FastaExplicit.hpp

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/*

Copyright (C) 2003-2009 Kevin Thornton, krthornt[]@[]uci.edu

Remove the brackets to email me.

This file is part of libsequence.

libsequence is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

libsequence is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
long with libsequence.  If not, see <http://www.gnu.org/licenses/>.

*/

#ifndef __FASTA_EXPLICIT_HPP_
#define __FASTA_EXPLICIT_HPP_

//include the relevant headers
#if __GNUG__ && __GNUC__ >= 3
#include <Sequence/Clustalw.hpp>
#include <Sequence/phylipData.hpp>
#include <Sequence/Fasta.hpp>
namespace Sequence
{
  namespace Alignment
  {
    extern template void GetData( std::vector<Sequence::Fasta> &,
                                  const char *);
    extern template std::istream & GetData( std::vector<Sequence::Fasta> &,
                                            std::istream & );
    extern template std::istream & ReadNObjects( std::vector<Sequence::Fasta> &,
                                                 unsigned, std::istream &);
    extern template bool Gapped(const std::vector<Sequence::Fasta> &);
    extern template bool IsAlignment(const std::vector<Sequence::Fasta> &);
    extern template bool validForPolyAnalysis(std::vector<Sequence::Fasta>::const_iterator beg,
                                              std::vector<Sequence::Fasta>::const_iterator end);
    extern template unsigned UnGappedLength(const std::vector<Sequence::Fasta> &);
    extern template void RemoveGaps(std::vector<Sequence::Fasta> &);
    extern template void RemoveTerminalGaps(std::vector<Sequence::Fasta> &);
    extern template void RemoveFixedOutgroupInsertions( std::vector<Sequence::Fasta> & data,
                                                        unsigned site,
                                                        const unsigned & ref );
    extern template std::vector<Sequence::Fasta>
    Trim(const std::vector<Sequence::Fasta> &, const std::vector<int> &);
    extern template std::vector<Sequence::Fasta>
    TrimComplement(const std::vector<Sequence::Fasta> &, const std::vector<int> & );
  }
  extern template class Sequence::ClustalW< Sequence::Fasta >;
  extern template class Sequence::phylipData< Sequence::Fasta >;
}
#endif

#endif

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