PolymorphismSequenceContainerTools.cpp

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//
// File: PolymorphismSequenceContainerTools.cpp
// Authors: Eric Bazin
//          Sylvain Gaillard
// Created on: Thursday July 29 2004
//

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

   This software is a computer program whose purpose is to provide classes
   for population genetics 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 "PolymorphismSequenceContainerTools.h"

using namespace bpp;
using namespace std;

PolymorphismSequenceContainerTools::~PolymorphismSequenceContainerTools() {}

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

PolymorphismSequenceContainer* PolymorphismSequenceContainerTools::read(const std::string& path, const Alphabet* alpha) throw (Exception)
{
  Mase ms;
  string key;
  const OrderedSequenceContainer* seqc = 0;
  try
  {
    seqc = dynamic_cast<OrderedSequenceContainer*>(ms.readSequences(path, alpha ));
  }
  catch (Exception& e)
  {
    if (seqc != 0)
      delete seqc;
    throw e;
  }
  PolymorphismSequenceContainer* psc = new PolymorphismSequenceContainer(*seqc);
  Comments maseFileHeader = seqc->getGeneralComments();
  delete seqc;
  map<string, size_t> groupMap = MaseTools::getAvailableSequenceSelections(maseFileHeader);
  for (map<string, size_t>::iterator mi = groupMap.begin(); mi != groupMap.end(); mi++)
  {
    key = mi->first;
    if (key.compare(0, 8, "OUTGROUP") == 0)
    {
      SequenceSelection ss;
      try
      {
        ss = MaseTools::getSequenceSet(maseFileHeader, key);
      }
      catch (IOException& ioe)
      {
        delete psc;
        throw ioe;
      }
      for (size_t i = 0; i != ss.size(); i++)
      {
        try
        {
          psc->setAsOutgroupMember(ss[i]);
        }
        catch (SequenceNotFoundException& snfe)
        {
          delete psc;
          throw snfe;
        }
      }
    }
  }
  return psc;
}

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

PolymorphismSequenceContainer* PolymorphismSequenceContainerTools::extractIngroup (const PolymorphismSequenceContainer& psc) throw (Exception)
{
  SequenceSelection ss;
  PolymorphismSequenceContainer* psci = dynamic_cast<PolymorphismSequenceContainer*>(psc.clone());
  for (size_t i = 0; i < psc.getNumberOfSequences(); i++)
  {
    if (!psc.isIngroupMember(i))
      ss.push_back(i);
  }
  if (ss.size() == psc.getNumberOfSequences())
  {
    delete psci;
    throw Exception("PolymorphismSequenceContainerTools::extractIngroup: no Ingroup sequences found.");
  }
  for (size_t i = ss.size(); i > 0; --i)
  {
    psci->deleteSequence(ss[i - 1]);
  }
  return psci;
}

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

PolymorphismSequenceContainer* PolymorphismSequenceContainerTools::extractOutgroup(const PolymorphismSequenceContainer& psc) throw (Exception)
{
  SequenceSelection ss;
  PolymorphismSequenceContainer* psci = dynamic_cast<PolymorphismSequenceContainer*>(psc.clone());
  for (size_t i = 0; i < psc.getNumberOfSequences(); i++)
  {
    if (psc.isIngroupMember(i) )
      ss.push_back(i);
  }
  if (ss.size() == psc.getNumberOfSequences())
  {
    delete psci;
    throw Exception("PolymorphismSequenceContainerTools::extractOutgroup: no Outgroup sequences found.");
  }
  for (size_t i = ss.size(); i > 0; i--)
  {
    psci->deleteSequence(ss[i - 1]);
  }
  return psci;
}

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

PolymorphismSequenceContainer* PolymorphismSequenceContainerTools::extractGroup(const PolymorphismSequenceContainer& psc, size_t group_id) throw (Exception)
{
  SequenceSelection ss;
  PolymorphismSequenceContainer* psci = dynamic_cast<PolymorphismSequenceContainer*>(psc.clone());
  for (size_t i = 0; i < psc.getNumberOfSequences(); i++)
  {
    if (psc.getGroupId(i) != group_id)
      ss.push_back(i);
  }
  if (ss.size() == psc.getNumberOfSequences())
  {
    delete psci;
    throw GroupNotFoundException("PolymorphismSequenceContainerTools::extractGroup: group_id not found.", group_id);
  }
  for (size_t i = ss.size(); i > 0; i--)
  {
    psci->deleteSequence(ss[i - 1]);
  }
  return psci;
}

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

PolymorphismSequenceContainer* PolymorphismSequenceContainerTools::getSelectedSequences(const PolymorphismSequenceContainer& psc, const SequenceSelection& ss)
{
  PolymorphismSequenceContainer* newpsc = new PolymorphismSequenceContainer(psc.getAlphabet());
  for (size_t i = 0; i < ss.size(); i++)
  {
    newpsc->addSequenceWithFrequency(psc.getSequence(ss[i]), psc.getSequenceCount(i), false);
    if (psc.isIngroupMember(i))
      newpsc->setAsIngroupMember(i);
    else
    {
      newpsc->setAsOutgroupMember(i);
      newpsc->setGroupId(i, psc.getGroupId(i));
    }
  }
  newpsc->setGeneralComments(psc.getGeneralComments());
  return newpsc;
}

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

PolymorphismSequenceContainer* PolymorphismSequenceContainerTools::sample(const PolymorphismSequenceContainer& psc, size_t n, bool replace)
{
  size_t nbSeq = psc.getNumberOfSequences();
  vector<size_t> v;
  for (size_t i = 0; i < nbSeq; ++i)
  {
    v.push_back(i);
  }
  vector<size_t> vv(n);
  RandomTools::getSample(v, vv, replace);
  PolymorphismSequenceContainer* newpsc = PolymorphismSequenceContainerTools::getSelectedSequences(psc, vv);
  return newpsc;
}

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

PolymorphismSequenceContainer* PolymorphismSequenceContainerTools::getSitesWithoutGaps (const PolymorphismSequenceContainer& psc)
{
  vector<string> seqNames = psc.getSequencesNames();
  PolymorphismSequenceContainer* noGapCont = new PolymorphismSequenceContainer(psc.getNumberOfSequences(), psc.getAlphabet());
  noGapCont->setSequencesNames(seqNames, false);
  size_t nbSeq = psc.getNumberOfSequences();
  for (size_t i = 0; i < nbSeq; i++)
  {
    noGapCont->setSequenceCount(i, psc.getSequenceCount(i));
    if (psc.isIngroupMember(i))
      noGapCont->setAsIngroupMember(i);
    else
    {
      noGapCont->setAsOutgroupMember(i);
      noGapCont->setGroupId(i, psc.getGroupId(i));
    }
  }
  NoGapSiteContainerIterator ngsi(psc);
  while (ngsi.hasMoreSites())
    noGapCont->addSite(*ngsi.nextSite());
  return noGapCont;
}

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

size_t PolymorphismSequenceContainerTools::getNumberOfNonGapSites(const PolymorphismSequenceContainer& psc, bool ingroup) throw (Exception)
{
  size_t count = psc.getNumberOfSites();
  PolymorphismSequenceContainer* npsc = 0;
  SimpleSiteContainerIterator* ssi;
  if (ingroup)
  {
    try
    {
      npsc = extractIngroup(psc);
    }
    catch (Exception& e)
    {
      if (npsc != NULL)
        delete npsc;
      throw e;
    }
    ssi = new SimpleSiteContainerIterator(*npsc);
  }
  else
    ssi = new SimpleSiteContainerIterator(psc);
  while (ssi->hasMoreSites())
    if (SiteTools::hasGap(*ssi->nextSite()))
      count--;
  delete ssi;
  return count;
}

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

size_t PolymorphismSequenceContainerTools::getNumberOfCompleteSites(const PolymorphismSequenceContainer& psc, bool ingroup) throw (Exception)
{
  size_t count = psc.getNumberOfSites();
  PolymorphismSequenceContainer* npsc = 0;
  SimpleSiteContainerIterator* ssi;
  if (ingroup)
  {
    try
    {
      npsc = extractIngroup(psc);
    }
    catch (Exception& e)
    {
      if (npsc != NULL)
        delete npsc;
      throw e;
    }
    ssi = new SimpleSiteContainerIterator(*npsc);
  }
  else
    ssi = new SimpleSiteContainerIterator(psc);
  while (ssi->hasMoreSites())
    if (!SiteTools::isComplete(*ssi->nextSite()))
      count--;
  delete ssi;
  return count;
}

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

PolymorphismSequenceContainer* PolymorphismSequenceContainerTools::getCompleteSites (const PolymorphismSequenceContainer& psc)
{
  vector<string> seqNames = psc.getSequencesNames();
  PolymorphismSequenceContainer* complete = new PolymorphismSequenceContainer(psc.getNumberOfSequences(), psc.getAlphabet());
  complete->setSequencesNames(seqNames, false);
  size_t nbSeq = psc.getNumberOfSequences();
  for (size_t i = 0; i < nbSeq; i++)
  {
    complete->setSequenceCount(i, psc.getSequenceCount(i));
    if (psc.isIngroupMember(i))
      complete->setAsIngroupMember(i);
    else
    {
      complete->setAsOutgroupMember(i);
      complete->setGroupId(i, psc.getGroupId(i));
    }
  }
  CompleteSiteContainerIterator csi(psc);
  while (csi.hasMoreSites())
    complete->addSite(*csi.nextSite());
  return complete;
}

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

PolymorphismSequenceContainer* PolymorphismSequenceContainerTools::excludeFlankingGap(const PolymorphismSequenceContainer& psc)
{
  PolymorphismSequenceContainer* psci = dynamic_cast<PolymorphismSequenceContainer*>(psc.clone());
  while (SiteTools::hasGap(psci->getSite(0)))
    psci->deleteSite(0);
  size_t i = 0;
  size_t n = psci->getNumberOfSites();
  while (SiteTools::hasGap(psci->getSite(n - i - 1)))
  {
    psci->deleteSite(n - i - 1);
    i++;
  }
  return psci;
}

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

PolymorphismSequenceContainer* PolymorphismSequenceContainerTools::getSelectedSites(const PolymorphismSequenceContainer& psc, const std::string& setName, bool phase)
{
  SiteContainer* pscc = MaseTools::getSelectedSites(psc, setName);
  Comments maseFileHeader = psc.getGeneralComments();
  if (phase)
  {
    for (size_t i = 1; i < MaseTools::getPhase(maseFileHeader, setName); i++)
    {
      pscc->deleteSite(0);
    }
  }
  PolymorphismSequenceContainer* psci = new PolymorphismSequenceContainer(*pscc);
  for (size_t i = 0; i < psc.getNumberOfSequences(); i++)
  {
    if (psc.isIngroupMember(i))
      psci->setAsIngroupMember(i);
    else
    {
      psci->setAsOutgroupMember(i);
      psci->setGroupId(i, psc.getGroupId(i));
    }
  }
  psci->deleteGeneralComments();
  delete pscc;
  return psci;
}

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

PolymorphismSequenceContainer* PolymorphismSequenceContainerTools::getNonCodingSites(const PolymorphismSequenceContainer& psc, const std::string& setName)
{
  SiteSelection ss;
  Comments maseFileHeader = psc.getGeneralComments();
  SiteSelection codss = MaseTools::getSiteSet(maseFileHeader, setName);
  for (size_t i = 0; i < psc.getNumberOfSites(); i++)
  {
    if (find(codss.begin(), codss.end(), i) == codss.end())
      ss.push_back(i);
  }
  const SiteContainer* sc = SiteContainerTools::getSelectedSites(psc, ss);
  PolymorphismSequenceContainer* psci = new PolymorphismSequenceContainer(*sc);
  for (size_t i = 0; i < psc.getNumberOfSequences(); i++)
  {
    if (psc.isIngroupMember(i))
      psci->setAsIngroupMember(i);
    else
    {
      psci->setAsOutgroupMember(i);
      psci->setGroupId(i, psc.getGroupId(i));
    }
  }
  delete sc;
  return psci;
}

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

PolymorphismSequenceContainer* PolymorphismSequenceContainerTools::getOnePosition(const PolymorphismSequenceContainer& psc, const std::string& setName, size_t pos)
{
  Comments maseFileHeader = psc.getGeneralComments();
  size_t start;
  try
  {
    start = MaseTools::getPhase(maseFileHeader, setName);
  }
  catch (Exception& e)
  {
    start = 1;
  }
  SiteSelection ss;
  size_t i;
  if ((int)pos - (int)start >= 0)
    i = pos - start;
  else
    i = pos - start + 3;
  while (i < psc.getNumberOfSites())
  {
    ss.push_back(i);
    i += 3;
  }
  const SiteContainer* sc = SiteContainerTools::getSelectedSites(psc, ss);
  PolymorphismSequenceContainer* newpsc = new PolymorphismSequenceContainer(*sc);
  for (size_t j = 0; j < psc.getNumberOfSequences(); j++)
  {
    if (psc.isIngroupMember(j))
      newpsc->setAsIngroupMember(j);
    else
    {
      newpsc->setAsOutgroupMember(j);
      newpsc->setGroupId(i, psc.getGroupId(j));
    }
  }
  delete sc;
  return newpsc;
}

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

PolymorphismSequenceContainer* PolymorphismSequenceContainerTools::getIntrons(
    const PolymorphismSequenceContainer& psc,
    const std::string& setName,
    const GeneticCode* gCode)
{
  Comments maseFileHeader = psc.getGeneralComments();
  SiteSelection ss;
  SiteSelection codss = MaseTools::getSiteSet(maseFileHeader, setName);
  size_t start;
  try
  {
    start = MaseTools::getPhase(maseFileHeader, setName);
  }
  catch (Exception& e)
  {
    throw e;
  }

  size_t first = 0, last = psc.getNumberOfSites();
  // Check if the first codon is AUG
  if (start == 1 &&
      psc.getSite(codss[0]).getValue(0) == 0 &&
      psc.getSite(codss[1]).getValue(0) == 3 &&
      psc.getSite(codss[2]).getValue(0) == 2)
    first = codss[0];
  // Check if the last codon is a STOP one
  int c1 = psc.getSite(codss[codss.size() - 3]).getValue(0);
  int c2 = psc.getSite(codss[codss.size() - 2]).getValue(0);
  int c3 = psc.getSite(codss[codss.size() - 1]).getValue(0);
  if (gCode->isStop(gCode->getSourceAlphabet()->getCodon(c1, c2, c3)))
    last = codss[codss.size() - 1];
  // Keep sites between AUG and STOP
  for (size_t i = first; i < last; i++)
  {
    if (find(codss.begin(), codss.end(), i) == codss.end())
    {
      ss.push_back(i);
    }
  }
  const SiteContainer* sc = SiteContainerTools::getSelectedSites(psc, ss);
  PolymorphismSequenceContainer* psci = new PolymorphismSequenceContainer(*sc);
  for (size_t i = 0; i < psc.getNumberOfSequences(); i++)
  {
    if (psc.isIngroupMember(i))
      psci->setAsIngroupMember(i);
    else
    {
      psci->setAsOutgroupMember(i);
      psci->setGroupId(i, psc.getGroupId(i));
    }
  }
  delete sc;
  return psci;
}

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

PolymorphismSequenceContainer* PolymorphismSequenceContainerTools::get5Prime(const PolymorphismSequenceContainer& psc, const std::string& setName)
{
  Comments maseFileHeader = psc.getGeneralComments();
  SiteSelection ss;
  SiteSelection codss = MaseTools::getSiteSet(maseFileHeader, setName);
  size_t start = MaseTools::getPhase(maseFileHeader, setName);
  size_t last = 0;
  // Check if the first Codon is AUG
  if (start == 1 &&
      psc.getSite(codss[0]).getValue(0) == 0 &&
      psc.getSite(codss[1]).getValue(0) == 3 &&
      psc.getSite(codss[2]).getValue(0) == 2)
    last = codss[0];
  for (size_t i = 0; i < last; i++)
  {
    if (find(codss.begin(), codss.end(), i) == codss.end())
    {
      ss.push_back(i);
    }
  }
  const SiteContainer* sc = SiteContainerTools::getSelectedSites(psc, ss);
  PolymorphismSequenceContainer* psci = new PolymorphismSequenceContainer(*sc);
  for (size_t i = 0; i < psc.getNumberOfSequences(); i++)
  {
    if (psc.isIngroupMember(i))
      psci->setAsIngroupMember(i);
    else
    {
      psci->setAsOutgroupMember(i);
      psci->setGroupId(i, psc.getGroupId(i));
    }
  }
  delete sc;
  return psci;
}

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

PolymorphismSequenceContainer* PolymorphismSequenceContainerTools::get3Prime(
    const PolymorphismSequenceContainer& psc,
    const std::string& setName,
    const GeneticCode* gCode)
{
  Comments maseFileHeader = psc.getGeneralComments();
  SiteSelection ss;
  SiteSelection codss = MaseTools::getSiteSet(maseFileHeader, setName);
  size_t first = psc.getNumberOfSites() - 1;
  // Check if the last codon is a STOP one
  int c1 = psc.getSite(codss[codss.size() - 3]).getValue(0);
  int c2 = psc.getSite(codss[codss.size() - 2]).getValue(0);
  int c3 = psc.getSite(codss[codss.size() - 1]).getValue(0);
  if (gCode->isStop(gCode->getSourceAlphabet()->getCodon(c1, c2, c3)))
    first = codss[codss.size() - 1];
  for (size_t i = first; i < psc.getNumberOfSites(); i++)
  {
    if (find(codss.begin(), codss.end(), i) == codss.end())
    {
      ss.push_back(i);
    }
  }
  const SiteContainer* sc = SiteContainerTools::getSelectedSites(psc, ss);
  PolymorphismSequenceContainer* psci = new PolymorphismSequenceContainer(*sc);
  for (size_t i = 0; i < psc.getNumberOfSequences(); i++)
  {
    if (psc.isIngroupMember(i))
      psci->setAsIngroupMember(i);
    else
    {
      psci->setAsOutgroupMember(i);
      psci->setGroupId(i, psc.getGroupId(i));
    }
  }
  delete sc;
  return psci;
}

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

string PolymorphismSequenceContainerTools::getIngroupSpeciesName(const PolymorphismSequenceContainer& psc)
{
  string key;
  string speciesName;
  Comments maseFileHeader = psc.getGeneralComments();
  if (!maseFileHeader.size())
    return speciesName;
  map<string, size_t> groupMap = MaseTools::getAvailableSequenceSelections(maseFileHeader);
  for (map<string, size_t>::iterator mi = groupMap.begin(); mi != groupMap.end(); mi++)
  {
    key = mi->first;
    if (key.compare(0, 7, "INGROUP") == 0)
    {
      StringTokenizer* sptk = new StringTokenizer(key, "_");
      speciesName = sptk->getToken(1) + " " + sptk->getToken(2);
    }
  }
  return speciesName;
}

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