// PdbToFasta.cpp


#include <fstream>
#include <iostream>
#include <map>
#include <set>
#include <stdexcept>
#include <string>
#include <cerrno>
#include <cstring>
#include <boost/scoped_ptr.hpp>
#include "GzipReader.hpp"
#include "PdbFinderWriter.hpp"
#include "PdbSeqresParser.hpp"
#include "SystemError.hpp"


using namespace NGBW;


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

		if(argc < 3 || argc > 4)
			throw std::invalid_argument("usage: fix-pdbfinder pdbseqres pdbfinder [ outputname ]");

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

		if(argc == 4 && std::memcmp(argv[3], "-", 2) != 0) {
			output_file.reset(new std::ofstream(argv[3]));

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

				message.append(argv[3]);

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

		SeqresMap sequences;
		GzipReader seqres_reader(argv[1]);
		PdbSeqresParser parser(seqres_reader);
		PdbSeqresRecord record;

		while (parser.Parse(record)) {
			SeqresMap::iterator entry(sequences.find(record.protein_id));

			if (entry == sequences.end()) {
				ChainSet new_set;

				new_set.insert(record);

				sequences.insert(SeqresMap::value_type(record.protein_id, new_set));
			}
			else
				(*entry).second.insert(record);
		}

		std::ostream &output = output_file ? *output_file : std::cout;
		GzipReader finder_reader(argv[2]);
		PdbFinderWriter writer(finder_reader, output);

		writer.Write(sequences);

		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;
	}
}