Dcse.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include <Bpp/Io/FileTools.h>
#include <Bpp/Text/StringTokenizer.h>
#include <Bpp/Text/TextTools.h>
 
#include "../Container/SequenceContainer.h"
#include "../Container/VectorSequenceContainer.h"
#include "../Sequence.h"
#include "AbstractIAlignment.h"
#include "Dcse.h"
 
using namespace bpp;
using namespace std;
 
void DCSE::appendAlignmentFromStream(istream& input, SequenceContainerInterface& sc) const
{
  // Checking the existence of specified file
  if (!input)
  {
    throw IOException ("DCSE::read : fail to open file");
  }
 
  // Initialization
  auto alphaPtr = sc.getAlphabet();
  string line, name, sequence = "";
 
  line = FileTools::getNextLine(input); // Copy current line in temporary string
  // StringTokenizer st(line);
  // st.nextToken();
  // First line ignored for now!
  // int n1 = TextTools::toInt(st.nextToken());
  // int n2 = TextTools::toInt(st.nextToken());
  // int nbSites = n2 - n1
  // cout << nbSpecies << " species and " << nbSites << " sites." << endl;
 
  // Main loop : for all file lines
  while (!input.eof())
  {
    line = FileTools::getNextLine(input); // Copy current line in temporary string
    if (line == "")
      break;
    string::size_type endOfSeq = line.find("     ");
    if (endOfSeq == line.npos)
      break;
    sequence = string(line.begin(), line.begin() + static_cast<ptrdiff_t>(endOfSeq));
    sequence = TextTools::removeWhiteSpaces(sequence);
    sequence = TextTools::removeChar(sequence, '{');
    sequence = TextTools::removeChar(sequence, '}');
    sequence = TextTools::removeChar(sequence, '[');
    sequence = TextTools::removeChar(sequence, ']');
    sequence = TextTools::removeChar(sequence, '(');
    sequence = TextTools::removeChar(sequence, ')');
    sequence = TextTools::removeChar(sequence, '^');
    name     = string(line.begin() + static_cast<ptrdiff_t>(endOfSeq + 1), line.end()),
    name     = TextTools::removeFirstWhiteSpaces(name);
    if (name.find("Helix numbering") == name.npos
        && name.find("mask") == name.npos)
    {
      auto seqPtr = make_unique<Sequence>(name, sequence, alphaPtr);
      sc.addSequence(name, seqPtr);
    }
  }
}
 
const string DCSE::getFormatName() const { return "DCSE"; }
 
const string DCSE::getFormatDescription() const { return "RNA structure format"; }