ToPS
DiscreteIIDModelCreator.hpp
00001 /*
00002  *       DiscreteIIDModelCreator.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 FINITE_DISCRETE_DISTRIBUTION_CREATOR_HPP
00026 #define FINITE_DISCRETE_DISTRIBUTION_CREATOR_HPP
00027 
00028 #include "crossplatform.hpp"
00029 
00030 #include "ProbabilisticModelCreator.hpp"
00031 #include "ProbabilisticModel.hpp"
00032 #include "DiscreteIIDModel.hpp"
00033 #include <boost/shared_ptr.hpp>
00034 
00035 namespace tops {
00037   class DLLEXPORT DiscreteIIDModelCreator : public ProbabilisticModelCreator
00038   {
00039   public:
00040     DiscreteIIDModelCreator() {}
00041     virtual ~DiscreteIIDModelCreator(){};
00042     virtual ProbabilisticModelPtr create(ProbabilisticModelParameters & parameters) const ;
00043     virtual DiscreteIIDModelPtr createDiscreteIIDModel(ProbabilisticModelParameters & parameters) const ;
00044 
00045     virtual std::string help() const
00046     {
00047       std::stringstream out;
00048       out << "\nUSAGE: " << std::endl;
00049       out << "Mandatory parameters: " << std::endl;
00050       out << "\tprobabilities = <a vector of doubles>" << std::endl;
00051       out << "Optional parameters: " << std::endl;
00052       out << "\talphabet = <a vector of strings>" << std::endl;
00053       out << "Example: " << std::endl;
00054       out << "\tcreate_model=\"DiscreteIIDModel\"" << std::endl;
00055       out << "\toutput_model_file=\"./example.model\"" << std::endl;
00056       out << "\talphabet= (\"A\", \"C\", \"G\", \"T\")" << std::endl;
00057       out << "\tprobabilities= (0.25, 0.25, 0.25)" << std::endl;
00058       return out.str();
00059     }
00060 
00061   };
00062   typedef boost::shared_ptr < DiscreteIIDModelCreator> DiscreteIIDModelCreatorPtr;
00063 }
00064 
00065 #endif