00001 /* 00002 00003 Copyright (C) 2003-2009 Kevin Thornton, krthornt[]@[]uci.edu 00004 00005 Remove the brackets to email me. 00006 00007 This file is part of libsequence. 00008 00009 libsequence is free software: you can redistribute it and/or modify 00010 it under the terms of the GNU General Public License as published by 00011 the Free Software Foundation, either version 3 of the License, or 00012 (at your option) any later version. 00013 00014 libsequence is distributed in the hope that it will be useful, 00015 but WITHOUT ANY WARRANTY; without even the implied warranty of 00016 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 00017 GNU General Public License for more details. 00018 00019 You should have received a copy of the GNU General Public License 00020 long with libsequence. If not, see <http://www.gnu.org/licenses/>. 00021 00022 */ 00023 00045 #ifndef KIMURA80_H 00046 #define KIMURA80_H 00047 00048 namespace Sequence 00049 { 00050 class Seq; 00051 class Kimura80 00052 { 00053 private: 00054 unsigned num_Ts, num_Tv; 00055 size_t seqlen; //total sequence length 00056 size_t sites_compared; //number of ungapped sites in the data 00057 void Compute (const Sequence::Seq *seq1, const Sequence::Seq *seq2); 00058 double divergence, P, Q; 00059 public: 00060 explicit Kimura80 (const Sequence::Seq * seqa,const Sequence::Seq * seqb); 00061 double K (); 00062 size_t sites (void); 00063 }; 00064 } 00065 #endif
1.6.3