ToPS: PhasedRunLengthDistributionCreator.cpp Source File

00001 /*
00002  *       PhasedRunLengthDistributionCreator.cpp
00003  *
00004  *       Copyright 2011 Andre Yoshiaki Kashiwabara <akashiwabara@usp.br>
00005  *                      �gor Bon�dio <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 #include "PhasedRunLengthDistributionCreator.hpp"
00026 #include "SequenceFactory.hpp"
00027 #include "SequenceFactory.hpp"
00028 #include "ProbabilisticModelCreatorClient.hpp"
00029 #include "PhasedRunLengthDistribution.hpp"
00030 
00031 namespace tops {
00032   ProbabilisticModelPtr PhasedRunLengthDistributionCreator::create( ProbabilisticModelParameters & parameters, const std::map<std::string,ProbabilisticModelPtr> & models) const {
00033     ProbabilisticModelParameterValuePtr iphasepar = parameters.getMandatoryParameterValue("input_phase");
00034     ProbabilisticModelParameterValuePtr ophasepar = parameters.getMandatoryParameterValue("output_phase");
00035     ProbabilisticModelParameterValuePtr nphasepar = parameters.getMandatoryParameterValue("number_of_phases");
00036     ProbabilisticModelParameterValuePtr  deltapar = parameters.getMandatoryParameterValue("delta");
00037     ProbabilisticModelParameterValuePtr  modelpar = parameters.getMandatoryParameterValue("model");
00038     if(
00039        (nphasepar == NULL) ||
00040        (deltapar == NULL) ||
00041        (iphasepar == NULL) ||
00042        (ophasepar == NULL) ||
00043        (modelpar == NULL) ) {
00044       exit(-1);
00045     }
00046     int iphase = iphasepar -> getInt();
00047     int ophase = ophasepar -> getInt();
00048     int nphase = nphasepar -> getInt();
00049     int delta = deltapar -> getInt();
00050     std::string modelstr = modelpar->getString();
00051 
00052 
00053     ConfigurationReader reader;
00054     ProbabilisticModelPtr m;
00055     std::map<std::string, ProbabilisticModelPtr>::const_iterator it = models.find(modelstr);
00056     if(it != models.end())
00057       m = it->second;
00058     else{
00059       std::cerr << "Model " << modelstr << " not loaded ! " << std::endl;
00060       std::exit(-1);
00061     }
00062 
00063     PhasedRunLengthDistributionPtr decorator = PhasedRunLengthDistributionPtr(new PhasedRunLengthDistribution(m));
00064     AlphabetPtr alpha = m->alphabet();
00065     decorator->initialize(delta, iphase, ophase, nphase);
00066     decorator->setAlphabet(m->alphabet());
00067     decorator->subModelName(modelstr);
00068     return decorator;
00069   }
00070 
00071   ProbabilisticModelPtr PhasedRunLengthDistributionCreator::create( ProbabilisticModelParameters & parameters) const {
00072     ProbabilisticModelParameterValuePtr iphasepar = parameters.getMandatoryParameterValue("input_phase");
00073     ProbabilisticModelParameterValuePtr ophasepar = parameters.getMandatoryParameterValue("output_phase");
00074     ProbabilisticModelParameterValuePtr nphasepar = parameters.getMandatoryParameterValue("number_of_phases");
00075     ProbabilisticModelParameterValuePtr  deltapar = parameters.getMandatoryParameterValue("delta");
00076     ProbabilisticModelParameterValuePtr  modelpar = parameters.getMandatoryParameterValue("model");
00077     if(
00078        (nphasepar == NULL) ||
00079        (deltapar == NULL) ||
00080        (iphasepar == NULL) ||
00081        (ophasepar == NULL) ||
00082        (modelpar == NULL) ) {
00083       exit(-1);
00084     }
00085     int iphase = iphasepar -> getInt();
00086     int ophase = ophasepar -> getInt();
00087     int nphase = nphasepar -> getInt();
00088     int delta = deltapar -> getInt();
00089     std::string modelstr = modelpar->getString();
00090 
00091     ProbabilisticModelCreatorClient creator;
00092     ConfigurationReader reader;
00093     ProbabilisticModelPtr m ;
00094     if((modelstr.size() > 0) && (modelstr[0] == '[') ){
00095       modelstr = modelstr.substr(1, modelstr.size() -2 );
00096       reader.load(modelstr);
00097       ProbabilisticModelParametersPtr par = reader.parameters();
00098       m = creator.create(*par);
00099     } else  {
00100         m = creator.create(modelstr) ;
00101         if(m == NULL) {
00102           std::cerr << "Can not load model file " << modelstr<< "!" << std::endl;
00103           exit(-1);
00104         }
00105       }
00106     PhasedRunLengthDistributionPtr decorator = PhasedRunLengthDistributionPtr(new PhasedRunLengthDistribution(m));
00107     AlphabetPtr alpha = m->alphabet();
00108     decorator->initialize(delta, iphase, ophase, nphase);
00109     decorator->setAlphabet(m->alphabet());
00110     return decorator;
00111 
00112   }
00113 
00114 }