// NrToFasta.cpp


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


using namespace NGBW;


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

		if(argc != 5)
			throw std::invalid_argument("usage: nr-to-fasta dataset blastoutputname luceneoutputname inputname");

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

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

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

				message.append(argv[2]);

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

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

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

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

				message.append(argv[3]);

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

		std::ostream &blast_output = blast_output_file ? *blast_output_file : std::cout;
		std::ostream &lucene_output = lucene_output_file ? *lucene_output_file : std::cout;
		FastaWriter blast_writer(argv[1], blast_output);
		FastaWriter lucene_writer(argv[1], lucene_output);
		GzipReader reader(argv[4]);
		NrParser parser(reader);
		NrFastaRecord nr_record;
		FastaRecord fasta_record;

		while (parser.Parse(nr_record)) {
			fasta_record.sequence.assign(nr_record.sequence);

			DeflineList::const_iterator defline(nr_record.deflines.begin());

			if (defline != nr_record.deflines.end()) {
				fasta_record.identity.assign((*defline).identity);
				fasta_record.description.assign((*defline).description);

				blast_writer.Write(fasta_record);
				lucene_writer.Write(fasta_record);

				while (++defline != nr_record.deflines.end()) {
					fasta_record.identity.assign((*defline).identity);
					fasta_record.description.assign((*defline).description);

					lucene_writer.Write(fasta_record);
				}
			}
		}

		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;
	}
}