// NtParser.cpp


#include <cstring>
#include "NtParser.hpp"


namespace NGBW {


// NtParser


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

	if (m_line == NULL)
		ReadNextLine();

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

		if (m_line[0] == '>') {
			ParseHeader(record);

			break;
		}

		ReadNextLine();
	}

	while (1) {
		if (m_input.Eof() || m_line[0] == '>')
			break;

		record.sequence.append(m_line);

		ReadNextLine();
	}

	return true;
}

void NtParser::ParseHeader(FastaRecord &record)
{
	size_t first = FindFirstOf('|', 1);

	if (first == std::string::npos)
		first = 1;
	else
		first += 1;

	size_t length = std::strlen(m_line);
	size_t last = FindFirstOf('|', first + 1);

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

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

	if (last < length) {
		first = FindFirstSpace(last + 1);

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

			record.description.assign(m_line + first, length - first);
		}
	}

	ReadNextLine();
}


} // namespace NGBW