libsequence  1.9.5
Snn.hpp
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.
8 
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.
13 
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.
18 
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/>.
21 
22 */
23 
24 #ifndef __SEQUENCE_SNN_HPP__
25 #define __SEQUENCE_SNN_HPP__
26 
27 #include <Sequence/Comparisons.hpp>
28 #include <Sequence/PolyTable.hpp>
29 #include <vector>
30 #include <utility>
31 #include <cassert>
32 
33 namespace Sequence
34 {
38  double Snn_statistic( const unsigned individuals[],
39  const std::vector< std::vector<double> > & dkj,
40  const unsigned config[],
41  const size_t & npop,
42  const unsigned & nsam )__attribute__ ((deprecated));
43 
44  template< typename shuffler >
45  std::pair<double,double>
46  Snn_test(const PolyTable & snpTable,
47  const unsigned config[],
48  const size_t & npop,
49  shuffler & s,
50  const unsigned & nperms = 10000)__attribute__ ((deprecated));
51 
52  template< typename shuffler >
53  std::vector< std::vector<double> >
54  Snn_test_pairwise(const PolyTable & snpTable,
55  const unsigned config[],
56  const size_t & npop,
57  shuffler & s,
58  const unsigned & nperms = 10000)__attribute__ ((deprecated));
59 }
60 #endif
61 #include <Sequence/bits/Snn.tcc>
double Snn_statistic(const unsigned individuals[], const std::vector< std::vector< double > > &dkj, const unsigned config[], const size_t &npop, const unsigned &nsam) __attribute__((deprecated))
Definition: Snn.cc:28
STL namespace.
Sequence::PolyTable, a virtual base class for polymorphism tables.
The namespace in which this library resides.
class __attribute__((deprecated)) FST
Functor to count the number of states, excluding gaps and missing data, in a range of characters...
Definition: FST.hpp:41
delcaration of routines for comparing DNA sequences This file declares a set of functions useful for ...