// GenbankToFasta.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 "GenbankParser.hpp"
#include "GzipReader.hpp"
#include "SystemError.hpp"


using namespace NGBW;


static void WriteFasta(const char *dataset, GenbankRecord &record, std::ostream &output) throw(std::ios_base::failure)
{
	output.write(">ngbw|", 6);

	output << dataset;

	output.put('|');

	output << record.accession;

	output.put('|');

	output << record.definition;

	output.put('\n');

	output << record.sequence;
}


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

		if(argc < 3)
			throw std::invalid_argument("usage: genbank-to-fasta dataset outputname inputname...");

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

		if(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::ostream &output = output_file ? *output_file : std::cout;

		output.exceptions(std::ios_base::badbit);

		for (int i = 3 ; i < argc ; i += 1) {
			GzipReader reader(argv[i]);
			GenbankParser parser(reader);
			GenbankRecord record;

			while (parser.Parse(record))
				WriteFasta(argv[1], record, output);
		}

		return 0;
	}
	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;
	}
}