DenseMatrix RMAExpressMatrixReader::read(std::istream& input, unsigned int opts) const
{
//TODO: interpret the passed options
if(readString_(input) != "RMAExpressionValues") {
return DenseMatrix(0,0);
}
uint32_t version;
input.read(reinterpret_cast<char*>(&version), 4);
if(version != 1) {
return DenseMatrix(0,0);
}
skipString_(input); // Skip the RMAExpress version number
skipString_(input); // Skip the chiptype
uint32_t nrows, ncols;
input.read(reinterpret_cast<char*>(&ncols), 4);
input.read(reinterpret_cast<char*>(&nrows), 4);
std::vector<std::string> colnames(ncols);
std::vector<std::string> rownames(nrows);
readStringVector_(input, colnames);
readStringVector_(input, rownames);
DenseMatrix result(std::move(rownames), std::move(colnames));
input.read(reinterpret_cast<char*>(result.matrix().data()), nrows * ncols * sizeof(double));
return result;
}
List maxmind_bindings::call_maxmind(std::vector < std::string > ip_addresses, const char* file,
std::vector < std::string > fields){
//Open file
MMDB_s geo_file;
int result;
result = MMDB_open(file, 0, &geo_file);
if(result != MMDB_SUCCESS){
throw std::range_error("The geolocation database could not be opened");
}
//Create references and holding
std::vector < std::string >& ip_ref = ip_addresses;
int input_size = ip_addresses.size();
IntegerVector rownames(input_size);
rownames = Rcpp::seq(1,input_size);
List output = lookup(ip_ref, &geo_file, fields);
output.attr("class") = "data.frame";
output.attr("names") = fields;
output.attr("row.names") = rownames;
//Close and return
MMDB_close(&geo_file);
return output;
}
SEXP rawSymmetricMatrixSubsetIndices(SEXP object_, SEXP i_, SEXP j_, SEXP drop_)
{
BEGIN_RCPP
Rcpp::S4 object = object_;
Rcpp::CharacterVector markers = object.slot("markers");
Rcpp::NumericVector levels = object.slot("levels");
Rcpp::RawVector data = object.slot("data");
Rcpp::IntegerVector i = i_;
Rcpp::IntegerVector j = j_;
bool drop = Rcpp::as<bool>(drop_);
if(drop)
{
if(i.size() == 1 && j.size() == 1)
{
R_xlen_t i = Rcpp::as<int>(i_);
R_xlen_t j = Rcpp::as<int>(j_);
if(i > j) std::swap(i, j);
Rbyte rawValue = data[(j*(j-(R_xlen_t)1))/(R_xlen_t)2 + i-(R_xlen_t)1];
if(rawValue == 0xff) return Rcpp::wrap(NA_REAL);
return Rcpp::wrap(levels[rawValue]);
}
else if(i.size() == 1)
{
Rcpp::NumericVector result(j.size());
R_xlen_t i = Rcpp::as<int>(i_);
Rcpp::CharacterVector names(j.size());
for(R_xlen_t jCounter = 0; jCounter < j.size(); jCounter++)
{
R_xlen_t iCopied = i;
R_xlen_t jValue = j[jCounter];
names[jCounter] = markers[jValue-(R_xlen_t)1];
if(iCopied > jValue) std::swap(iCopied, jValue);
Rbyte rawValue = data[(jValue*(jValue-(R_xlen_t)1))/(R_xlen_t)2 + iCopied-(R_xlen_t)1];
if(rawValue == 0xff) result[jCounter] = NA_REAL;
else result[jCounter] = levels[rawValue];
}
result.attr("names") = names;
return result;
}
else if(j.size() == 1)
{
Rcpp::NumericVector result(i.size());
R_xlen_t j = Rcpp::as<int>(j_);
Rcpp::CharacterVector names(i.size());
for(R_xlen_t iCounter = 0; iCounter < i.size(); iCounter++)
{
R_xlen_t jCopied = j;
R_xlen_t iValue = i[iCounter];
names[iCounter] = markers[iValue-(R_xlen_t)1];
if(iValue > jCopied) std::swap(iValue, jCopied);
Rbyte rawValue = data[(jCopied*(jCopied-(R_xlen_t)1))/(R_xlen_t)2 + iValue-(R_xlen_t)1];
if(rawValue == 0xff) result[iCounter] = NA_REAL;
else result[iCounter] = levels[rawValue];
}
result.attr("names") = names;
return result;
}
}
Rcpp::NumericMatrix result((int)i.size(), (int)j.size());
Rcpp::CharacterVector rownames(i.size()), colnames(j.size());
for(R_xlen_t iCounter = 0; iCounter < i.size(); iCounter++)
{
rownames[iCounter] = markers[i[iCounter]-(R_xlen_t)1];
for(R_xlen_t jCounter = 0; jCounter < j.size(); jCounter++)
{
R_xlen_t iCopied = i[iCounter], jCopied = j[jCounter];
if(iCopied > jCopied) std::swap(iCopied, jCopied);
Rbyte rawValue = data[(jCopied*(jCopied-(R_xlen_t)1))/(R_xlen_t)2 + iCopied-(R_xlen_t)1];
if(rawValue == 0xff) result(iCounter, jCounter) = NA_REAL;
else result(iCounter, jCounter) = levels[rawValue];
}
}
for(R_xlen_t jCounter = 0; jCounter < j.size(); jCounter++)
{
colnames[jCounter] = markers[j[jCounter]-(R_xlen_t)1];
}
result.attr("dimnames") = Rcpp::List::create(rownames, colnames);
return result;
END_RCPP
}
