ToPS
TargetModel.hpp
00001 /*
00002  *       TargetModel.hpp
00003  *
00004  *       Copyright 2011 Andre Yoshiaki Kashiwabara <akashiwabara@usp.br>
00005  *                      Ígor Bonádio <ibonadio@ime.usp.br>
00006  *                      Vitor Onuchic <vitoronuchic@gmail.com>
00007  *                      Alan Mitchell Durham <aland@usp.br>
00008  *
00009  *       This program 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  *       This program 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  *       along with this program; if not, write to the Free Software
00021  *       Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
00022  *       MA 02110-1301, USA.
00023  */
00024 
00025 #ifndef TargetModel_H
00026 #define TargetModel_H
00027 
00028 #include "crossplatform.hpp"
00029 
00030 #include "Sequence.hpp"
00031 #include "Alphabet.hpp"
00032 
00033 #include "ProbabilisticModel.hpp"
00034 #include "FactorableModel.hpp"
00035 #include "TargetModelCreator.hpp"
00036 #include "util.hpp"
00037 #include <cstdarg>
00038 #include <vector>
00039 
00040 namespace tops {
00041 
00043   class DLLEXPORT TargetModel : public ProbabilisticModel
00044   {
00045   public:
00046 
00047     TargetModel()  {
00048     };
00049 
00050     virtual ~TargetModel() {}
00051     virtual void initialize (const ProbabilisticModelParameters & p ) ;
00052     virtual ProbabilisticModelParameters parameters() const;
00053     virtual std::string model_name() const {
00054       return "TargetModel";
00055     }
00056 
00058     virtual double evaluate(const Sequence & s, unsigned int begin, unsigned int end) const;
00059 
00060     virtual ProbabilisticModelCreatorPtr getFactory () const{
00061           return TargetModelCreatorPtr(new TargetModelCreator());
00062     }
00063 
00064     virtual std::string str() const;
00065 
00066 
00067   };
00068 
00069   typedef boost::shared_ptr<TargetModel> TargetModelPtr;
00070 }
00071 
00072 
00073 #endif