// PdbToFasta.cpp


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


using namespace NGBW;


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

		if(argc != 4)
			throw std::invalid_argument("usage: pdb-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;
		FastaWriter writer(argv[1], output);
		GzipReader reader(argv[3]);
		PdbFinderParser parser(reader);
		PdbFinderRecord pdb_record;
		FastaRecord fasta_record;

		while (parser.Parse(pdb_record)) {
			fasta_record.organism.assign(pdb_record.organism);
			fasta_record.description.assign(pdb_record.description);

			for (ChainList::const_iterator i = pdb_record.chains.begin() ; i != pdb_record.chains.end() ; i++) {
				fasta_record.identity.assign(pdb_record.identity);
				fasta_record.identity.push_back('-');
				fasta_record.identity.append((*i).identity);
				fasta_record.sequence.assign((*i).sequence);

				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;
	}
}