// GenbankParser.cpp


#include <string>
#include <cctype>
#include <cstring>
#include "GenbankParser.hpp"


namespace NGBW {


// GenbankParser


bool GenbankParser::Parse(FastaRecord &record)
{
	record.clear();

	ReadNextLine();

	while (1) {
		if (m_input.Eof())
			return false;

		if (std::memcmp(m_line, "LOCUS", 5) == 0) {
			ReadNextLine();

			break;
		}

		IgnoreField();
	}

	while (1) {
		if (m_input.Eof())
			return false;

		if (std::memcmp(m_line, "DEFINITION", 10) == 0) {
			ParseDefinition(record);

			break;
		}

		IgnoreField();
	}

	while (1) {
		if (m_input.Eof())
			return false;

		if (std::memcmp(m_line, "ACCESSION", 9) == 0) {
			ParseAccession(record);

			break;
		}

		IgnoreField();
	}

	while (1) {
		if (m_input.Eof())
			return false;

		if (std::memcmp(m_line, "SOURCE", 6) == 0) {
			ParseSource(record);

			break;
		}

		IgnoreField();
	}

	while (1) {
		if (m_input.Eof())
			return false;

		if (std::memcmp(m_line, "ORIGIN", 6) == 0) {
			ParseOrigin(record);

			break;
		}

		IgnoreField();
	}

	while (1) {
		if (m_input.Eof())
			return false;

		if (FindEndToken())
			break;

		IgnoreField();
	}

	return true;
}

void GenbankParser::ParseDefinition(FastaRecord &record)
{
	size_t first = FindFirstNotSpace(11);

	if (first == std::string::npos)
		return;

	record.description.assign(m_line + first);

	while (1) {
		ReadNextLine();

		if (m_input.Eof() || !std::isspace(m_line[0]))
			return;

		size_t last = FindLastNotSpace();

		if (last != std::string::npos) {
			first = FindFirstNotSpace(1);

			record.description.append(m_line + first, last - first);
		}
	}
}

void GenbankParser::ParseAccession(FastaRecord &record)
{
	size_t first = FindFirstNotSpace(10);

	if (first == std::string::npos)
		return;

	size_t last = FindFirstSpace(first + 1);

	if (last == std::string::npos)
		last = std::strlen(m_line);

	record.identity.assign(m_line + first, last - first);

	ReadNextLine();
}

void GenbankParser::ParseSource(FastaRecord &record)
{
	size_t first = FindFirstNotSpace(7);

	if (first == std::string::npos)
		return;

	record.organism.assign(m_line + first);

	IgnoreField();
}

void GenbankParser::ParseOrigin(FastaRecord &record)
{
	while (1) {
		ReadNextLine();

		if (m_input.Eof() || !std::isspace(m_line[0]))
			return;

		size_t first = FindFirstNotSpace(1);

		if (m_line[first] == '/' && m_line[first + 1] == '/')
			return;

		size_t last = FindFirstNotDigit(first);
		size_t length = std::strlen(m_line);

		while (1) {
			first = FindFirstNotSpace(last + 1);
			last = FindFirstSpace(first + 1);

			if (last == std::string::npos)
				last = length;

			record.sequence.append(m_line + first, last - first);

			if (last == length)
				break;
		}
	}
}

void GenbankParser::IgnoreField()
{
	while (1) {
		ReadNextLine();

		if (m_input.Eof() || !std::isspace(m_line[0]))
			return;
	}
}

bool GenbankParser::FindEndToken()
{
	size_t first = FindFirstNotSpace();

	if (first == std::string::npos)
		return false;

	if (m_line[first] == '/' && m_line[first + 1] == '/')
		return true;

	return false;
}


} // namespace NGBW