int main(int argc, char *argv[])
{
char *file_name;
uint8_t i;
screensize(&screen_width, &screen_height);
/*
printf("width=%d height=%d\n", screen_width, screen_height);
*/
if (argc <= 1) {
/* ProDOS doesn't support piping input/output so, if there are no
arguments, ask for a file name. */
file_name = input_file_name();
if (file_name != NULL && strcmp(file_name,"")!=0) {
more(file_name);
}
}
else {
/* If there are arguments, process them. */
for (i = 1; i < argc; ++i) {
more(argv[i]);
}
}
return EXIT_SUCCESS;
}
void read_kemoview_data_glut(){
char file_name[LENGTHBUF];
char file_head[LENGTHBUF];
char file_head2[LENGTHBUF];
char file_ext[LENGTHBUF];
char pick_command[LENGTHBUF];
int iflag_datatype;
input_file_name(file_name);
kemoview_get_ext_from_file_name(file_name, file_head, file_ext);
printf("file name: %s\n", file_name);
printf("file_head %s\n", file_head);
printf("file_ext %s\n", file_ext);
if ( (file_ext[0] == 'g' && file_ext[1] == 'z')
|| (file_ext[0] == 'G' && file_ext[1] == 'Z') ){
kemoview_get_ext_from_file_name(file_head, file_head2, file_ext);
if (file_ext[0] == '0' && file_ext[1] == '\0') {
return;
}
} else if (file_ext[0] == '0' && file_ext[1] == '\0') {
set_pickup_command(pick_command);
kemoview_set_pick_surface_command(pick_command);
}
iflag_datatype = kemoview_open_data(file_name);
return;
};
int main()
{
string input_file_name("seed.txt");
string output_file_name("crawled_links.txt");
CCrawl crawl(input_file_name.c_str(),output_file_name.c_str());
crawl.DoCrawl();
}
void C_arg::read_args() {
std::cout << "RECKONER ver. " << VERSION << std::endl;
if (num_args == 1) {
print_usage();
exit(EXIT_SUCCESS);
}
//--------------------------------------------------
// parse arguments
//--------------------------------------------------
for (int it_arg = 1; it_arg < num_args; it_arg++) {
if (strcmp(args[it_arg], "-help") == 0) {
print_usage();
exit(EXIT_SUCCESS);
}
else if (strcmp(args[it_arg], "-read") == 0) {
if (it_arg <= num_args - 2) {
read_files_names.push_back(args[it_arg + 1]);
it_arg++;
}
else {
std::cout << std::endl << "ERROR: The read file name is not specified" << std::endl << std::endl;
exit(EXIT_FAILURE);
}
}
else if (strcmp(args[it_arg], "-prefix") == 0) {
if (it_arg <= num_args - 2) {
prefix = args[it_arg + 1];
it_arg++;
}
else {
std::cout << std::endl << "ERROR: The prefix is not specified" << std::endl << std::endl;
exit(EXIT_FAILURE);
}
}
else if (strcmp(args[it_arg], "-kmerlength") == 0) {
if (it_arg <= num_args - 2) {
kmer_length = atoi(args[it_arg + 1]);
it_arg++;
}
else {
std::cout << std::endl << "ERROR: The k-mer length is not specified" << std::endl << std::endl;
exit(EXIT_FAILURE);
}
}
else if (strcmp(args[it_arg], "-extend") == 0) {
if (it_arg <= num_args - 2) {
extend = atoi(args[it_arg + 1]);
it_arg++;
}
else {
std::cout << std::endl << "ERROR: The max extension is not specified" << std::endl << std::endl;
exit(EXIT_FAILURE);
}
}
else if (strcmp(args[it_arg], "-threads") == 0) {
if (it_arg <= num_args - 2) {
n_threads = atoi(args[it_arg + 1]);
it_arg++;
}
else {
std::cout << std::endl << "ERROR: The number of threads is not specified" << std::endl << std::endl;
exit(EXIT_FAILURE);
}
}
else if (strcmp(args[it_arg], "-nowrite") == 0) {
nowrite = true;
}
else {
std::cout << std::endl << "ERROR: Illegal option " << args[it_arg] << std::endl << std::endl;
exit(EXIT_FAILURE);
}
}
//--------------------------------------------------
// check options
//--------------------------------------------------
if (read_files_names.empty()) {
std::cout << std::endl << "ERROR: No read file name is specified." << std::endl << std::endl;
exit(EXIT_FAILURE);
}
if (prefix.empty()) {
prefix = ".";
}
if (kmer_length == 0) {
std::cout << std::endl << "ERROR: k-mer length not specified" << std::endl << std::endl;
exit(EXIT_FAILURE);
}
else if (kmer_length < MIN_KMER_LENGTH) {
std::cout << std::endl << "ERROR: k-mer length should be >= " << MIN_KMER_LENGTH << std::endl << std::endl;
exit(EXIT_FAILURE);
}
if (extend < 1) {
std::cout << std::endl << "ERROR: The max extension should be >= 1" << std::endl << std::endl;
exit(EXIT_FAILURE);
}
//--------------------------------------------------
// file names
//--------------------------------------------------
read_files_types.resize(read_files_names.size(), FileReader::NOT_DEFINED);
for (std::size_t it = 0; it < read_files_names.size(); ++it) {
std::ifstream f_tmp;
f_tmp.open(read_files_names[it].c_str());
if (f_tmp.is_open() == false) {
std::cout << std::endl << "ERROR: Cannot open " << read_files_names[it] << std::endl << std::endl;
exit(EXIT_FAILURE);
}
f_tmp.close();
std::size_t slash_pos = read_files_names[it].find_last_of("/");
std::string input_file_name(slash_pos == std::string::npos ? read_files_names[it] : read_files_names[it].substr(slash_pos + 1));
std::string last_extension, pre_last_extension;
std::size_t dot_pos = input_file_name.find_last_of(".");
if (dot_pos != std::string::npos) {
last_extension = input_file_name.substr(dot_pos);
input_file_name = input_file_name.substr(0, dot_pos);
dot_pos = input_file_name.find_last_of(".");
if (dot_pos != std::string::npos) {
pre_last_extension = input_file_name.substr(dot_pos);
input_file_name = input_file_name.substr(0, dot_pos);
}
}
if (log_file_name.empty()) {
// set a log file name
log_file_name = prefix + "/" + input_file_name + LOG_FILE_EXTENSION;
}
// set error_correction information file names
error_correction_info_files_names.push_back(prefix + "/" + input_file_name + CORRECTION_FILE_EXTENSION);
// set error_corrected read file names
corrected_read_files_names.push_back(prefix + "/" + input_file_name + CORRECTED_FILE_EXTENSION + pre_last_extension + last_extension);
std::transform(last_extension.begin(), last_extension.end(), last_extension.begin(), ::tolower);
if (last_extension == GZ_FILE_EXTENSION) {
read_files_types[it] = FileReader::GZIP;
}
else {
read_files_types[it] = FileReader::RAW;
}
}
Log::open_log_file(log_file_name);
//--------------------------------------------------
// print options
//--------------------------------------------------
std::ofstream& f_log = Log::get_stream();
std::cout << std::endl;
std::cout << "Parsing arguments is finished" << std::endl;
for (std::size_t it = 0; it < read_files_names.size(); ++it) {
std::cout << " Read File " << (it + 1) << std::endl;
std::cout << " Name: : " << read_files_names[it] << std::endl;
std::string compressed = "N";
if (read_files_types[it] == FileReader::GZIP) {
compressed = "Y (GZIP)";
}
std::cout << " Compressed: : " << compressed << std::endl;
}
std::cout << " Log File Name : " << log_file_name << std::endl;
std::cout << " K-mer Length : " << kmer_length << std::endl;
std::cout << " Number of Threads : " << n_threads << std::endl;
std::cout << std::endl;
f_log << "RECKONER ver. " << VERSION << std::endl;
f_log << std::endl;
f_log << "Parsing arguments is finished" << std::endl;
for (std::size_t it = 0; it < read_files_names.size(); ++it) {
f_log << " Read File " << (it + 1) << std::endl;
f_log << " Name: : " << read_files_names[it] << std::endl;
std::string compressed = "N";
if (read_files_types[it] == FileReader::GZIP) {
compressed = "Y (GZIP)";
}
f_log << " Compressed: : " << compressed << std::endl;
}
f_log << " Log File Name : " << log_file_name << std::endl;
f_log << " K-mer Length : " << kmer_length << std::endl;
f_log << " Number of Threads : " << n_threads << std::endl;
f_log << std::endl;
}
