    throw ParameterNotFoundException("AbstractParameterAliasable::aliasParameters", p1);
  if (!hasParameter(p2))
    throw ParameterNotFoundException("AbstractParameterAliasable::aliasParameters", p2);
  if (!independentParameters_.hasParameter(getNamespace() + p2))
    throw Exception("AbstractParameterAliasable::aliasParameters. Parameter " + p2 + " does not exist in independent parameters. Perhaps it is already aliased to a parameter and can't be aliased twice.");
 
  string id = "__alias_" + p2 + "_to_" + p1;
  string idCheck = "__alias_" + p1 + "_to_" + p2;
 
  if (aliasListenersRegister_.find(idCheck) != aliasListenersRegister_.end())
    throw Exception("AbstractParameterAliasable::aliasParameters. Trying to alias parameter " + p2 + " to " + p1 + ", but parameter " + p1 + " is already aliased to parameter " + p2 + ".");
  Parameter* param1 = &getParameter_(p1);
  Parameter* param2 = &getParameter_(p2);
 
  if (!param1->hasConstraint())
  {
    if (param2->hasConstraint())
    {
      ApplicationTools::displayWarning("Aliasing parameter " + p2 + " to " + p1 + ". " + p1 + " gets the constraints of " + p2 + ": " + param2->getConstraint()->getDescription());
      param1->setConstraint(param2->getConstraint());
    }
  }
  else
  // We use a small trick here, we test the constraints on the basis of their string description (C++ does not provide a default operator==() :( ).
  if (param2->hasConstraint() && (param1->getConstraint()->getDescription() != param2->getConstraint()->getDescription()))
  {
    std::shared_ptr<Constraint> nc(*param2->getConstraint() & *param1->getConstraint());
    ApplicationTools::displayWarning("Aliasing parameter " + p2 + " to " + p1 + " with different constraints. They get the intersection of both constraints : " + nc->getDescription());
 
    param2->setConstraint(nc);
    param1->setConstraint(nc);
  }
 
  // Every thing seems ok, let's create the listener and register it:
 
  AliasParameterListener* aliasListener = new AliasParameterListener(id, getParameters().whichParameterHasName(getNamespace() + p2), &getParameters_(), p1);
 
  aliasListenersRegister_[id] = aliasListener;
 
  // Now we add it to the appropriate parameter, that is p1.
  // The parameter will not own the listener, the bookkeeping being achieved by the register:
  param1->addParameterListener(aliasListener, false);
 
  // Finally we remove p2 from the list of independent parameters:
  independentParameters_.deleteParameter(getNamespace() + p2);
}
 
void AbstractParameterAliasable::aliasParameters(map<string, string>& unparsedParams, bool verbose)
{
  const ParameterList& pl = getParameters();
  ParameterList plpars;
 
  for (size_t i = 0; i < pl.size(); i++)
  {
    if (unparsedParams.find(pl[i].getName()) == unparsedParams.end())
      plpars.addParameter(pl[i].clone());
  }
 
  size_t unp_s = unparsedParams.size();
  while (unp_s != 0)
  {
    auto it = unparsedParams.begin();
    while (it != unparsedParams.end())
    {
      Parameter* pp = 0;
      try
      {
        pp = &plpars.getParameter(it->second);
      }
      catch (ParameterNotFoundException& e)
      {
        if (!pl.hasParameter(it->second))
          throw ParameterNotFoundException("Unknown aliasing parameter", it->first + "->" + it->second);
        continue;
      }
      unique_ptr<Parameter> p2(pp->clone());
      p2->setName(it->first);
      plpars.addParameter(p2.release());
      plpars.getParameter(it->first);
      aliasParameters(it->second, it->first);
      if (verbose)
        ApplicationTools::displayResult("Parameter alias found", it->first + " -> " + it->second + " = " + TextTools::toString(pp->getValue()));
      it = unparsedParams.erase(it);
    }
 
    if (unparsedParams.size() == unp_s)
      throw Exception("Error, there is a cycle in aliasing starting with " + unparsedParams.begin()->first);
    else
      unp_s = unparsedParams.size();
  }
 
  matchParametersValues(plpars);
}
 
 
void AbstractParameterAliasable::unaliasParameters(const std::string& p1, const std::string& p2)
{
  if (!hasParameter(p1))
    throw ParameterNotFoundException("AbstractParameterAliasable::unaliasParameters", p1);
  if (!hasParameter(p2))
    throw ParameterNotFoundException("AbstractParameterAliasable::unaliasParameters", p2);
 
  string id = "__alias_" + p2 + "_to_" + p1;
  map<string, AliasParameterListener*>::iterator it = aliasListenersRegister_.find(id);
  if (it == aliasListenersRegister_.end())
    throw Exception("AbstractParameterAliasable::unaliasParameters. Parameter " + p2 + " is not aliased to parameter " + p1 + ".");
  // Remove the listener:
  getParameter_(p1).removeParameterListener(id);
  delete it->second;
  aliasListenersRegister_.erase(it);
  // Finally we re-add p2 to the list of independent parameters:
  independentParameters_.shareParameter(getSharedParameter(p2));
}
 
void AbstractParameterAliasable::setNamespace(const std::string& prefix)
{
  string currentName;
 
  // We modify all the listeners
  for (map<string, AliasParameterListener*>::iterator it = aliasListenersRegister_.begin();
       it != aliasListenersRegister_.end();
       it++)
  {
    currentName = it->second->getName();
    if (TextTools::startsWith(currentName, getNamespace()))
      it->second->rename(prefix + currentName.substr(getNamespace().size()));
    else
      it->second->rename(prefix + currentName);
  }
 
// Finally we notify the mother class:
  AbstractParametrizable::setNamespace(prefix);
}
 
vector<string> AbstractParameterAliasable::getAlias(const string& name) const
{
  vector<string> aliases;
 
  for (map<string, AliasParameterListener*>::const_iterator it = aliasListenersRegister_.begin();
       it != aliasListenersRegister_.end();
       it++)
  {
    if (it->second->getFrom() == name)
    {
      string alias = it->second->getAlias();
      aliases.push_back(alias);
      if (alias != name)
      {
        vector<string> chainAliases = getAlias(alias);
        VectorTools::append(aliases, chainAliases);
      }
    }
  }
  return aliases;
}
 
 
std::map<std::string, std::string> AbstractParameterAliasable::getAliases() const
{
  map<string, string> aliases;
 
  for (map<string, AliasParameterListener*>::const_iterator it = aliasListenersRegister_.begin();
       it != aliasListenersRegister_.end();
       it++)
  {
    string name = it->second->getFrom();
 
    vector<string> alias = getAlias(name);
 
    for (size_t i = 0; i < alias.size(); i++)
    {
      aliases[alias[i]] = name;
    }
  }
 
  return aliases;
}
 
ParameterList AbstractParameterAliasable::getAliasedParameters(const ParameterList& pl) const
{
  ParameterList aliases;
  bool b = false;
 
  for (map<string, AliasParameterListener*>::const_iterator it = aliasListenersRegister_.begin();
       it != aliasListenersRegister_.end();
       it++)
  {
    if ((pl.hasParameter(it->second->getFrom()) ||
         aliases.hasParameter(it->second->getFrom()))
        && !(aliases.hasParameter(it->second->getAlias()) ||
             pl.hasParameter(it->second->getAlias())))
    {
      b = true;
      aliases.addParameter(getParameter(it->second->getAlias()));
    }
  }
 
  while (b)
  {
    b = false;
 
    for (map<string, AliasParameterListener*>::const_iterator it = aliasListenersRegister_.begin();
         it != aliasListenersRegister_.end();
         it++)
    {
      if (aliases.hasParameter(it->second->getFrom())
          && !(aliases.hasParameter(it->second->getAlias()) ||
               pl.hasParameter(it->second->getAlias())))
      {
        b = true;
        aliases.addParameter(getParameter(it->second->getAlias()));
      }
    }
  }
 
  return aliases;
}
 
string AbstractParameterAliasable::getFrom(const string& name) const
{
  string from = "";
 
  for (map<string, AliasParameterListener*>::const_iterator it = aliasListenersRegister_.begin();
       it != aliasListenersRegister_.end();
       it++)
  {
    if (it->second->getName() == name)
    {
      from = it->second->getFrom();
      break;
    }
  }
 
  return from;
}
 
 
ParameterList AbstractParameterAliasable::getFromParameters(const ParameterList& pl) const
{
  ParameterList from;
  bool b = false;
 
  for (map<string, AliasParameterListener*>::const_iterator it = aliasListenersRegister_.begin();
       it != aliasListenersRegister_.end();
       it++)
  {
    if ((pl.hasParameter(it->second->getAlias()) ||
         from.hasParameter(it->second->getAlias()))
        && !(from.hasParameter(it->second->getFrom()) ||
             pl.hasParameter(it->second->getFrom())))
    {
      b = true;
      from.addParameter(getParameter(it->second->getFrom()));
    }
  }
 
  while (b)
  {
    b = false;
 
    for (map<string, AliasParameterListener*>::const_iterator it = aliasListenersRegister_.begin();
         it != aliasListenersRegister_.end();
         it++)
    {
      if (from.hasParameter(it->second->getAlias())
          && !(from.hasParameter(it->second->getFrom()) ||
               pl.hasParameter(it->second->getFrom())))
      {
        b = true;
        from.addParameter(getParameter(it->second->getFrom()));
      }
    }
  }
 
  return from;
}