ToPS: GeneralizedPairHiddenMarkovModelCreator.hpp Source File

00001 #ifndef GENERALIZED_PAIR_HIDDEN_MARKOV_MODEL_CREATOR_HPP
00002 #define GENERALIZED_PAIR_HIDDEN_MARKOV_MODEL_CREATOR_HPP
00003 
00004 #include "ProbabilisticModelCreator.hpp"
00005 #include "ProbabilisticModel.hpp"
00006 #include <boost/shared_ptr.hpp>
00007 
00008 namespace tops {
00009   class GeneralizedPairHiddenMarkovModelCreator : public ProbabilisticModelCreator 
00010   {
00011   public:
00012     GeneralizedPairHiddenMarkovModelCreator() {}
00013     virtual ~GeneralizedPairHiddenMarkovModelCreator(){};
00014     virtual ProbabilisticModelPtr create(ProbabilisticModelParameters & parameters) const ;
00015 
00016     virtual std::string help() const 
00017     {
00018       std::stringstream out;
00019       out << "\nUSAGE: " << std::endl;
00020       out << "Mandatory parameters: " << std::endl;
00021       out << "\tstate_names" << std::endl;
00022       out << "\tobservation_symbols" << std::endl;
00023       out << "\tinitial_probabilities" << std::endl;
00024       out << "\tend_probabilities" << std::endl;
00025       out << "\tnumber_of_emissions" << std::endl;
00026       out << "\tduration_probabilities" << std::endl;
00027       out << "\ttransitions" << std::endl;
00028       out << "\temission_models" << std::endl;
00029       out << "Example: " << std::endl;
00030       out << "\tmodel_name = \"GeneralizedPairHiddenMarkovModel\"" << std::endl;
00031       out << "\tstate_names = (\"N\",\"C\")" << std::endl;
00032       out << "\tobservation_symbols = (\"A\",\"T\",\"C\",\"G\")" << std::endl;
00033       out << "\ttransitions = (\"N\" | \"N\": 0.899;" << std::endl;
00034       out << "\t \"C\" | \"N\": 0.1;" << std::endl;
00035       out << "\t \"N\" | \"C\": 0.999;" << std::endl;
00036       out << "\t(\"C\" : \"codingEmissionModel.txt\";" << std::endl;
00037       out << "\t\"N\" : \"noncodingEmissionModel.txt\";)" << std::endl;
00038       out << "\tinitial_probabilities = (\"N\":  0.9;" << std::endl;
00039       out << "\t \"C\": 0.1)" << std::endl;
00040       out << "end_probabilities = (\"N\" = 0.0001;" << std::endl;
00041       out << "\"C\" = 0.0001;)" << std::endl;
00042       out << "number_of_emissions = (\"C\" : \"1-1000,1-1000\";" << std::endl;
00043       out << "\"N\" : \"0-1,0-1\";)" << std::endl;
00044       out << "duration_probabilities = (\"C\" : \"durationCoding.txt\";)" << std::endl;
00045       return out.str();
00046     }
00047 
00048 
00049   };
00050   typedef boost::shared_ptr <GeneralizedPairHiddenMarkovModelCreator> GeneralizedPairHiddenMarkovModelCreatorPtr;
00051 }
00052 
00053 #endif