SequenceContainerTools.cpp

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//
// File: SequenceContainerTools.cpp
// Authors:
//   Julien Dutheil
// Created: 2003-10-04 09:18:34
//
 
/*
  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 "../Alphabet/CodonAlphabet.h"
#include "../SymbolListTools.h"
#include "ProbabilisticSequenceContainer.h"
#include "SequenceContainerTools.h"
#include "VectorSequenceContainer.h"
 
// From bpp-core:
#include <Bpp/Text/TextTools.h>
 
using namespace bpp;
 
// From the STL:
#include <iostream>
 
using namespace std;
 
/******************************************************************************/
 
SequenceContainer* SequenceContainerTools::createContainerOfSpecifiedSize(const Alphabet* alphabet, size_t size)
{
  VectorSequenceContainer* vsc = new VectorSequenceContainer(alphabet);
  for (size_t i = 0; i < size; ++i)
  {
    vsc->addSequence(BasicSequence(TextTools::toString(i), "", alphabet), false);
  }
  return vsc;
}
 
/******************************************************************************/
 
SequenceContainer* SequenceContainerTools::createContainerWithSequenceNames(
  const Alphabet* alphabet,
  const vector<string>& seqNames)
{
  SequenceContainer* sc = createContainerOfSpecifiedSize(alphabet, seqNames.size());
  sc->setSequenceNames(seqNames, true);
  return sc;
}
 
/******************************************************************************/
 
void SequenceContainerTools::getSelectedSequences(
  const OrderedSequenceContainer& sequences,
  const SequenceSelection& selection,
  SequenceContainer& outputCont)
{
  bool checkNames = outputCont.getNumberOfSequences() > 0;
  for (size_t i = 0; i < selection.size(); i++)
  {
    outputCont.addSequence(sequences.getSequence(selection[i]), checkNames);
  }
}
 
/******************************************************************************/
 
void SequenceContainerTools::getSelectedSequences(
  const SequenceContainer& sequences,
  const std::vector<std::string>& selection,
  SequenceContainer& outputCont, bool strict)
{
  bool checkNames = outputCont.getNumberOfSequences() > 0;
  for (size_t i = 0; i < selection.size(); i++)
  {
    if (strict)
    {
      outputCont.addSequence(sequences.getSequence(selection[i]), checkNames);
    }
    else
    {
      if (sequences.hasSequence(selection[i]))
        outputCont.addSequence(sequences.getSequence(selection[i]), checkNames);
    }
  }
}
 
/******************************************************************************/
 
void SequenceContainerTools::keepOnlySelectedSequences(
  OrderedSequenceContainer& sequences,
  const SequenceSelection& selection)
{
  vector<string> names = sequences.getSequenceNames();
  for (size_t i = 0; i < names.size(); i++)
  {
    // We need to do this because after removal the indices will not be the same!
    // another solution would be to sort decreasingly the indices...
    bool test = false;
    for (size_t j = 0; j < selection.size() && !test; j++)
    {
      test = (selection[j] == i);
    }
    if (!test)
      sequences.removeSequence(names[i]);
    // WARNING: what if selection contains several times the same indice? ...
  }
}
 
/******************************************************************************/
 
bool SequenceContainerTools::sequencesHaveTheSameLength(const SequenceContainer& sequences)
{
  vector<string> seqNames = sequences.getSequenceNames();
  if (seqNames.size() <= 1)
    return true;
  size_t length = sequences.getSequence(seqNames[0]).size();
  for (size_t i = 1; i < seqNames.size(); i++)
  {
    if (sequences.getSequence(seqNames[i]).size() != length)
      return false;
  }
  return true;
}
 
/******************************************************************************/
 
void SequenceContainerTools::getFrequencies(const SequencedValuesContainer& sequences, std::map<int, double>& f, double pseudoCount)
{
  double n = 0;
 
  const SequenceContainer* sc = dynamic_cast<const SequenceContainer*>(&sequences);
  const ProbabilisticSequenceContainer* psc = dynamic_cast<const ProbabilisticSequenceContainer*>(&sequences);
 
  for (const auto& name: sequences.getSequenceNames())
  {
    if (sc)
    {
      const Sequence& seq = sc->getSequence(name);
      SymbolListTools::getCounts(seq, f, true);
      n += static_cast<double>(seq.size());
    }
    else if (psc)
    {
      const ProbabilisticSequence& seq = psc->getSequence(name);
      SymbolListTools::getCounts(seq, f, true);
      n += static_cast<double>(seq.size());
    }
    else
      throw Exception("SequenceContainerTools::getFrequencies : unknown SequenceContainer type.");
  }
 
  if (pseudoCount != 0)
  {
    const Alphabet* pA = sequences.getAlphabet();
    for (int i = 0; i < static_cast<int>(pA->getSize()); i++)
    {
      f[i] += pseudoCount;
    }
 
    n += pseudoCount * static_cast<double>(pA->getSize());
  }
 
  for (auto& i : f)
  {
    i.second = i.second / n;
  }
}
 
/******************************************************************************/
 
void SequenceContainerTools::getCounts(const SequenceContainer& sequences, std::map<int, int>& f)
{
  for (const auto& name: sequences.getSequenceNames())
  {
    const Sequence& seq = sequences.getSequence(name);
    for (size_t i = 0; i < seq.size(); i++)
    {
      f[seq[i]]++;
    }
  }
}
 
/******************************************************************************/
 
SequenceContainer* SequenceContainerTools::getCodonPosition(const SequenceContainer& sequences, size_t pos)
{
  const CodonAlphabet* calpha = dynamic_cast<const CodonAlphabet*>(sequences.getAlphabet());
  if (!calpha)
    throw AlphabetException("SequenceContainerTools::getCodonPosition. Input sequences should be of type codon.");
  VectorSequenceContainer* newcont = new VectorSequenceContainer(calpha->getNucleicAlphabet());
  for (const auto& name: sequences.getSequenceNames())
  {
    const Sequence& seq = sequences.getSequence(name);
    vector<int> newseq(seq.size());
    for (size_t i = 0; i < seq.size(); i++)
    {
      newseq[i] = calpha->getNPosition(seq[i], pos);
    }
    BasicSequence s(name, newseq, sequences.getComments(name), calpha->getNucleicAlphabet());
    newcont->addSequence(s);
  }
  return newcont;
}
 
/******************************************************************************/