TNT_Script/src_tnt2figtree/tnt2figtree.cpp

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2024-01-14 22:30:04 +08:00
#include <fstream>
#include <iostream>
#include <regex>
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#include <sstream>
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std::string remove_useless(std::string input_str1)
{
std::string result_str1 =
std::regex_replace(input_str1, std::regex(" /*"), " ");
result_str1 = std::regex_replace(result_str1, std::regex("\\["), "{");
result_str1 = std::regex_replace(result_str1, std::regex("\\]"), "}");
return result_str1;
}
std::string add_support(std::string input_str2)
{
std::string result_str2 = "";
size_t i = 0;
while (i < input_str2.length()) {
if (input_str2[i] == ')') {
result_str2 += input_str2[i];
i++;
std::string support_str = "";
while (i < input_str2.length() &&
std::regex_match(std::string(1, input_str2[i]),
std::regex("[/0-9{}?]"))) {
support_str += input_str2[i];
i++;
}
result_str2 += "[&support=\"" + support_str + "\"]";
}
else {
result_str2 += input_str2[i];
i++;
}
}
return result_str2;
}
std::string add_blen(std::string input_str3)
{
std::string result_str3 = "";
int i = 0;
for (char c : input_str3) {
if (c == '(') {
i++;
result_str3 += c;
}
else if (c == ')') {
result_str3 += ":" + std::to_string(i) + c;
i--;
}
else if (c == ',') {
result_str3 += ":" + std::to_string(i) + c;
}
else {
result_str3 += c;
}
}
return result_str3;
}
std::string remove_slash(std::string input_str4)
{
std::string result_str4 = std::regex_replace(
input_str4, std::regex("\\[&support=\"[\\/\\s]*\"\\]"), "");
return result_str4;
}
std::vector<std::string> get_lines(std::string filename)
{
std::ifstream file(filename);
if (!file.is_open()) {
std::cout << "Failed to open the input file." << std::endl;
}
std::vector<std::string> lines;
std::string line;
while (std::getline(file, line)) {
lines.push_back(line);
}
file.close();
return lines;
}
std::vector<std::string> process_line(std::vector<std::string> lines,
size_t lineNum)
{
std::string line = remove_useless(lines[lineNum]);
line = add_blen(line);
line = add_support(line);
lines[lineNum] = remove_slash(line);
return lines;
}
void write_lines(const std::vector<std::string>& lines,
const std::string& filename)
{
std::ofstream outfile(filename);
if (!outfile.is_open()) {
std::cout << "Failed to open the output file." << std::endl;
}
for (const std::string& line : lines) {
outfile << line << std::endl;
}
outfile.close();
}
void interactive_commands(std::vector<std::string> lines)
{
std::string command, filename1, filename2;
std::cout
<< "~|~|\\ |~|~~)|~o(~|~|~._ _ _\n | | \\| | /_|~| _| | | }_}_"
<< std::endl;
std::cout << "TNT2FigTree\nMIT, Guoyi Zhang, 2024\nplease type help "
"to see more commands"
<< std::endl;
while (true) {
std::cout << "tnt2figtree> ";
getline(std::cin, command);
if (command == "help") {
std::cout << "help\t\t\tshow interactive commands "
"help\nimport <filename>\timport a TNT "
"output nexus format tree by TNT export "
"command\nexport <filename>\texport a "
"nexus format tree file\nquit\t\t\tquit "
"the program\nexit\t\t\texit the program"
<< std::endl;
}
else if (command.find("import ") == 0) {
std::stringstream ss(command.substr(7));
ss >> filename1;
if (filename1.empty()) {
std::cout << "tnt2figtree> please specify a "
"filename."
<< std::endl;
}
else {
lines = get_lines(filename1);
}
}
else if (command.find("export ") == 0) {
std::stringstream ss(command.substr(7));
ss >> filename2;
if (filename2.empty()) {
std::cout << "tnt2figtree> please specify a "
"filename."
<< std::endl;
}
else {
for (size_t i = 0; i < lines.size(); i++) {
if (lines[i][0] == '(') {
lines = process_line(lines, i);
}
}
write_lines(lines, filename2);
}
}
else if (command == "quit" || command == "exit") {
break;
}
else {
std::cout << "tnt2figtree> unrecognized command. Type "
"'help' for "
"a list of commands."
<< std::endl;
}
}
}
int main(int argc, char* argv[])
{
std::vector<std::string> lines;
if (argc == 1) {
interactive_commands(lines);
return 0;
}
else if (argc == 3) {
lines = get_lines(argv[1]);
for (size_t i = 0; i < lines.size(); i++) {
if (lines[i][0] == '(') {
lines = process_line(lines, i);
}
}
write_lines(lines, argv[2]);
}
else {
std::cout << "Usage: " << argv[0]
<< " <input_tnt_treefile> <output_nexus_treefile>"
<< std::endl;
}
return 0;
}