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00001 /* 00002 * InhomogeneousMarkovChainCreator.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 IHM_CREATOR_HPP 00026 #define IHM_CREATOR_HPP 00027 00028 #include "crossplatform.hpp" 00029 00030 #include "ProbabilisticModelCreator.hpp" 00031 #include "ProbabilisticModel.hpp" 00032 #include <boost/shared_ptr.hpp> 00033 00034 namespace tops { 00036 class DLLEXPORT InhomogeneousMarkovChainCreator : public ProbabilisticModelCreator 00037 { 00038 public: 00039 InhomogeneousMarkovChainCreator() {} 00040 virtual ~InhomogeneousMarkovChainCreator(){}; 00041 virtual ProbabilisticModelPtr create(ProbabilisticModelParameters & parameters) const ; 00042 virtual std::string help() const { 00043 std::stringstream out; 00044 out << "\nUSAGE: " << std::endl; 00045 out << "Mandatory parameters: " << std::endl; 00046 out << "\tposition_specific_distribution" << std::endl; 00047 out << "\tphased" << std::endl; 00048 out << "\talphabet" << std::endl; 00049 out << "Example: " << std::endl; 00050 out << "\tmodel_name=\"InhomogeneousMarkovChain\"" << std::endl; 00051 out << "\talphabet=(\"0\", \"1\")" << std::endl; 00052 out << "\tprob1 = (\"0\" | \".\": 0.5; # Pr(X_0 = 0)" << std::endl; 00053 out << "\t \"1\" | \".\": 0.5; # Pr(X_0 = 1)" << std::endl; 00054 out << "\t \"0\" | \"0\": 0.1; # Pr(X_n = 0 | X_{n-1} = 0)" << std::endl; 00055 out << "\t \"1\" | \"0\": 0.9; # Pr(X_n = 1 | X_{n-1} = 0)" << std::endl; 00056 out << "\t \"0\" | \"1\": 0.5; # Pr(X_n = 0 | X_{n-1} = 1)" << std::endl; 00057 out << "\t \"1\" | \"1\": 0.5; # Pr(X_n = 1 | X_{n-1} = 1)" << std::endl; 00058 out << "\t \"0\" | \"1 0\": 0.7; # Pr(X_n = 0 | X_{n-1} = 1, X_{n-2} = 0)" << std::endl; 00059 out << "\t \"1\" | \"1 0\": 0.3; # Pr(X_n = 1 | X_{n-1} = 1, X_{n-2} = 0)" << std::endl; 00060 out << "\t \"0\" | \"1 1\": 0.4; # Pr(X_n = 0 | X_{n-1} = 1, X_{n-2} = 1)" << std::endl; 00061 out << "\t \"1\" | \"1 1\": 0.6) # Pr(X_n = 0 | X_{n-1} = 1, X_{n-2} = 1)" << std::endl; 00062 out << "\tprob2 = (\"0\" | \".\": 0.5; # Pr(X_0 = 0)" << std::endl; 00063 out << "\t \"1\" | \".\": 0.5; # Pr(X_0 = 1)" << std::endl; 00064 out << "\t \"0\" | \"0\": 0.9; # Pr(X_n = 0 | X_{n-1} = 0)" << std::endl; 00065 out << "\t \"1\" | \"0\": 0.1; # Pr(X_n = 1 | X_{n-1} = 0)" << std::endl; 00066 out << "\t \"0\" | \"1\": 0.5; # Pr(X_n = 0 | X_{n-1} = 1)" << std::endl; 00067 out << "\t \"1\" | \"1\": 0.5; # Pr(X_n = 1 | X_{n-1} = 1)" << std::endl; 00068 out << "\t \"0\" | \"1 0\": 0.3; # Pr(X_n = 0 | X_{n-1} = 1, X_{n-2} = 0)" << std::endl; 00069 out << "\t \"1\" | \"1 0\": 0.7; # Pr(X_n = 1 | X_{n-1} = 1, X_{n-2} = 0)" << std::endl; 00070 out << "\t \"0\" | \"1 1\": 0.6; # Pr(X_n = 0 | X_{n-1} = 1, X_{n-2} = 1)" << std::endl; 00071 out << " t \"1\" | \"1 1\": 0.4) # Pr(X_n = 0 | X_{n-1} = 1, X_{n-2} = 1)" << std::endl; 00072 out << "\tposition_specific_distribution = (\"prob1\", \"prob2\")" << std::endl; 00073 return out.str(); 00074 } 00075 00076 }; 00077 typedef boost::shared_ptr < InhomogeneousMarkovChainCreator> InhomogeneousMarkovChainCreatorPtr; 00078 } 00079 00080 #endif
1.8.0