Mase.cpp

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//
// File Mase.cpp
// Author : Guillaume Deuchst
//          Julien Dutheil
// Last modification: Tuesday August 21 2003
//

/*
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 "Mase.h"
#include "../StringSequenceTools.h"

using namespace bpp;
using namespace std;

/****************************************************************************************/

void Mase::appendSequencesFromStream(std::istream& input, SequenceContainer& vsc) const throw (Exception)
{
  if (!input) { throw IOException ("Mase::read : fail to open file"); }
  
  // Initialization
  Comments seqComments, fileComments;
  string temp, name, sequence = "";
  bool comments = false;

  // Get current general comments is VectorSequenceContainer
  fileComments = vsc.getGeneralComments();

  // Main loop : for all file lines
  while (!input.eof())
  {
    getline(input, temp, '\n');  // Copy current line in temporary string
    
    // If first character is ;
    if (temp[0] == ';')
    {
      // If second character is also ;
      if (temp[1] == ';')
      {
        // File comments isolation
        temp.erase(0,2);  // Characters ;; deletion
        if(temp != "") fileComments.push_back(temp);
      }
      else
      {
        // If a name and a sequence were founded
        if ((name != "") && (sequence != ""))
        {
          // New sequence creation, and addition in existing VectorSequenceContainer
          vsc.addSequence(BasicSequence(name, sequence, seqComments, vsc.getAlphabet()), checkNames_);
          name = "";
          sequence = "";
          seqComments.clear();
        }
        
        // Sequence commentaries isolation
        temp.erase(temp.begin());  // Character ; deletion
        if (temp != "") seqComments.push_back(temp);
        comments = true;
      }
    }
    else
    {
      // If sequence commentaries were just isolated
      if (comments)
      {
        // Sequence name isolation
        name = temp;
        comments = false;
      }
      else sequence += temp;  // Sequence isolation
    }
  }
  
  // Addition of the last sequence in file
  if ((name != "") && (sequence != ""))
  {
    vsc.addSequence(BasicSequence(name, sequence, seqComments, vsc.getAlphabet()), checkNames_);
  }

  // Set new general comments in VectorSequenceContainer (old + new comments)
  vsc.setGeneralComments(fileComments);
}

/****************************************************************************************/

void Mase::writeSequences(ostream& output, const SequenceContainer& sc) const throw (Exception)
{
  // Checking the existence of specified file, and possibility to open it in write mode
  if (!output) { throw IOException ("Mase::write : failed to open file"); }

  Comments comments = sc.getGeneralComments();

  // Writing all general comments in file
  if (comments.size() == 0) {
    output << ";;" << endl;
  }
  for (unsigned int i = 0 ; i < comments.size() ; i++) {
    output << ";;" << comments[i] << endl;
  }

  string seq, temp = "";  // Initialization

  // Main loop : for all sequences
  vector<string> names = sc.getSequencesNames();
  for (unsigned int i = 0 ; i < names.size() ; i ++)
  {
    comments = sc.getComments(names[i]);

    // Writing all sequence comments in file
    // If no comments are associated with current sequence, an empy commentary line will be writed
    if (comments.size() == 0)
    {
      output << ";" << endl;
    }
    else
    {
      for (unsigned int j = 0 ; j < comments.size() ; j++)
      {
        output << ";" << comments[j] << endl;
      }
    }

    // Sequence name writing
    output << names[i] << endl;

    // Sequence cutting to specified characters number per line
    seq = sc.toString(names[i]);
    while (seq != "")
    {
      if (seq.size() > charsByLine_)
      {
        temp = seq;
        temp.erase(temp.begin() + charsByLine_ , temp.end());
        output << temp  << endl;
        seq.erase(seq.begin(), seq.begin() + charsByLine_);
      }
      else
      {
        output << seq << endl;
        seq = "";
      }
    }
  }
}

/****************************************************************************************/

void Mase::readHeader_(std::istream& input, MaseHeader& header) const throw (Exception)
{
  do {
    //Check if the line is a header line:
    if (input.peek() == ';') {
      char c;
      input.get(c);
      if (input.peek() == ';') {
        input.get(c);
        string line = FileTools::getNextLine(input);
        
        //Check the type of line...

        //Site selection:
        string::size_type index = line.find("# of");
        if (index < line.npos) {
          StringTokenizer st(string(line.begin() + static_cast<ptrdiff_t>(index + 4), line.end()), " \t=;");
          st.nextToken(); //skip next word: may be 'regions' or 'segments' or else ;-)
          unsigned int numberOfSegments = TextTools::to<unsigned int>(st.nextToken());
          string name = st.unparseRemainingTokens();
          //Then look for the set definition:
          MultiRange<size_t> siteSelection;
          while (siteSelection.size() < numberOfSegments) {
            line = FileTools::getNextLine(input);
            if (line[0] != ';' || line[1] != ';')
              throw Exception("Mase::readHeader_(): corrupted file, site selection " + name + " is incomplete. Aborting.");
            line = line.substr(2);
            StringTokenizer st2(line);
            while (st2.hasMoreToken()) {
              StringTokenizer st3(st2.nextToken(), ",");
              unsigned int begin = TextTools::to<unsigned int>(st3.nextToken());
              unsigned int end   = TextTools::to<unsigned int>(st3.nextToken());
              //WARNING!!! In the mase+ format, sites numerotation is 1-based, including, while ranges are 0-based, [a, b[:
              siteSelection.addRange(Range<size_t>(begin - 1, end));
            }
            if (siteSelection.size() > numberOfSegments)
              throw Exception("Mase::readHeader_(): incorrected file, found " + TextTools::toString(siteSelection.size()) + "segments while expected " + TextTools::toString(numberOfSegments));
          }
          header.setSiteSelection(name, siteSelection);
        } else {
          //Sequence selection:
          index = line.find("@ of");
          if (index < line.npos) {
            StringTokenizer st(line.substr(index + 4), " \t=;");
            st.nextToken(); //skip next word: may be 'sequences' or else ;-)
            unsigned int numberOfSequences = TextTools::to<unsigned int>(st.nextToken());
            string name = st.unparseRemainingTokens();
            //The look for the set definition:
            vector<size_t> sequenceSelection;
            while (sequenceSelection.size() < numberOfSequences) {
              line = FileTools::getNextLine(input);
              if (line[0] != ';' || line[1] != ';')
                throw Exception("Mase::readHeader_(): corrupted file, sequence selection " + name + " is incomplete. Aborting.");
              line = line.substr(2);
              StringTokenizer st2(line, ", ");
              while (st2.hasMoreToken()) {
                unsigned int pos = TextTools::to<unsigned int>(st2.nextToken());
                //WARNING!!! In the mase+ format, sequence numerotation is 1-based 
                sequenceSelection.push_back(pos);
            }
            if (sequenceSelection.size() > numberOfSequences)
              throw Exception("Mase::readHeader_(): incorrected file, found " + TextTools::toString(sequenceSelection.size()) + "sequences while expected " + TextTools::toString(numberOfSequences));
            }
            header.setSequenceSelection(name, sequenceSelection);
          } else {
            //Tree:
            index = line.find("$");
            if (index < line.npos) {
              string name = TextTools::removeSurroundingWhiteSpaces(line.substr(index + 1));
              //Here we stop if the line ends with a ";"
              string tree = "";
              do {
                line = FileTools::getNextLine(input);
                if (line[0] != ';' || line[1] != ';')
                  throw Exception("Mase::readHeader_(): corrupted file, tree " + name + " is incomplete. Aborting.");
                line = TextTools::removeSurroundingWhiteSpaces(line.substr(2));
                tree += line;
              } while (! TextTools::endsWith(line, ";"));
              header.setTree(name, tree);
            }
          }
        }
      } else {
        input.putback(c);
        break;
      }
    }
  } while (true);
}

/****************************************************************************************/

void Mase::writeHeader_(std::ostream& output, const MaseHeader& header) const
{
  //Write trees:
  vector<string> treeNames = header.getTreeNames();
  for (size_t i = 0; i < treeNames.size(); ++i) {
    output << ";;$ " + treeNames[i] << endl;
    output << ";;" + header.getTree(treeNames[i]);
    output << endl;
  }

  //Write site selections:
  vector<string> siteSelectionNames = header.getSiteSelectionNames();
  for (size_t i = 0; i < siteSelectionNames.size(); ++i) {
    MultiRange<size_t> ranges = header.getSiteSelection(siteSelectionNames[i]);
    output << ";;# of segments=" << ranges.size() << " " << siteSelectionNames[i] << endl;
    output << ";;";
    for (unsigned int j = 0; j < ranges.size(); ++j) {
      output << " " << (ranges.getRange(j).begin() + 1) << "," << ranges.getRange(j).end();
      if ((j + 1) % 10 == 0)
        output << endl << ";;";
    }
    output << endl;
  }

  //Write sequence selections:
  vector<string> sequenceSelectionNames = header.getSequenceSelectionNames();
  for (size_t i = 0; i < sequenceSelectionNames.size(); ++i) {
    vector<size_t> set = header.getSequenceSelection(sequenceSelectionNames[i]);
    output << ";;@ of species=" << set.size() << " " << sequenceSelectionNames[i] << endl;
    output << ";;";
    for (unsigned int j = 0; j < set.size(); ++j) {
      output << " " << set[j];
      if ((j + 1) % 10 == 0)
        output << endl << ";;";
    }
    output << endl;
  }
}

/****************************************************************************************/