PhredPhd.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include <Bpp/Text/StringTokenizer.h>
#include <Bpp/Text/TextTools.h>
 
#include "PhredPhd.h"
 
using namespace bpp;
 
/******************************************************************************/
 
// PhredPhd::PhredPhd() {}
 
/******************************************************************************/
 
bool PhredPhd::nextSequence(std::istream& input, Sequence& seq) const
{
  std::vector<size_t> pos;
  return nextSequence(input, seq, pos);
}
 
/******************************************************************************/
 
bool PhredPhd::nextSequence(std::istream& input, Sequence& seq, std::vector<size_t>& pos) const
{
  if (!input)
  {
    throw IOException ("PhredPhd::read: fail to open stream");
  }
 
  bool flag = false;
  std::string name, sequence = "";  // Initialization
  std::vector<int> q;
  std::vector<size_t> p;
 
  flag = parseFile_(input, name, sequence, q, p);
  // Sequence creation
  if (name == "")
    throw Exception("PhredPhd::read: sequence without name!");
  seq.setName(name);
  seq.setContent(sequence);
  try
  {
    SequenceWithQuality& sq = dynamic_cast<SequenceWithQuality&>(seq);
    sq.setQualities(q);
  }
  catch (...)
  {}
  return flag;
}
 
/******************************************************************************/
 
bool PhredPhd::parseFile_(std::istream& input, std::string& name, std::string& sequence, std::vector<int>& qual, std::vector<size_t>& pos) const
{
  bool readSeqFlag = false;
  std::string temp;
  // Read sequence info
  // Main loop : for all lines
  while (!input.eof())
  {
    std::getline(input, temp, '\n');  // Copy current line in temporary string
    StringTokenizer st(temp, " ");
    if (st.hasMoreToken())
    {
      if (st.getToken(0) == "BEGIN_SEQUENCE")
      {
        name = st.getToken(1);
      }
      std::string flag = st.getToken(0);
      while (flag != "END_SEQUENCE" && !input.eof())
      {
        getline(input, temp, '\n');
        StringTokenizer st2(temp, " ");
        if (st2.hasMoreToken())
        {
          flag = st2.getToken(0);
        }
        if (flag == "BEGIN_DNA")
        {
          readSeqFlag = parseDNA_(input, sequence, qual, pos);
          break; // End the whole loop after parsing DNA
        }
      }
    }
  }
  return readSeqFlag;
}
 
/******************************************************************************/
 
bool PhredPhd::parseDNA_(std::istream& input, std::string& sequence, std::vector<int>& qual, std::vector<size_t>& pos) const
{
  bool readSeqFlag = false;
  std::string line_buffer;
  std::string flag;
  sequence.clear();
  qual.clear();
  pos.clear();
  while (flag != "END_DNA" && !input.eof())
  {
    std::getline(input, line_buffer, '\n');
    StringTokenizer st(line_buffer, " ");
    if (st.hasMoreToken())
    {
      flag = TextTools::toUpper(st.getToken(0));
      if (st.numberOfRemainingTokens() == 3)
      {
        sequence += flag;
        qual.push_back(TextTools::toInt(st.getToken(1)));
        pos.push_back(TextTools::to<size_t>(st.getToken(2)));
        readSeqFlag = true;
      }
    }
  }
  return readSeqFlag;
}
 
/******************************************************************************/