// NrParser.cpp


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


namespace NGBW {


// NrParser


bool NrParser::Parse(NrFastaRecord &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 NrParser::ParseHeader(NrFastaRecord &record)
{
	size_t first = 1;
	size_t length = std::strlen(m_line);

	while (1) {
		size_t last = FindFirstOf('\x01', first);
		NrDefline new_defline;

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

		ParseDefline(first, last, new_defline);

		record.deflines.push_back(new_defline);

		if (last == length)
			break;

		first = last + 1;
	}

	ReadNextLine();
}

void NrParser::ParseDefline(size_t offset, size_t end, NrDefline &defline)
{
	size_t first = FindFirstOf('|', offset);

	if (first >= end || first == std::string::npos)
		first = offset;
	else
		first += 1;

	size_t last = FindFirstOf('|', first + 1);

	if (last >= end || last == std::string::npos)
		last = end;

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

	if (last == end)
		return;

	first = last + 1;
	last = FindFirstOf('|', first + 1);

	if (last >= end || last == std::string::npos)
		return;

	defline.database.assign(m_line + first, last - first);

 	first = FindFirstSpace(last + 1);

	if (first >= end || first == std::string::npos)
		return;

	first += 1;

	defline.description.assign(m_line + first, end - first);
}


} // namespace NGBW