// Copyright 2013, 2014, 2015, 2016 Ramon Diaz-Uriarte
// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
// You should have received a copy of the GNU General Public License
// along with this program. If not, see <http://www.gnu.org/licenses/>.
// This code is not being used in production. It was used during
// development, to see what C++ was thinking about what R was passing to
// it. It is left here, but is now all commented out.
// // [[Rcpp::export]]
// void readFitnessEffects(Rcpp::List rFE,
// bool echo) {
// // fitnessEffectsAll fitnessEffects;
// // convertFitnessEffects(rFE, fitnessEffects);
// fitnessEffectsAll fitnessEffects = convertFitnessEffects(rFE);
// if(echo) {
// printFitnessEffects(fitnessEffects);
// }
// }
// void printPoset(const std::vector<Poset_struct>& Poset) {
// int counterInfs = 0;
// int counterNegInfs = 0;
// Rcpp::Rcout << "\n ********** Poset or Restriction table (internal) *******"
// << std::endl;
// if(!Poset.size()) {
// Rcpp::Rcout << "No posets: restriction table of size 0"<< std::endl;
// } else {
// Rcpp::Rcout << "Size = " << (Poset.size() - 1) << std::endl;
// for(size_t i = 1; i != Poset.size(); ++i) {
// // We do not show the Poset[0]
// Rcpp::Rcout <<"\t Dependent Module or gene (child) " << i
// << ". childNumID: " << Poset[i].childNumID
// << ". child full name: " << Poset[i].child
// << std::endl;
// Rcpp::Rcout <<"\t\t typeDep = " << depToString(Poset[i].typeDep) << ' ' ;
// Rcpp::Rcout <<"\t s = " << Poset[i].s << " ";
// Rcpp::Rcout <<"\t sh = " << Poset[i].sh << std::endl;
// if(std::isinf(Poset[i].sh))
// ++counterInfs;
// if(std::isinf(Poset[i].sh) && (Poset[i].sh < 0))
// ++counterNegInfs;
// Rcpp::Rcout << "\t\t Number of parent modules or genes = " <<
// Poset[i].parents.size() << std::endl;
// Rcpp::Rcout << "\t\t\t Parents IDs: ";
// for(auto const &c : Poset[i].parentsNumID)
// Rcpp::Rcout << c << "; ";
// Rcpp::Rcout << std::endl;
// Rcpp::Rcout << "\t\t\t Parents names: ";
// for(auto const &c : Poset[i].parents)
// Rcpp::Rcout << c << "; ";
// Rcpp::Rcout << std::endl;
// // for(size_t j = 0; j != Poset[i].deps.size(); ++j) {
// // Rcpp::Rcout << "\t\t\t\t Module " << (j + 1) << ": "
// // << Poset[i].deps[j] << std::endl;
// }
// Rcpp::Rcout << std::endl;
// if(counterInfs) {
// Rcpp::Rcout << "In sh there were " << counterNegInfs
// << " negative infinites and "
// << (counterInfs - counterNegInfs)
// << " positive infinites" << std::endl;
// }
// }
// }
// void printGene_Module_table(const
// std::vector<Gene_Module_struct>& Gene_Module_tabl,
// const bool gMOneToOne) {
// // Rcpp::Rcout <<
// // "\n\n******** geneModule table (internal) *******:\nGene name\t Gene NumID\t Module name\t Module NumID\n";
// // for(auto it = Gene_Module_tabl.begin(); it != Gene_Module_tabl.end(); ++it) {
// // Rcpp::Rcout << '\t' << it->GeneName << '\t' << it->GeneNumID << '\t'
// // << it->ModuleName << '\t' << it->ModuleNumID << std::endl;
// // }
// Rcpp::Rcout <<
// "\n\n******** geneModule table (internal) *******:\n" <<
// std::setw(14) << std::left << "Gene name" << std::setw(14) << "Gene NumID" << std::setw(14)
// << "Module name" << std::setw(14) << "Module NumID" << "\n";
// for(auto it = Gene_Module_tabl.begin(); it != Gene_Module_tabl.end(); ++it) {
// Rcpp::Rcout << std::setw(14) << std::left << it->GeneName << std::setw(14)
// << it->GeneNumID << std::setw(14) << it->ModuleName
// << std::setw(14) << it->ModuleNumID << std::endl;
// }
// if(gMOneToOne)
// Rcpp::Rcout << "This is a dummy module table: each module is one gene."
// << std::endl;
// }
// void printOtherEpistasis(const std::vector<epistasis>& Epistasis,
// const std::string effectName,
// const std::string sepstr) {
// Rcpp::Rcout << "\n ********** General " << effectName << "s (internal) *******"
// << std::endl;
// if(!Epistasis.size()) {
// Rcpp::Rcout << "No general " << effectName << std::endl;
// } else {
// Rcpp::Rcout << " Number of " << effectName <<"s = " << Epistasis.size();
// for(size_t i = 0; i != Epistasis.size(); ++i) {
// Rcpp::Rcout << "\n\t " << effectName << " " << i + 1 << ": " <<
// ". Modules or Genes (names) = " << Epistasis[i].names[0];
// for(size_t j = 1; j != Epistasis[i].NumID.size(); ++j) {
// Rcpp::Rcout << sepstr << Epistasis[i].names[j] ;
// }
// Rcpp::Rcout << ".\t Modules or Genes (NumID) = " << Epistasis[i].NumID[0];
// for(size_t j = 1; j != Epistasis[i].NumID.size(); ++j) {
// Rcpp::Rcout << sepstr << Epistasis[i].NumID[j] ;
// }
// Rcpp::Rcout << ".\t s = " << Epistasis[i].s;
// }
// }
// Rcpp::Rcout << std::endl;
// }
// void printNoInteractionGenes(const genesWithoutInt& genesNoInt) {
// Rcpp::Rcout << "\n ********** All remaining genes without interactions (internal) *******"
// << std::endl;
// if(genesNoInt.shift <= 0) {
// Rcpp::Rcout << "No other genes without interactions" << std::endl;
// } else {
// Rcpp::Rcout << std::setw(14) << std::left << "Gene name" << std::setw(14)
// << "Gene NumID" << std::setw(14) << "s" << std::endl;
// for(size_t i = 0; i != genesNoInt.NumID.size(); ++i) {
// Rcpp::Rcout << std::setw(14) << std::left << genesNoInt.names[i]
// << std::setw(14) << genesNoInt.NumID[i]
// << std::setw(14) << genesNoInt.s[i] << '\n';
// }
// }
// }
// void printAllOrderG(const std::vector<int> ge) {
// Rcpp::Rcout << "\n ********** NumID of genes/modules in the order restrict. (internal) *******"
// << std::endl;
// for(auto const &g : ge)
// Rcpp::Rcout << g << " ";
// Rcpp::Rcout << std::endl;
// }
// void printFitnessEffects(const fitnessEffectsAll& fe) {
// printGene_Module_table(fe.Gene_Module_tabl, fe.gMOneToOne);
// printPoset(fe.Poset);
// printOtherEpistasis(fe.orderE, "order effect", " > ");
// printOtherEpistasis(fe.Epistasis, "epistatic interaction", ", ");
// printNoInteractionGenes(fe.genesNoInt);
// printAllOrderG(fe.allOrderG);
// }
