Stockholm.cpp

Go to the documentation of this file.

// 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 "../StringSequenceTools.h"
#include "Stockholm.h"
 
using namespace bpp;
using namespace std;
 
/******************************************************************************/
 
void Stockholm::writeAlignment(ostream& output, const SiteContainerInterface& sc) const
{
  if (!output)
    throw IOException("Stockholm::writeAlignment: can't write to ostream output");
 
  output << "# STOCKHOLM 1.0" << endl;
  // Loop for all general comments
  for (size_t i = 0; i < sc.getComments().size(); ++i)
  {
    output << "#=GF CC " << sc.getComments()[i] << endl;
  }
 
  // Main loop : for all sequences in vector container
  vector<string> names = sc.getSequenceNames();
  size_t maxSize = 0;
  for (size_t i = 0; i < names.size(); ++i)
  {
    names[i] = TextTools::removeWhiteSpaces(names[i]);
    if (names[i].size() > maxSize)
      maxSize = names[i].size();
  }
  if (maxSize > 255)
    maxSize = 255;
  for (size_t i = 0; i < sc.getNumberOfSequences(); ++i)
  {
    output << TextTools::resizeRight(names[i], maxSize) << " " << sc.sequence(i).toString() << endl;
  }
  output << "//" << endl;
}
 
/******************************************************************************/