ProbabilisticSymbolList.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include <Bpp/Text/TextTools.h>
 
#include "Alphabet/AlphabetTools.h"
#include "ProbabilisticSymbolList.h"
 
using namespace bpp;
using namespace std;
 
/****************************************************************************************/
 
ProbabilisticSymbolList::ProbabilisticSymbolList(shared_ptr<const Alphabet>& alpha) :
  alphabet_(alpha), content_(alpha->getResolvedChars().size(), 0)
{
  content_.setRowNames(alphabet_->getResolvedChars());
}
 
ProbabilisticSymbolList::ProbabilisticSymbolList(const DTable& list, shared_ptr<const Alphabet>& alpha) :
  alphabet_(alpha), content_(alpha->getResolvedChars().size(), 0)
{
  content_.setRowNames(alpha->getResolvedChars());
  setContent(list);
}
 
ProbabilisticSymbolList::ProbabilisticSymbolList(const vector< vector<double>>& list, shared_ptr<const Alphabet>& alpha) :
  alphabet_(alpha), content_(alpha->getResolvedChars().size(), 0)
{
  content_.setRowNames(alpha->getResolvedChars());
  setContent(list);
}
 
/****************************************************************************************/
 
ProbabilisticSymbolList::ProbabilisticSymbolList(const ProbabilisticSymbolListInterface& list) :
  alphabet_(list.getAlphabet()), content_(list.getContent())
{}
 
ProbabilisticSymbolList::ProbabilisticSymbolList(const ProbabilisticSymbolList& list) :
  alphabet_(list.alphabet_), content_(list.content_)
{}
 
ProbabilisticSymbolList::ProbabilisticSymbolList(const CruxSymbolListInterface& list) :
  alphabet_(list.getAlphabet()), content_(list.getAlphabet()->getResolvedChars().size(), list.size())
{
  size_t nbc = getAlphabet()->getResolvedChars().size();
  content_.setRowNames(alphabet_->getResolvedChars());
 
  for (size_t i = 0; i < size(); ++i)
  {
    for (size_t s = 0; s < nbc; ++s)
    {
      content_(s, i) = list.getStateValueAt(i, static_cast<int>(s));
    }
  }
}
 
ProbabilisticSymbolList& ProbabilisticSymbolList::operator=(const ProbabilisticSymbolListInterface& list)
{
  alphabet_ = list.getAlphabet();
  setContent(list.getContent());
  return *this;
}
 
ProbabilisticSymbolList& ProbabilisticSymbolList::operator=(const ProbabilisticSymbolList& list)
{
  alphabet_ = list.alphabet_;
  content_ = list.content_;
  return *this;
}
 
/****************************************************************************************/
 
void ProbabilisticSymbolList::setContent(const DTable& list)
{
  if (list.hasRowNames())
  {
    if (list.getRowNames().size() != alphabet_->getResolvedChars().size())
      throw DimensionException("ProbabilisticSymbolList::setContent. ", list.getRowNames().size(), alphabet_->getResolvedChars().size());
 
    std::vector<std::string> column_names = list.getRowNames();
    std::vector<std::string> resolved_chars = alphabet_->getResolvedChars();
    for (std::size_t i = 0; i < list.getRowNames().size(); ++i)
    {
      if (column_names[i] != resolved_chars[i])
        throw Exception("ProbabilisticSymbolList::setContent. Row names / resolved characters of alphabet mismatch at " + TextTools::toString(column_names[i]) + " and " + TextTools::toString(resolved_chars[i]) + ".");
    }
  }
  else // DTable has no row names
 
  {
    if (list.getNumberOfRows() != alphabet_->getResolvedChars().size())
      throw DimensionException("ProbabilisticSymbolList::setContent. ", list.getNumberOfRows(), alphabet_->getResolvedChars().size());
  }
 
  content_ = list; // final check passes, content_ becomes DTable
 
  if (!list.hasRowNames())
  {
    content_.setRowNames(alphabet_->getResolvedChars());
  }
}
 
/****************************************************************************************/
 
string ProbabilisticSymbolList::toString() const
{
  stringstream ss;
  ss.precision(10);
 
  for (size_t j = 0; j < content_.getNumberOfColumns(); ++j)
  {
    if (j != 0)
      ss << "|";
 
    for (size_t i = 0; i < content_.getNumberOfRows(); ++i)
    {
      ss << content_.getRowName(i) << "(";
      ss << content_(i, j) << ")";
    }
  }
 
  string st;
  ss >> st;
  return st;
}
 
/****************************************************************************************/
 
void ProbabilisticSymbolList::setContent(const std::vector<std::vector<double>>& list)
{
  if (list.size() == 0)
    return;
 
  if (list[0].size() != alphabet_->getResolvedChars().size())
    throw DimensionException("BasicProbabilisticSymbolList::setContent. ", list[0].size(), alphabet_->getResolvedChars().size());
 
  content_ = list; // final check passes, content_ becomes DTable
  content_.setRowNames(alphabet_->getResolvedChars());
}
 
/****************************************************************************************/
 
void ProbabilisticSymbolList::addElement(const std::vector<double>& element)
{
  // now we add this 'row', to the content DTable, padding the end
  // with 0's should its length be smaller than the width of this DTable
  if (element.size() < content_.getNumberOfRows())
  {
    std::vector<double> padded_element(element);
 
    padded_element.resize(content_.getNumberOfRows(), 0.);
 
    content_.addColumn(padded_element);
  }
  else
  {
    if (element.size() > content_.getNumberOfRows())
    {
      throw BadSizeException("ProbabilisticSymbolList::addElement: too long element: ",
            element.size(),
            content_.getNumberOfRows());
    }
    else
      content_.addColumn(element);
  }
}
 
void ProbabilisticSymbolList::addElement(size_t pos, const std::vector<double>& element)
{
  // now we add this 'row', to the content DTable, padding the end
  // with 0's should its length be smaller than the width of this DTable
  if (element.size() < content_.getNumberOfRows())
  {
    std::vector<double> padded_element(element);
 
    padded_element.resize(content_.getNumberOfRows(), 0.);
    content_.addColumn(padded_element, (int)pos);
  }
  else
  {
    content_.addColumn(element, (int)pos);
  }
}
 
void ProbabilisticSymbolList::setElement(size_t pos, const std::vector<double>& element)
{
  if (element.size() < content_.getNumberOfRows())
  {
    std::vector<double> padded_element(element);
 
    padded_element.resize(content_.getNumberOfRows(), 0.);
    content_.setColumn(padded_element, pos);
  }
  else
  {
    content_.setColumn(element, pos);
  }
}