libsequence: PolySNPimpl.hpp Source File

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 
00024 #include <Sequence/PolyTable.hpp>
00025 #include <Sequence/stateCounter.hpp>
00026 #include <string>
00027 
00028 namespace Sequence
00029 {
00030   struct _PolySNPImpl
00037   {
00038     const PolyTable* _data;
00039     unsigned _nsites,_nsam,_outgroup;
00040     bool _haveOutgroup, _totMuts;
00041     unsigned _totsam;
00042     unsigned _DVK;
00043     double _DVH;
00044     bool _counted_singletons;
00045     bool _know_pi;
00046     bool _CalculatedDandV;
00047     double _pi;
00048     unsigned _singletons;
00049     unsigned _walls_Bprime,_NumPoly;
00050     double _walls_B,_walls_Q;
00051     bool _calculated_wall_stats;
00052     std::vector< Sequence::stateCounter > _counts;
00053     std::vector< std::pair< bool, Sequence::stateCounter > > _derivedCounts;
00054     bool _preprocessed;
00055     void preprocess(void);
00056 
00057     _PolySNPImpl (const Sequence::PolyTable * data, bool haveOutgroup ,
00058                   unsigned outgroup, bool totMuts);
00059   };
00060 }