PolyTableFunctions.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 __POLYTABLE_FUNCTIONS_HPP__
#define __POLYTABLE_FUNCTIONS_HPP__

#include <Sequence/PolyTable.hpp>

namespace Sequence
{
  bool containsCharacter(const PolyTable * t,const char ch)__attribute__ ((deprecated));

  bool polyTableValid(const PolyTable * t)__attribute__ ((deprecated));

  template<typename T> T copyPolyTable(const T & t)
  {
    return T(std::vector<double>(t.pbegin(),t.pend()),
             std::vector<std::string>(t.begin(),t.end()));
  }
  
  template<typename T,typename F> T removeColumns( const T & t, const F & f, const bool skipAnc = false, const unsigned anc = 0,const char gapchar = '-' )__attribute__ ((deprecated));
  template<typename T> T removeGaps( const T & t, const bool skipAnc = false, const unsigned anc = 0,const char gapchar = '-' )__attribute__ ((deprecated));
  template<typename T> T removeInvariantPos(const T & t, const bool skipAnc = false, const unsigned anc = 0,
                                            const char gapchar = '-')__attribute__ ((deprecated));
  template<typename T> T removeAmbiguous(const T & t, const bool skipAnc = false, const unsigned anc = 0,
                                         const char gapchar = '-')__attribute__ ((deprecated));
  template<typename T> T removeMissing(const T & t, const bool skipAnc = false, const unsigned anc = 0,
                                       const char gapchar = '-')__attribute__ ((deprecated));
  template<typename T> T removeMultiHits(const T & t, const bool skipAnc = false, const unsigned anc = 0,
                                         const char gapchar = '-')__attribute__ ((deprecated));
  template<typename T> T polyTableToBinary(const T & t, const unsigned ref = 0, const char gapchar = '-')__attribute__ ((deprecated));
  template<typename T> T polyTableFreqFilter(const T & t, const unsigned mincount,const bool skipAnc = false, const unsigned anc = 0 , const char gapchar = '-')__attribute__ ((deprecated));
}
#include <Sequence/bits/PolyTableFunctions.tcc>
#endif