// UpdateUniprot.cpp


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

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

#endif


#include <fstream>
#include <iostream>
#include <string>
#include <cctype>
#include <cerrno>
#include <cstring>
#include <boost/scoped_ptr.hpp>
#include "GzipReader.hpp"
#include "SystemError.hpp"
#include "UniprotParser.hpp"


using namespace NGBW;


static void WriteFasta(const char *dataset, UniprotRecord &record, std::ostream &output) throw(std::ios_base::failure)
{
	std::string description;

	if (record.description.compare(0, 8, "RecName:", 8) == 0) {
		size_t equals_sign = record.description.find_first_of('=', 8) + 1;
		size_t semi_colon = record.description.find_first_of(';', equals_sign);

		description.assign(record.description.substr(equals_sign, semi_colon - equals_sign));

		size_t flags_line = record.description.find("Flags:", semi_colon + 1, 6);

		if (flags_line != std::string::npos) {
			flags_line += 6;

			semi_colon = record.description.find_first_of(';', flags_line);

			std::string flag(record.description.substr(flags_line, semi_colon - flags_line));

			for (std::string::const_iterator i = flag.begin() ; i != flag.end() ; i++)
				description.push_back(std::tolower(*i));
		}
	}
	else
		description.assign(record.description);

	output.write(">ngbw|", 6);

	output << dataset;

	output.put('|');

	output << record.accession;

	output.put('|');

	output << record.organism;

	output.put('|');

	output << description;

	output.put('\n');

	output << record.sequence;
}


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

		if(argc != 4)
			throw std::invalid_argument("usage: uniprot-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;
		GzipReader reader(argv[3]);
		UniprotParser parser(reader);
		UniprotRecord record;

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

		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;
	}
}