// Hennig86ToNexus.cpp


#if defined(_WIN32) || defined(_WIN64)

// C4290 - the compiler ignores exception specifications
#pragma warning(disable: 4290)

#endif


#include <fstream>
#include <iostream>
#include <string>
#include <cerrno>
#include <cstring>
#include <boost/scoped_ptr.hpp>
#include "Hennig86Reader.hpp"
#include "NexusWriter.hpp"
#include "SystemError.hpp"


using namespace Cipres;
using namespace Cipres::SequenceFormats;


int main(int argc, char **argv)
{
	try {
		std::ios_base::sync_with_stdio(false);

		if(argc > 3)
			throw std::invalid_argument("usage: hennig86-to-nexus [ inputname [ outputname ]]");

		boost::scoped_ptr<std::ifstream> input_file;
		boost::scoped_ptr<std::ofstream> output_file;

		if(argc > 1) {
			if(std::memcmp(argv[1], "-", 2) != 0) {
				input_file.reset(new std::ifstream(argv[1]));

				if(!input_file->good()) {
					std::string message("can't open ");

					message.append(argv[1]);

					throw SystemError("main", message, errno);
				}
			}

			if(argc == 3 && std::memcmp(argv[2], "-", 2) != 0) {
				output_file.reset(new std::ofstream(argv[2]));

				if(!output_file->good()) {
					std::string message("can't open ");

					message.append(argv[2]);

					throw SystemError("main", message, errno);
				}
			}
		}

		std::istream &input = input_file ? *input_file : std::cin;
		std::ostream &output = output_file ? *output_file : std::cout;
		Hennig86Reader reader;
		NexusWriter writer;

		reader.Read(input, writer);
		writer.Write(output);

		return 0;
	}
	catch(const std::ios_base::failure &io_err) {
		std::cerr << "a std::ios_base::failure was thrown: " << io_err.what() << std::endl;

		return 1;
	}
	catch(const std::exception &err) {
		std::cerr << err.what() << std::endl;

		return 1;
	}
	catch(...) {
		std::cerr << "an unknown exception was thrown" << std::endl;

		return 1;
	}
}