CompressedVectorSiteContainer.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include <Bpp/Text/TextTools.h>
#include <iostream>
 
#include "CompressedVectorSiteContainer.h"
 
using namespace std;
 
using namespace bpp;
 
CompressedVectorSiteContainer::CompressedVectorSiteContainer(
    std::vector< unique_ptr<Site>>& vs,
    shared_ptr<const Alphabet>& alphabet) :
  AbstractTemplateSequenceContainer<Sequence>(alphabet),
  siteContainer_(),
  sequenceContainer_(),
  sequenceNames_(),
  sequenceComments_(),
  index_(0)
{
  if (vs.size() == 0)
    throw Exception("CompressedVectorSiteContainer::CompressedVectorSiteContainer. Empty site set.");
  // Seq names and comments:
  size_t nbSeq = vs[0]->size();
  for (size_t i = 0; i < nbSeq; ++i)
  {
    sequenceNames_.push_back("Seq_" + TextTools::toString(i));
    sequenceContainer_.appendObject(nullptr, "Seq_" + TextTools::toString(i));
  }
 
  // Now try to add each site:
  for (auto& site : vs)
  {
    addSite(site);
  }
}
 
/******************************************************************************/
 
CompressedVectorSiteContainer::CompressedVectorSiteContainer(
    size_t size,
    shared_ptr<const Alphabet>& alphabet) :
  AbstractTemplateSequenceContainer<Sequence>(alphabet),
  siteContainer_(),
  sequenceContainer_(),
  sequenceNames_(),
  sequenceComments_(),
  index_(0)
{
  // Seq names and comments:
  for (size_t i = 0; i < size; ++i)
  {
    sequenceNames_.push_back("Seq_" + TextTools::toString(i));
    sequenceContainer_.appendObject(nullptr, "Seq_" + TextTools::toString(i));
  }
}
 
/******************************************************************************/
 
CompressedVectorSiteContainer::CompressedVectorSiteContainer(
    const std::vector<std::string>& sequenceKeys,
    shared_ptr<const Alphabet>& alphabet) :
  AbstractTemplateSequenceContainer(alphabet),
  siteContainer_(),
  sequenceContainer_(),
  sequenceNames_(),
  sequenceComments_(),
  index_(0)
{
  unsigned int i = 0;
  for (auto key : sequenceKeys)
  {
    ++i;
    sequenceNames_.push_back("Seq_" + TextTools::toString(i));
    sequenceContainer_.appendObject(nullptr, key);
  }
}
 
/******************************************************************************/
 
CompressedVectorSiteContainer::CompressedVectorSiteContainer(shared_ptr<const Alphabet>& alphabet) :
  AbstractTemplateSequenceContainer<Sequence>(alphabet),
  siteContainer_(),
  sequenceContainer_(),
  sequenceNames_(),
  sequenceComments_(),
  index_(0)
{}
 
/******************************************************************************/
 
CompressedVectorSiteContainer::CompressedVectorSiteContainer(const CompressedVectorSiteContainer& vsc) :
  AbstractTemplateSequenceContainer<Sequence>(vsc),
  siteContainer_(),
  sequenceContainer_(),
  sequenceNames_(vsc.sequenceNames_),
  sequenceComments_(vsc.sequenceComments_),
  index_(vsc.index_)
{
  for (const auto& name: vsc.sequenceNames_)
  {
    sequenceContainer_.appendObject(nullptr, name);
  }
 
  // Copy the compressed data:
  for (size_t i = 0; i < vsc.siteContainer_.getSize(); ++i)
  {
    auto sitePtr = std::shared_ptr<Site>(vsc.siteContainer_.getObject(i)->clone());
    siteContainer_.appendObject(sitePtr);
  }
}
 
/******************************************************************************/
 
CompressedVectorSiteContainer::CompressedVectorSiteContainer(const SiteContainerInterface& sc) :
  AbstractTemplateSequenceContainer<Sequence>(sc),
  siteContainer_(),
  sequenceContainer_(),
  sequenceNames_(sc.getSequenceNames()),
  sequenceComments_(sc.getSequenceComments()),
  index_(0)
{
  for (const auto& name: sc.getSequenceNames())
  {
    sequenceContainer_.appendObject(nullptr, name);
  }
 
  // Now try to add each site:
  for (size_t i = 0; i < sc.getNumberOfSites(); ++i)
  {
    auto sitePtr = std::unique_ptr<Site>(sc.site(i).clone());
    addSite(sitePtr, false);
  }
}
 
/******************************************************************************/
 
CompressedVectorSiteContainer& CompressedVectorSiteContainer::operator=(const CompressedVectorSiteContainer& vsc)
{
  clear();
  AbstractTemplateSequenceContainer<Sequence>::operator=(vsc);
 
  for (const auto& name: vsc.getSequenceNames())
  {
    sequenceContainer_.appendObject(nullptr, name);
  }
 
  // Copy the compressed data:
  index_ = vsc.index_;
  for (size_t i = 0; i < vsc.siteContainer_.getSize(); ++i)
  {
    auto sitePtr = std::shared_ptr<Site>(vsc.siteContainer_.getObject(i)->clone());
    siteContainer_.appendObject(sitePtr);
  }
 
  sequenceNames_ = vsc.sequenceNames_;
  sequenceComments_ = vsc.sequenceComments_;
 
  return *this;
}
 
/******************************************************************************/
 
CompressedVectorSiteContainer& CompressedVectorSiteContainer::operator=(const SiteContainerInterface& sc)
{
  clear();
  AbstractTemplateSequenceContainer<Sequence>::operator=(sc);
 
  // Now try to add each site:
  for (size_t i = 0; i < sc.getNumberOfSites(); ++i)
  {
    auto sitePtr = std::unique_ptr<Site>(sc.site(i).clone());
    addSite(sitePtr, false);
  }
 
  sequenceNames_ = sc.getSequenceNames();
  sequenceComments_ = sc.getSequenceComments();
 
  return *this;
}
 
/******************************************************************************/
 
void CompressedVectorSiteContainer::setSite(size_t sitePosition, unique_ptr<Site>& site, bool checkCoordinate)
{
  if (sitePosition >= getNumberOfSites())
    throw IndexOutOfBoundsException("CompressedVectorSiteContainer::setSite.", sitePosition, 0, getNumberOfSites() - 1);
 
  // Check size:
  if (site->size() != getNumberOfSequences())
    throw SiteException("AlignedSequenceContainer::setSite. Site does not have the appropriate length", site.get());
 
  // New site's alphabet and site container's alphabet matching verification
  if (site->getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
    throw AlphabetMismatchException("CompressedVectorSiteContainer::setSite", getAlphabet(), site->getAlphabet());
 
  size_t current = index_[sitePosition];
  size_t siteIndex = getSiteIndex_(*site);
  if (siteIndex == current)
  {
    // Nothing to do here, this is the same site.
  }
  else if (siteIndex < getNumberOfUniqueSites())
  {
    // The new site is already in the list, si we just update the index:
    index_[sitePosition] = siteIndex;
 
    // We have to check if the previous pattern was unique, and if so, remove it and update indices:
    bool test = true;
    for (size_t i = 0; test && i < index_.size(); ++i)
    {
      if (index_[i] == current)
      {
        // There is another site, so nothing to do...
        test = false;
      }
    }
    if (test)
    {
      // There was no other site pointing toward this pattern, so we remove it.
      siteContainer_.deleteObject(current);
      // Now we have to correct all indices:
      for (size_t i = 0; i < index_.size(); ++i)
      {
        if (index_[i] > current)
          index_[i]--;
      }
    }
  }
  else
  {
    // This is a new pattern, and we have to add it to the list.
    // Now we have to check if the previous pattern was unique, and if so,
    // replace it with the new one. Otherwise, add the new site at the end of the list.
    bool test = true;
    for (size_t i = 0; test && i < index_.size(); ++i)
    {
      if (i != sitePosition && index_[i] == current)
      {
        // There is another site
        test = false;
      }
    }
    if (test)
    {
      // we relace the site
      siteContainer_.addObject(std::move(site), current, false);
    }
    else
    {
      // We add the site at the end:
      siteContainer_.appendObject(std::move(site));
      index_[sitePosition] = siteIndex;
    }
  }
 
  // Clean Sequence Container cache
  sequenceContainer_.clear();
}
 
/******************************************************************************/
 
std::unique_ptr<Site> CompressedVectorSiteContainer::removeSite(size_t siteIndex)
{
  if (siteIndex >= getNumberOfSites())
    throw IndexOutOfBoundsException("CompressedVectorSiteContainer::removeSite.", siteIndex, 0, getNumberOfSites() - 1);
  // Here we need to check whether the pattern corresponding to this site is unique:
 
  auto sitePtr = siteContainer_.getObject(index_[siteIndex]);
  std::get_deleter< SwitchDeleter<Site>>(sitePtr)->off();
 
  size_t current = index_[siteIndex];
  bool test = true;
  for (size_t j = 0; test && j < index_.size(); ++j)
  {
    if (j != siteIndex && index_[j] == current)
    {
      // There is another site, so nothing to erase
      test = false;
    }
  }
  if (test)
  {
    // There was no other site pointing toward this pattern, so we remove it.
    siteContainer_.removeObject(index_[siteIndex]);
 
    // Now we have to correct all indices:
    for (size_t j = 0; j < index_.size(); ++j)
    {
      if (index_[j] > current)
        index_[j]--;
    }
  }
  index_.erase(index_.begin() + static_cast<ptrdiff_t>(siteIndex));
 
  // Clean Sequence Container cache
  sequenceContainer_.clear();
 
  return std::unique_ptr<Site>(sitePtr.get());
}
 
/******************************************************************************/
 
void CompressedVectorSiteContainer::deleteSite(size_t siteIndex)
{
  if (siteIndex >= getNumberOfSites())
    throw IndexOutOfBoundsException("CompressedVectorSiteContainer::deleteSite.", siteIndex, 0, getNumberOfSites() - 1);
  // Here we need to check whether the pattern corresponding to this site is unique:
 
  removeSite(siteIndex); // This effectively delete the object as the unique_ptr is not forwarded and will be destroyed.
}
 
/******************************************************************************/
 
void CompressedVectorSiteContainer::deleteSites(size_t siteIndex, size_t length)
{
  // This may be optimized later:
  for (size_t i = 0; i < length; ++i)
  {
    deleteSite(siteIndex + i);
  }
}
 
/***************************************************************************/
 
void CompressedVectorSiteContainer::addSite(std::unique_ptr<Site>& site, bool checkCoordinate)
{
  // Check size:
  if (getNumberOfSequences() != 0 && site->size() != getNumberOfSequences())
    throw SiteException("CompressedVectorSiteContainer::addSite. Site does not have the appropriate length", site.get());
 
  // New site's alphabet and site container's alphabet matching verification
  if (site->getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
  {
    throw AlphabetMismatchException("CompressedVectorSiteContainer::addSite", getAlphabet(), site->getAlphabet());
  }
 
  size_t n = site->size();
 
  size_t siteIndex = getSiteIndex_(*site);
  if (siteIndex == getNumberOfUniqueSites())
  {
    // This is a new pattern:
    std::shared_ptr<Site> sitePtr(site.release(), SwitchDeleter<Site>());
    siteContainer_.appendObject(sitePtr);
  }
 
  index_.push_back(siteIndex);
 
  // Clean Sequence Container cache
  if (getNumberOfSequences() == 0)
  {
    sequenceNames_.resize(n);
    sequenceComments_.resize(n);
    for (size_t i = 0; i < n; ++i)
    {
      sequenceNames_[i] = "Seq_" + TextTools::toString(i);
      sequenceContainer_.appendObject(nullptr, sequenceNames_[i]);
    }
  }
  else
  {
    sequenceContainer_.nullify();
  }
}
 
/******************************************************************************/
 
void CompressedVectorSiteContainer::addSite(std::unique_ptr<Site>& site, size_t siteIndex, bool checkCoordinates)
{
  if (siteIndex >= getNumberOfSites())
    throw IndexOutOfBoundsException("CompressedVectorSiteContainer::addSite", siteIndex, 0, getNumberOfSites() - 1);
 
  // Check size:
  if (site->size() != getNumberOfSequences())
    throw SiteException("CompressedVectorSiteContainer::addSite. Site does not have the appropriate length", site.get());
 
  // New site's alphabet and site container's alphabet matching verification
  if (site->getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
  {
    throw AlphabetMismatchException("CompressedVectorSiteContainer::addSite", getAlphabet(), site->getAlphabet());
  }
 
  size_t n = site->size();
 
  size_t index = getSiteIndex_(*site);
  if (index == getNumberOfUniqueSites())
  {
    // This is a new pattern:
    std::shared_ptr<Site> sitePtr(site.release(), SwitchDeleter<Site>());
    siteContainer_.appendObject(sitePtr);
  }
 
  index_.insert(index_.begin() + static_cast<ptrdiff_t>(siteIndex), index);
 
  // Clean Sequence Container cache
  if (getNumberOfSequences() == 0)
  {
    sequenceNames_.resize(n);
    sequenceComments_.resize(n);
    for (size_t i = 0; i < n; ++i)
    {
      sequenceNames_[i] = "Seq_" + TextTools::toString(i);
      sequenceContainer_.appendObject(nullptr, sequenceNames_[i]);
    }
  }
  else
  {
    sequenceContainer_.nullify();
  }
}
 
/******************************************************************************/
 
void CompressedVectorSiteContainer::reindexSites()
{
  for (size_t i = 0; i < siteContainer_.getSize(); ++i)
  {
    getSite_(i).setCoordinate(static_cast<int>(i) + 1);
  }
}
 
/******************************************************************************/
 
void CompressedVectorSiteContainer::setSiteCoordinates(const Vint& vCoordinates)
{
  if (vCoordinates.size() != getNumberOfSites())
    throw BadSizeException("CompressedVectorSiteContainer::setSitePositions bad size of positions vector", vCoordinates.size(), getNumberOfSites());
 
  for (size_t i = 0; i < vCoordinates.size(); ++i)
  {
    getSite_(i).setCoordinate(vCoordinates[i]);
  }
}
 
/******************************************************************************/
 
Vint CompressedVectorSiteContainer::getSiteCoordinates() const
{
  size_t n = getNumberOfSites();
  Vint coordinates(n);
  for (size_t i = 0; i < n; i++)
  {
    coordinates[i] = siteContainer_.getObject(index_[i])->getCoordinate();
  }
  return coordinates;
}
 
/******************************************************************************/
 
const Sequence& CompressedVectorSiteContainer::sequence(size_t sequencePosition) const
{
  if (sequencePosition >= getNumberOfSequences())
    throw IndexOutOfBoundsException("CompressedVectorSiteContainer::getSequence.", sequencePosition, 0, getNumberOfSequences() - 1);
 
  // If Sequence already exists
  auto name = sequenceContainer_.getObjectName(sequencePosition);
  if (!sequenceContainer_.isAvailableName(name))
    return *sequenceContainer_.getObject(sequencePosition);
 
  // Main loop : for all sites
  size_t n = getNumberOfSites();
  vector<int> sequence(n);
  for (size_t j = 0; j < n; ++j)
  {
    sequence[j] = (*siteContainer_.getObject(index_[j]))[sequencePosition];
  }
 
  auto alphaPtr = getAlphabet();
  auto ns = std::make_shared<Sequence>(
        sequenceNames_[sequencePosition],
        sequence,
        sequenceComments_[sequencePosition],
        alphaPtr);
 
  sequenceContainer_.addObject_(ns, sequencePosition, sequenceKey(sequencePosition), false);
 
  return *ns;
}
 
/******************************************************************************/
 
size_t CompressedVectorSiteContainer::getSiteIndex_(const Site& site)
{
  size_t pos = getNumberOfUniqueSites();
  bool test;
  for (size_t i = 0; i < getNumberOfUniqueSites(); ++i)
  {
    test = true;
    const Site& siteI = *siteContainer_.getObject(i);
 
    for (size_t j = 0; test && j < site.size(); ++j) // site is supposed to have the correct size, that is the same as all the ones in the container.
    {
      if (site[j] != siteI[j])
        test = false;
    }
 
    if (test)
    {
      pos = i;
      break;
    }
  }
  return pos;
}
 
/******************************************************************************/