C++ SiteContainer::addSequence方法代碼示例

void DCSE::appendAlignmentFromStream(istream& input, SiteContainer& sc) const throw (Exception)
{
  // Checking the existence of specified file
  if (!input) { throw IOException ("DCSE::read : fail to open file"); }

  // Initialization
  const Alphabet * alpha = 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)
      sc.addSequence(BasicSequence(name, sequence, alpha), true);
  }
}

int main() {
  //ProteicAlphabet* alpha = new ProteicAlphabet;
  RNA* alpha = new RNA();
  SiteContainer* sites = new VectorSiteContainer(alpha);
  BasicSequence seq1("seq1", "----AUGCCG---GCGU----UUU----G--G-CCGACGUGUUUU--", alpha);
  BasicSequence seq2("seq2", "---GAAGGCG---G-GU----UUU----GC-GACCGACG--UUUU--", alpha);
  sites->addSequence(seq1, false);
  sites->addSequence(seq2, false);

  cout << sites->getNumberOfSites() << endl;
  cout << sites->toString("seq1") << endl;
  cout << sites->toString("seq2") << endl;
  SiteContainerTools::removeGapOnlySites(*sites);
  cout << endl;
  
  cout << sites->getNumberOfSites() << endl;
  cout << sites->toString("seq1") << endl;
  cout << sites->toString("seq2") << endl;

  return (sites->getNumberOfSites() == 30 ? 0 : 1);
}

void Clustal::appendAlignmentFromStream(std::istream& input, SiteContainer & sc) const throw (Exception)
{
  // Checking the existence of specified file
  if (!input) { throw IOException ("Clustal::read : fail to open file"); }

  const Alphabet * alpha = sc.getAlphabet();
  vector<BasicSequence> sequences;

  string lineRead("");

  Comments comments(1);
  comments[0] = FileTools::getNextLine(input); // First line gives file generator.

  lineRead = FileTools::getNextLine(input); // This is the first sequence of the first block.
    
  string::size_type beginSeq = 0;
  unsigned int count = 0;
  for (size_t i = lineRead.size(); i > 0; i--) {
    char c = lineRead[i-1];
    if (c == ' ') {
      count++;
      if (count == nbSpacesBeforeSeq_) {
        beginSeq = i - 1 + nbSpacesBeforeSeq_;
        break;
      }
    }
    else count = 0;
  }
  if (beginSeq == 0) throw IOException("Clustal::read. Bad intput file.");

  unsigned int countSequences = 0;

  //Read first sequences block:
  bool test = true;
  do {
    sequences.push_back(BasicSequence(TextTools::removeSurroundingWhiteSpaces(lineRead.substr(0, beginSeq - nbSpacesBeforeSeq_)), lineRead.substr(beginSeq), alpha));
    getline(input, lineRead, '\n');
    countSequences++;
    test = !TextTools::isEmpty(lineRead) && !TextTools::isEmpty(lineRead.substr(0, beginSeq - nbSpacesBeforeSeq_));
  }
  while (input && test);

  // Read other blocks
  lineRead = FileTools::getNextLine(input); // Read first sequence of next block.
  while (!TextTools::isEmpty(lineRead)) {
    // Read next block:
    for (unsigned int i = 0; i < countSequences; ++i) {
      // Complete sequences
      if (TextTools::isEmpty(lineRead))
        throw IOException("Clustal::read. Bad intput file.");
       sequences[i].append(lineRead.substr(beginSeq));
      getline(input, lineRead, '\n');
    }
    //At this point, lineRead is the first line after the current block.
    lineRead = FileTools::getNextLine(input);
  }

  for (unsigned int i = 0; i < countSequences; ++i)
    sc.addSequence(sequences[i], checkNames_);
  sc.setGeneralComments(comments);
}