Phylip.h

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//
// File: Phylip.h
// Created by: Julien Dutheil
// Created on: Mon Oct 27 12:22:56 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.
*/

#ifndef _PHYLIP_H_
#define _PHYLIP_H_

#include "AbstractIAlignment.h"
#include "AbstractOAlignment.h"
#include "../Sequence.h"
#include "../Container/SequenceContainer.h"
#include "../Container/VectorSequenceContainer.h"
#include "../Container/AlignedSequenceContainer.h"

// From the STL:
#include <iostream>

namespace bpp
{

class Phylip :
  public AbstractIAlignment,
  public AbstractOAlignment,
  public virtual ISequence
{
  private:

    /* this class allows two kinds of Phylip format:
     * traditional, with names limited to 10 chars,
     * and 'extended', defined by PAML, with names separated from sequences by at least 6 white spaces.
     */
    bool extended_;
    /* tells if sequences are in the seuqential or the interleave format/
     */
    bool sequential_;

    unsigned int charsByLine_;

    bool checkNames_;

    std::string namesSplit_;
  
  public:
    Phylip(bool extended = true, bool sequential = true, unsigned int charsByLine = 100, bool checkSequenceNames = true, const std::string& split = "  "):
      extended_(extended), sequential_(sequential), charsByLine_(charsByLine), checkNames_(checkSequenceNames), namesSplit_(split) {}

    virtual ~Phylip() {}

  public:

    void appendAlignmentFromStream(std::istream& input, SiteContainer& sc) const throw (Exception);
    virtual SequenceContainer* readSequences(std::istream& input, const Alphabet* alpha) const throw (Exception) {
      return readAlignment(input, alpha);
    }
    virtual SequenceContainer* readSequences(const std::string& path, const Alphabet* alpha) const throw (Exception) {
      return readAlignment(path, alpha);
    }
    unsigned int getNumberOfSequences(const std::string& path) const throw (IOException);

    void writeAlignment(std::ostream& output, const SiteContainer& sc) const throw (Exception);
    void writeAlignment(const std::string& path, const SiteContainer& sc, bool overwrite) const throw (Exception)
    {
      AbstractOAlignment::writeAlignment(path, sc, overwrite);
    }
    const std::string getFormatName() const;
    const std::string getFormatDescription() const;
    bool checkNames() const { return checkNames_; }

    void checkNames(bool yn) { checkNames_ = yn; }

    const std::string& getSplit() const { return namesSplit_; }

    void setSplit(const std::string& split) { namesSplit_ = split; }
     
  protected:
    //Reading tools:
    const std::vector<std::string> splitNameAndSequence(const std::string& s) const throw (Exception); 
    void readSequential (std::istream& in, SiteContainer& asc) const throw (Exception);
    void readInterleaved(std::istream& in, SiteContainer& asc) const throw (Exception);
    //Writing tools:
    std::vector<std::string> getSizedNames(const std::vector<std::string>& names) const;
    void writeSequential(std::ostream& out, const SequenceContainer& sc) const;
    void writeInterleaved(std::ostream& out, const SequenceContainer& sc) const;
};

} //end of namespace bpp.

#endif  //_PHYLIP_H_