ParameterList.cpp

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//
// File: ParameterList.cpp
// Authors:
//   Julien Dutheil
// Created: 2003-10-15 18:17:29
//
 
/*
  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.
  
  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
  requirements in conditions enabling the security of their systems and/or
  data to be ensured and, more generally, to use and operate it in the
  same conditions as regards security.
  
  The fact that you are presently reading this means that you have had
  knowledge of the CeCILL license and that you accept its terms.
*/
 
 
#include "../Text/StringTokenizer.h"
#include "ParameterList.h"
 
using namespace bpp;
 
#include <iostream>
#include <algorithm>
using namespace std;
 
ParameterList::ParameterList(const ParameterList& pl) :
  parameters_(pl.size())
{
  // Now copy all parameters:
  for (size_t i = 0; i < size(); i++)
  {
    parameters_[i] = shared_ptr<Parameter>(pl.parameters_[i]->clone());
  }
}
 
ParameterList& ParameterList::operator=(const ParameterList& pl)
{
  // Then resize the vector:
  parameters_.resize(pl.size());
 
  // Now copy all parameters:
  for (size_t i = 0; i < pl.size(); i++)
  {
    parameters_[i] = shared_ptr<Parameter>(pl.parameters_[i]->clone());
  }
 
  return *this;
}
 
ParameterList::~ParameterList()
{
  // Delete all parameter objects.
  reset();
}
 
/******************************************************************************/
 
const Parameter& ParameterList::getParameter(const std::string& name) const
{
  for (size_t i = 0; i < size(); i++)
  {
    const Parameter* p = parameters_[i].get();
    if (p->getName() == name)
      return *p;
  }
  throw ParameterNotFoundException("ParameterList::getParameter('name').", name);
}
 
/******************************************************************************/
 
const shared_ptr<Parameter>& ParameterList::getSharedParameter(const std::string& name) const
{
  for (size_t i = 0; i < size(); i++)
  {
    const shared_ptr<Parameter>& p = parameters_[i];
    if (p->getName() == name)
      return p;
  }
  throw ParameterNotFoundException("ParameterList::getSharedParameter('name').", name);
}
 
 
/******************************************************************************/
 
double ParameterList::getParameterValue(const std::string& name) const
{
  for (size_t i = 0; i < size(); i++)
  {
    const Parameter* p = parameters_[i].get();
    if (p->getName() == name)
      return p->getValue();
  }
  throw ParameterNotFoundException("ParameterList::getParameterValue('name').", name);
}
 
/******************************************************************************/
 
Parameter& ParameterList::getParameter(const std::string& name)
{
  for (size_t i = 0; i < size(); i++)
  {
    Parameter* p = parameters_[i].get();
    if (p->getName() == name)
      return *p;
  }
  throw ParameterNotFoundException("ParameterList::getParameter('name').", name);
}
 
/******************************************************************************/
 
shared_ptr<Parameter>& ParameterList::getSharedParameter(const std::string& name)
{
  for (size_t i = 0; i < size(); i++)
  {
    shared_ptr<Parameter>& p = parameters_[i];
    if (p->getName() == name)
      return p;
  }
  throw ParameterNotFoundException("ParameterList::getSharedParameter('name').", name);
}
 
 
/******************************************************************************/
 
ParameterList ParameterList::createSubList(const std::vector<std::string>& names) const
{
  ParameterList pl;
  for (size_t i = 0; i < names.size(); i++)
  {
    Parameter param = getParameter(names[i]);
    pl.addParameter(param);
  }
  return pl;
}
 
/******************************************************************************/
 
ParameterList ParameterList::shareSubList(const std::vector<std::string>& names) const
{
  ParameterList pl;
  for (const auto& name:names)
  {
    pl.shareParameter(getSharedParameter(name));
  }
 
  return pl;
}
 
/******************************************************************************/
 
ParameterList ParameterList::createSubList(const std::string& name) const
{
  ParameterList pl;
  Parameter param = getParameter(name);
  pl.addParameter(param);
  return pl;
}
 
/******************************************************************************/
 
ParameterList ParameterList::createSubList(const std::vector<size_t>& parameters) const
{
  ParameterList pl;
  for (auto iparam : parameters)
  {
    if (iparam < size())
      pl.parameters_.push_back(shared_ptr<Parameter>(parameters_[iparam]->clone()));
  }
  return pl;
}
 
/******************************************************************************/
 
ParameterList ParameterList::shareSubList(const std::vector<size_t>& parameters) const
{
  ParameterList pl;
  for (auto iparam : parameters)
  {
    if (iparam < size())
      pl.shareParameter(parameters_[iparam]);
  }
 
  return pl;
}
 
/******************************************************************************/
 
ParameterList ParameterList::createSubList(size_t parameter) const
{
  ParameterList pl;
  if (parameter < size())
    pl.parameters_.push_back(shared_ptr<Parameter>(parameters_[parameter]->clone()));
  return pl;
}
 
/******************************************************************************/
 
ParameterList ParameterList::getCommonParametersWith(const ParameterList& params) const
{
  ParameterList pl;
  for (size_t i = 0; i < params.size(); i++)
  {
    const Parameter& p = params[i];
    if (hasParameter(p.getName()))
      pl.parameters_.push_back(shared_ptr<Parameter>(p.clone()));
    // We use push_back instead of addParameter because we are sure the name is not duplicated.
  }
 
  return pl;
}
 
/******************************************************************************/
 
std::vector<std::string> ParameterList::getParameterNames() const
{
  vector<string> pNames(size());
  for (size_t i = 0; i < size(); i++)
  {
    pNames[i] = parameters_[i]->getName();
  }
  return pNames;
}
 
/****************************************************************************/
 
vector<string> ParameterList::getMatchingParameterNames(const string& pattern) const
{
  vector<string> pNames;
  for (size_t i = 0; i < size(); i++)
  {
    string name = parameters_[i]->getName();
 
    StringTokenizer stj(pattern, "*", true, false);
    size_t pos1, pos2;
    bool flag(true);
    string g = stj.nextToken();
    pos1 = name.find(g);
    if (pos1 != 0)
      flag = false;
    pos1 += g.length();
    while (flag && stj.hasMoreToken())
    {
      g = stj.nextToken();
      pos2 = name.find(g, pos1);
      if (pos2 == string::npos)
      {
        flag = false;
        break;
      }
      pos1 = pos2 + g.length();
    }
    if (flag &&
        ((g.length() == 0) || (pos1 == name.length()) || (name.rfind(g) == name.length() - g.length())))
      pNames.push_back(name);
  }
 
  return pNames;
}
 
/******************************************************************************/
 
void ParameterList::addParameter(const Parameter& param)
{
  if (hasParameter(param.getName()))
    throw ParameterException("ParameterList::addParameter. Parameter with name '" + param.getName() + "' already exists.", &param);
  parameters_.push_back(shared_ptr<Parameter>(param.clone()));
}
 
/******************************************************************************/
 
void ParameterList::addParameter(Parameter* param)
{
  if (hasParameter(param->getName()))
    throw ParameterException("ParameterList::addParameter. Parameter with name '" + param->getName() + "' already exists.", param);
  parameters_.push_back(shared_ptr<Parameter>(param));
}
 
/******************************************************************************/
 
void ParameterList::shareParameter(const std::shared_ptr<Parameter>& param)
{
  if (hasParameter(param->getName()))
    setParameterValue(param->getName(), param->getValue());
  else
    parameters_.push_back(param);
}
 
 
/******************************************************************************/
 
void ParameterList::setParameter(size_t index, const Parameter& param)
{
  if (index >= size())
    throw IndexOutOfBoundsException("ParameterList::setParameter.", index, 0, size());
  parameters_[index] = shared_ptr<Parameter>(param.clone());
}
 
 
/******************************************************************************/
 
void ParameterList::includeParameters(const ParameterList& params)
{
  for (size_t i = 0; i < params.size(); i++)
  {
    if (hasParameter(params[i].getName()))
      setParameterValue(params[i].getName(), params[i].getValue());
    else
      parameters_.push_back(shared_ptr<Parameter>(params[i].clone()));
  }
}
 
/******************************************************************************/
 
void ParameterList::addParameters(const ParameterList& params)
{
  for (size_t i = 0; i < params.size(); i++)
  {
    addParameter(params[i]);
  }
}
 
/******************************************************************************/
 
void ParameterList::shareParameters(const ParameterList& params)
{
  for (size_t i = 0; i < params.size(); i++)
  {
    shareParameter(params.getSharedParameter(i));
  }
}
 
/******************************************************************************/
 
void ParameterList::setParameterValue(const string& name, double value)
{
  Parameter* p = &getParameter(name);
  p->setValue(value);
}
 
/******************************************************************************/
 
void ParameterList::setAllParametersValues(const ParameterList& params)
{
  // First we check if all values are correct:
  for (vector<shared_ptr<Parameter> >::iterator it = parameters_.begin(); it < parameters_.end(); it++)
  {
    const Parameter* p = &params.getParameter((*it)->getName());
    if ((*it)->hasConstraint() && !(*it)->getConstraint()->isCorrect(p->getValue()))
      throw ConstraintException("ParameterList::setParametersValues()", (*it).get(), p->getValue());
  }
 
  // If all values are ok, we set them:
  for (vector<shared_ptr<Parameter> >::iterator it = parameters_.begin(); it < parameters_.end(); it++)
  {
    const Parameter* p = &params.getParameter((*it)->getName());
    (*it)->setValue(p->getValue());
  }
}
 
/******************************************************************************/
 
void ParameterList::setParametersValues(const ParameterList& params)
{
  // First we check if all values are correct:
  for (vector<shared_ptr<Parameter> >::const_iterator it = params.parameters_.begin(); it < params.parameters_.end(); it++)
  {
    if (hasParameter((*it)->getName()))
    {
      Parameter* p = &getParameter((*it)->getName());
      if (p->hasConstraint() && !p->getConstraint()->isCorrect((*it)->getValue()))
        throw ConstraintException("ParameterList::setParametersValues()", p, (*it)->getValue());
    }
  }
 
  // If all values are ok, we set them:
  {
    for (vector<shared_ptr<Parameter> >::const_iterator it = params.parameters_.begin(); it < params.parameters_.end(); it++)
    {
      if (hasParameter((*it)->getName()))
      {
        Parameter* p = &getParameter((*it)->getName());
        p->setValue((*it)->getValue());
      }
    }
  }
}
 
/******************************************************************************/
 
bool ParameterList::testParametersValues(const ParameterList& params) const
{
  // First we check if all values are correct:
  for (vector<shared_ptr<Parameter> >::const_iterator it = params.parameters_.begin(); it < params.parameters_.end(); it++)
  {
    if (hasParameter((*it)->getName()))
    {
      const Parameter* p = &getParameter((*it)->getName());
      if (p->hasConstraint() && !p->getConstraint()->isCorrect((*it)->getValue()))
        throw ConstraintException("ParameterList::testParametersValues()", p, (*it)->getValue());
    }
  }
 
  // If all values are ok, we test them:
  bool ch = 0;
 
  for (vector<shared_ptr<Parameter> >::const_iterator it = params.parameters_.begin(); it < params.parameters_.end(); it++)
  {
    if (hasParameter((*it)->getName()))
    {
      const Parameter* p = &getParameter((*it)->getName());
      if (p->getValue() != (*it)->getValue())
        ch |= 1;
    }
  }
  return ch;
}
 
/******************************************************************************/
 
bool ParameterList::matchParametersValues(const ParameterList& params, vector<size_t>* updatedParameters)
{
  // First we check if all values are correct:
  for (vector<shared_ptr<Parameter> >::const_iterator it = params.parameters_.begin(); it < params.parameters_.end(); it++)
  {
    if (hasParameter((*it)->getName()))
    {
      Parameter* p = &getParameter((*it)->getName());
      if (p->hasConstraint() && !p->getConstraint()->isCorrect((*it)->getValue()))
        throw ConstraintException("ParameterList::matchParametersValues()", p, (*it)->getValue());
    }
  }
 
  // If all values are ok, we set them:
  bool ch = 0;
 
  size_t pos = 0;
  for (vector<shared_ptr<Parameter> >::const_iterator it = params.parameters_.begin(); it < params.parameters_.end(); it++)
  {
    if (hasParameter((*it)->getName()))
    {
      Parameter* p = &getParameter((*it)->getName());
      if (p->getValue() != (*it)->getValue())
      {
        ch |= 1;
        p->setValue((*it)->getValue());
        if (updatedParameters)
          updatedParameters->push_back(pos);
      }
    }
    pos++;
  }
  return ch;
}
 
/******************************************************************************/
void ParameterList::setAllParameters(const ParameterList& params)
{
  for (vector<shared_ptr<Parameter> >::iterator it = parameters_.begin(); it < parameters_.end(); it++)
  {
    const Parameter* p = &params.getParameter((*it)->getName());
    **it = *p;
  }
}
 
/******************************************************************************/
void ParameterList::setParameters(const ParameterList& params)
{
  for (vector<shared_ptr<Parameter> >::const_iterator it = params.parameters_.begin(); it < params.parameters_.end(); it++)
  {
    Parameter* p = &getParameter((*it)->getName());
    *p = **it;
  }
}
 
/******************************************************************************/
bool ParameterList::hasParameter(const std::string& name) const
{
  for (unsigned int i = 0; i < size(); i++)
  {
    const Parameter* p = parameters_[i].get();
    if (p->getName() == name)
      return true;
  }
  return false;
}
 
/******************************************************************************/
void ParameterList::matchParameters(const ParameterList& params)
{
  for (vector<shared_ptr<Parameter> >::const_iterator it = params.parameters_.begin(); it < params.parameters_.end(); it++)
  {
    if (hasParameter((*it)->getName()))
    {
      Parameter* p = &getParameter((*it)->getName());
      *p = **it;
    }
  }
}
 
/******************************************************************************/
void ParameterList::deleteParameter(const std::string& name)
{
  for (auto it = parameters_.begin(); it != parameters_.end(); ++it)
  {
    if ((*it)->getName() == name)
    {
      it = parameters_.erase(it);
      return;
    }
  }
  throw ParameterNotFoundException("ParameterList::deleteParameter", name);
}
 
/******************************************************************************/
void ParameterList::deleteParameters(const std::vector<std::string>& names, bool mustExist)
{
  for (auto it = names.begin(); it != names.end(); ++it)
  {
    try
    {
      deleteParameter(*it);
    }
    catch (ParameterNotFoundException& e)
    {
      if (mustExist)
        throw ParameterNotFoundException(e);
      else
        continue;
    }
  }
}
 
/******************************************************************************/
void ParameterList::deleteParameter(size_t index)
{
  if (index >= size())
    throw IndexOutOfBoundsException("ParameterList::deleteParameter.", index, 0, size());
  parameters_.erase(parameters_.begin() + static_cast<ptrdiff_t>(index));
}
 
/******************************************************************************/
void ParameterList::deleteParameters(const std::vector<size_t>& indices)
{
  vector<size_t> tmp(indices);
  sort(tmp.begin(), tmp.end());
  for (vector<size_t>::reverse_iterator i = tmp.rbegin(); i != tmp.rend(); i++)
  {
    size_t index = *i;
    if (index >= size())
      throw IndexOutOfBoundsException("ParameterList::deleteParameter.", index, 0, size());
//    Parameter* p = parameters_[index].get();
//    delete p;
    parameters_.erase(parameters_.begin() + static_cast<ptrdiff_t>(index));
  }
}
 
/******************************************************************************/
size_t ParameterList::whichParameterHasName(const std::string& name) const
{
  for (size_t i = 0; i < size(); i++)
  {
    if (parameters_[i]->getName() == name)
      return i;
  }
  throw ParameterNotFoundException("ParameterList::whichParameterHasName.", name);
}
 
/******************************************************************************/
void ParameterList::printParameters(OutputStream& out) const
{
  (out << "Name:\tValue:\tConstraint:").endLine();
  (out << "_________________________________________________").endLine();
  for (unsigned int i = 0; i < size(); i++)
  {
    out << parameters_[i]->getName();
    out << "\t" << parameters_[i]->getValue();
    out << (parameters_[i]->hasConstraint() ? "\t" + parameters_[i]->getConstraint()->getDescription() : string(""));
    out.endLine();
  }
}
 
/******************************************************************************/
void ParameterList::reset()
{
  parameters_.resize(0);
}
 
/******************************************************************************/