SiteTools.cpp

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//
// File SiteTools.cpp
// Author : Julien Dutheil
//          Guillaume Deuchst
// Created on: Friday August 8 2003
//

/*
   Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)

   This software is a computer program whose purpose is to provide classes
   for sequences 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
   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 "SiteTools.h"
#include "Alphabet/CodonAlphabet.h"
#include <Bpp/Utils/MapTools.h>
#include <Bpp/Numeric/NumTools.h>
#include <Bpp/Numeric/VectorTools.h>

using namespace bpp;

// From the STL:
#include <cmath>

using namespace std;

/******************************************************************************/

bool SiteTools::hasGap(const Site& site)
{
  // Main loop : for all characters in site
  for (size_t i = 0; i < site.size(); i++)
  {
    if (site.getAlphabet()->isGap(site[i]))
      return true;
  }
  return false;
}

/******************************************************************************/

bool SiteTools::isGapOnly(const Site& site)
{
  // Main loop : for all characters in site
  for (size_t i = 0; i < site.size(); i++)
  {
    if (!site.getAlphabet()->isGap(site[i]))
      return false;
  }
  return true;
}

/******************************************************************************/

bool SiteTools::isGapOrUnresolvedOnly(const Site& site)
{
  // Main loop : for all characters in site
  for (size_t i = 0; i < site.size(); i++)
  {
    if (!site.getAlphabet()->isGap(site[i]) && !site.getAlphabet()->isUnresolved(site[i]))
      return false;
  }
  return true;
}

/******************************************************************************/

bool SiteTools::hasUnknown(const Site& site)
{
  // Main loop : for all characters in site
  for (size_t i = 0; i < site.size(); i++)
  {
    if (site[i] == site.getAlphabet()->getUnknownCharacterCode())
      return true;
  }
  return false;
}

/******************************************************************************/

bool SiteTools::hasStopCodon(const Site& site)
{
  // Main loop : for all characters in site
  const CodonAlphabet* pca = dynamic_cast<const CodonAlphabet*>(site.getAlphabet());
  if (pca == 0)
    return false;
  for (size_t i = 0; i < site.size(); i++)
  {
    if (pca->isStop(site[i]))
      return true;
  }
  return false;
}

/******************************************************************************/

bool SiteTools::isComplete(const Site& site)
{
  // Main loop : for all characters in site
  for (size_t i = 0; i < site.size(); i++)
  {
    if (site.getAlphabet()->isGap(site[i]) || site.getAlphabet()->isUnresolved(site[i]))
      return false;
  }
  return true;
}

/******************************************************************************/

bool SiteTools::areSitesIdentical(const Site& site1, const Site& site2)
{
  // Site's size and content checking
  if (site1.getAlphabet()->getAlphabetType() != site2.getAlphabet()->getAlphabetType())
    return false;
  if (site1.size() != site2.size())
    return false;
  else
  {
    for (size_t i = 0; i < site1.size(); i++)
    {
      if (site1[i] != site2[i])
        return false;
    }
    return true;
  }
}

/******************************************************************************/

bool SiteTools::isConstant(const Site& site, bool ignoreUnknown, bool unresolvedRaisesException) throw (EmptySiteException)
{
  // Empty site checking
  if (site.size() == 0)
    throw EmptySiteException("SiteTools::isConstant: Incorrect specified site, size must be > 0", &site);

  // For all site's characters
  int gap = site.getAlphabet()->getGapCharacterCode();
  if (ignoreUnknown)
  {
    int s = site[0];
    int unknown = site.getAlphabet()->getUnknownCharacterCode();
    size_t i = 0;
    while (i < site.size() && (s == gap || s == unknown))
    {
      s = site[i];
      i++;
    }
    if (s == unknown || s == gap)
    {
      if (unresolvedRaisesException)
        throw EmptySiteException("SiteTools::isConstant: Site is only made of gaps or generic characters.");
      else
        return false;
    }
    while (i < site.size())
    {
      if (site[i] != s && site[i] != gap && site[i] != unknown)
        return false;
      i++;
    }
  }
  else
  {
    int s = site[0];
    size_t i = 0;
    while  (i < site.size() && s == gap)
    {
      s = site[i];
      i++;
    }
    if (s == gap)
    {
      if (unresolvedRaisesException)
        throw EmptySiteException("SiteTools::isConstant: Site is only made of gaps.");
      else
        return false;
    }
    while (i < site.size())
    {
      if (site[i] != s && site[i] != gap)
        return false;
      i++;
    }
  }

  return true;
}

/******************************************************************************/

double SiteTools::variabilityShannon(const Site& site, bool resolveUnknown) throw (EmptySiteException)
{
  // Empty site checking
  if (site.size() == 0)
    throw EmptySiteException("SiteTools::variabilityShannon: Incorrect specified site, size must be > 0", &site);
  map<int, double> p;
  getFrequencies(site, p, resolveUnknown);
  // We need to correct frequencies for gaps:
  double s = 0.;
  for (int i = 0; i < static_cast<int>(site.getAlphabet()->getSize()); i++)
  {
    double f = p[i];
    if (f > 0)
      s += f * log(f);
  }
  return -s;
}

/******************************************************************************/

double SiteTools::mutualInformation(const Site& site1, const Site& site2, bool resolveUnknown) throw (DimensionException, EmptySiteException)
{
  // Empty site checking
  if (site1.size() == 0)
    throw EmptySiteException("SiteTools::mutualInformation: Incorrect specified site, size must be > 0", &site1);
  if (site2.size() == 0)
    throw EmptySiteException("SiteTools::mutualInformation: Incorrect specified site, size must be > 0", &site2);
  if (site1.size() != site2.size())
    throw DimensionException("SiteTools::mutualInformation: sites must have the same size!", site1.size(), site2.size());
  vector<double> p1(site1.getAlphabet()->getSize());
  vector<double> p2(site2.getAlphabet()->getSize());
  map<int, map<int, double> > p12;
  getCounts(site1, site2, p12, resolveUnknown);
  double mi = 0, tot = 0, pxy;
  // We need to correct frequencies for gaps:
  for (size_t i = 0; i < site1.getAlphabet()->getSize(); i++)
  {
    for (size_t j = 0; j < site2.getAlphabet()->getSize(); j++)
    {
      pxy = p12[static_cast<int>(i)][static_cast<int>(j)];
      tot += pxy;
      p1[i] += pxy;
      p2[j] += pxy;
    }
  }
  for (size_t i = 0; i < site1.getAlphabet()->getSize(); i++)
  {
    p1[i] /= tot;
  }
  for (size_t j = 0; j < site2.getAlphabet()->getSize(); j++)
  {
    p2[j] /= tot;
  }
  for (size_t i = 0; i < site1.getAlphabet()->getSize(); i++)
  {
    for (size_t j = 0; j < site2.getAlphabet()->getSize(); j++)
    {
      pxy = p12[static_cast<int>(i)][static_cast<int>(j)] / tot;
      if (pxy > 0)
        mi += pxy * log(pxy / (p1[i] * p2[j]));
    }
  }
  return mi;
}

/******************************************************************************/

double SiteTools::jointEntropy(const Site& site1, const Site& site2, bool resolveUnknown) throw (DimensionException, EmptySiteException)
{
  // Empty site checking
  if (site1.size() == 0)
    throw EmptySiteException("SiteTools::jointEntropy: Incorrect specified site, size must be > 0", &site1);
  if (site2.size() == 0)
    throw EmptySiteException("SiteTools::jointEntropy: Incorrect specified site, size must be > 0", &site2);
  if (site1.size() != site2.size())
    throw DimensionException("SiteTools::jointEntropy: sites must have the same size!", site1.size(), site2.size());
  map<int, map<int, double> > p12;
  getCounts(site1, site2, p12, resolveUnknown);
  double tot = 0, pxy, h = 0;
  // We need to correct frequencies for gaps:
  for (size_t i = 0; i < site1.getAlphabet()->getSize(); i++)
  {
    for (size_t j = 0; j < site2.getAlphabet()->getSize(); j++)
    {
      pxy = p12[static_cast<int>(i)][static_cast<int>(j)];
      tot += pxy;
    }
  }
  for (size_t i = 0; i < site1.getAlphabet()->getSize(); i++)
  {
    for (size_t j = 0; j < site2.getAlphabet()->getSize(); j++)
    {
      pxy = p12[static_cast<int>(i)][static_cast<int>(j)] / tot;
      if (pxy > 0)
        h += pxy * log(pxy);
    }
  }
  return -h;
}

/******************************************************************************/

double SiteTools::variabilityFactorial(const Site& site) throw (EmptySiteException)
{
  // Empty site checking
  if (site.size() == 0)
    throw EmptySiteException("SiteTools::variabilityFactorial: Incorrect specified site, size must be > 0", &site);
  map<int, size_t> p;
  getCounts(site, p);
  vector<size_t> c = MapTools::getValues(p);
  size_t s = VectorTools::sum(c);
  long double l = static_cast<long double>(NumTools::fact(s)) / static_cast<long double>(VectorTools::sum(VectorTools::fact(c)));
  return (static_cast<double>(std::log(l)));
}

/******************************************************************************/

double SiteTools::heterozygosity(const Site& site) throw (EmptySiteException)
{
  // Empty site checking
  if (site.size() == 0)
    throw EmptySiteException("SiteTools::heterozygosity: Incorrect specified site, size must be > 0", &site);
  map<int, double> p;
  getFrequencies(site, p);
  vector<double> c = MapTools::getValues(p);
  double n = VectorTools::norm<double, double>(MapTools::getValues(p));
  return 1. - n * n;
}

/******************************************************************************/

size_t SiteTools::getNumberOfDistinctCharacters(const Site& site) throw (EmptySiteException)
{
  // Empty site checking
  if (site.size() == 0)
    throw EmptySiteException("SiteTools::getNumberOfDistinctCharacters(): Incorrect specified site, size must be > 0", &site);
  // For all site's characters
  if (SiteTools::isConstant(site))
    return 1;
  map<int, size_t> counts;
  SymbolListTools::getCounts(site, counts);
  int s = 0;
  for (map<int, size_t>::iterator it = counts.begin(); it != counts.end(); it++)
  {
    if (it->second != 0)
      s++;
  }
  return s;
}

/******************************************************************************/

bool SiteTools::hasSingleton(const Site& site) throw (EmptySiteException)
{
  // Empty site checking
  if (site.size() == 0)
    throw EmptySiteException("SiteTools::hasSingleton: Incorrect specified site, size must be > 0", &site);
  // For all site's characters
  if (SiteTools::isConstant(site))
    return false;
  map<int, size_t> counts;
  getCounts(site, counts);
  for (map<int, size_t>::iterator it = counts.begin(); it != counts.end(); it++)
  {
    if (it->second == 1)
      return true;
  }
  return false;
}

/******************************************************************************/

bool SiteTools::isParsimonyInformativeSite(const Site& site) throw (EmptySiteException)
{
  // Empty site checking
  if (site.size() == 0)
    throw EmptySiteException("SiteTools::isParsimonyInformativeSite: Incorrect specified site, size must be > 0", &site);
  // For all site's characters
  if (SiteTools::isConstant(site, false, false))
    return false;
  map<int, size_t> counts;
  SymbolListTools::getCounts(site, counts);
  size_t npars = 0;
  for (map<int, size_t>::iterator it = counts.begin(); it != counts.end(); it++)
  {
    if (it->second > 1)
      npars++;
  }
  if (npars > 1)
    return true;
  return false;
}

/******************************************************************************/

bool SiteTools::isTriplet(const Site& site) throw (EmptySiteException)
{
  // Empty site checking
  if (site.size() == 0)
    throw EmptySiteException("SiteTools::isTriplet: Incorrect specified site, size must be > 0", &site);
  // For all site's characters
  if (SiteTools::getNumberOfDistinctCharacters(site) >= 3)
    return true;
  else
    return false;
}

/******************************************************************************/