string read_sequence_from_file (string filename) {
ifstream fileReader (filename.c_str());
if (fileReader == 0) { // couldn't open file
throw(stacktrace() + "\n\nCould not open " + filename + "\n");
}
string mySequence;
char c_line [MAX_LINE_LENGTH];
fileReader.getline(c_line, MAX_LINE_LENGTH);
while (! fileReader.eof() ) {
if (c_line[0] != '>') {
string s_line (c_line);
for (unsigned int i = 0; i < strlen(c_line); i++) {
char c = tolower(c_line[i]);
if (c == ' ' || c == '\t' || c == '\n') { continue;}
mySequence += c;
}
}
fileReader.getline(c_line, MAX_LINE_LENGTH);
}
return (mySequence);
}
std::array<ublas::matrix<double>, 3> get_iris(std::string filename){
std::ifstream fs(filename);
ASSERT(!fs.bad() && fs.good(), "Failed to open the file.");
std::array<ublas::matrix<double>, 3> datas;
for (int i = 0; i < 3; ++i){
datas[i] = ublas::matrix<double>(4, 50);
for (int j = 0; j < 50; ++j){
char *line = new char[100];
fs.getline(line, 100);
std::vector<string> nums;
string s_line(line);
boost::split(nums, s_line, boost::is_any_of(","));
delete[] line;
ASSERT(nums.size() == 5, "Failed to parse the date.");
for (int k = 0; k < 4; ++k){
datas[i](k, j) = boost::lexical_cast<double, string>(nums[k]);
}
}
}
return datas;
}
