libsequence  1.9.5
PolySites.hpp
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1 /*
2 
3 Copyright (C) 2003-2009 Kevin Thornton, krthornt[]@[]uci.edu
4 
5 Remove the brackets to email me.
6 
7 This file is part of libsequence.
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9 libsequence is free software: you can redistribute it and/or modify
10 it under the terms of the GNU General Public License as published by
11 the Free Software Foundation, either version 3 of the License, or
12 (at your option) any later version.
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14 libsequence is distributed in the hope that it will be useful,
15 but WITHOUT ANY WARRANTY; without even the implied warranty of
16 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17 GNU General Public License for more details.
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19 You should have received a copy of the GNU General Public License
20 long with libsequence. If not, see <http://www.gnu.org/licenses/>.
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22 */
23 
24 #ifndef POLYSITES_H
25 #define POLYSITES_H
26 
29 #include <Sequence/PolyTable.hpp>
30 namespace Sequence
31  {
32  class Fasta;
33  class PolySites : public PolyTable
34  {
35  private:
39  template<class __DataType>
40  void fillIt(const std::vector < __DataType >&alignment,
41  bool strictInfSites = 0,
42  bool ignoregaps = 1,bool skipMissing=false,
43  unsigned freqfilter=0);
44  public:
45  PolySites (void);
46  template<typename __DataType>
47  PolySites (const std::vector < __DataType >&alignment,
48  bool strictInfSites = 0,
49  bool ignoregaps = 1,
50  bool skipMissing=false,
51  bool skipAdjSNP=false,
52  unsigned freqfilter=0);
53  //PolySites (const std::vector < double > &List, const std::vector < std::string > &stringList);
54  PolySites ( std::vector < double > List, std::vector < std::string > stringList);
55  PolySites (PolyTable::const_site_iterator beg,
56  PolyTable::const_site_iterator end);
57  PolySites( PolySites && );
58  PolySites( const PolySites & );
59  PolySites & operator=( PolySites && );
60  PolySites & operator=( const PolySites & );
61  ~PolySites(void){};
62  std::istream & read(std::istream &s) ;
63  std::ostream & print(std::ostream &stream) const;
64  };
65 }
66 #include <Sequence/bits/PolySites.tcc>
67 #endif
The base class for polymorphism tables.
Polymorphism tables for sequence data.
Definition: PolySites.hpp:33
Sequence::PolyTable, a virtual base class for polymorphism tables.
std::ostream & print(std::ostream &stream) const
output a tab-delimited array of positions and character states
Definition: PolySites.cc:191
The namespace in which this library resides.